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commit/galaxy-central: greg: Fix for managing sample datasets in the sample tracking admin UI.
by Bitbucket 29 Mar '12

29 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9f5750e19c1e/ changeset: 9f5750e19c1e user: greg date: 2012-03-29 15:17:34 summary: Fix for managing sample datasets in the sample tracking admin UI. affected #: 1 file diff -r 04ed074ef9d21888bfd68235707b5ec0b9a70a10 -r 9f5750e19c1ea88fa0c694bb42642589659b0750 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py +++ b/lib/galaxy/web/controllers/requests_admin.py @@ -199,6 +199,11 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + sample_id = params.get( 'sample_id', None ) + try: + sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) ) + except: + return invalid_id_redirect( trans, 'requests_admin', sample_id, 'sample' ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() sample_dataset_id = params.get( 'id', None ) @@ -269,11 +274,6 @@ **kwd ) ) # Render the grid view - sample_id = params.get( 'sample_id', None ) - try: - sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id ( sample_id ) ) - except: - return invalid_id_redirect( trans, 'requests_admin', sample_id, 'sample' ) request_id = trans.security.encode_id( sample.request.id ) library_id = trans.security.encode_id( sample.library.id ) self.datatx_grid.title = 'Manage "%s" datasets' % sample.name Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Make ldda.templates_json able to set use_name flag in call to templates_dict.
by Bitbucket 28 Mar '12

28 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04ed074ef9d2/ changeset: 04ed074ef9d2 user: dan date: 2012-03-28 18:05:00 summary: Make ldda.templates_json able to set use_name flag in call to templates_dict. affected #: 1 file diff -r 0c6cf4f53c4efad46fe7716587ca5a2dddff049c -r 04ed074ef9d21888bfd68235707b5ec0b9a70a10 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1554,8 +1554,8 @@ tmp_dict[ name ] = content[ field[ 'name' ] ] template_data[template.name] = tmp_dict return template_data - def templates_json( self ): - return simplejson.dumps( self.templates_dict() ) + def templates_json( self, use_name=False ): + return simplejson.dumps( self.templates_dict( use_name=use_name ) ) def get_display_name( self ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add use_name flag to ldda.templates_dict() that will return a dictionary using the form field names instead of labels.
by Bitbucket 28 Mar '12

28 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0c6cf4f53c4e/ changeset: 0c6cf4f53c4e user: dan date: 2012-03-28 18:01:44 summary: Add use_name flag to ldda.templates_dict() that will return a dictionary using the form field names instead of labels. affected #: 1 file diff -r 15bd01c59c24eae40026470459c5577cba063768 -r 0c6cf4f53c4efad46fe7716587ca5a2dddff049c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1536,17 +1536,22 @@ else: return template.get_widgets( trans.user ) return [] - def templates_dict( self ): + def templates_dict( self, use_name=False ): """ Returns a dict of template info """ + #TODO: Should have a method that allows names and labels to be returned together in a structured way template_data = {} for temp_info in self.info_association: template = temp_info.template content = temp_info.info.content tmp_dict = {} for field in template.fields: - tmp_dict[field['label']] = content[field['name']] + if use_name: + name = field[ 'name' ] + else: + name = field[ 'label' ] + tmp_dict[ name ] = content[ field[ 'name' ] ] template_data[template.name] = tmp_dict return template_data def templates_json( self ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 28 Mar '12

28 Mar '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cc2605facf6b/ changeset: cc2605facf6b user: jgoecks date: 2012-03-28 16:58:38 summary: Enable set_metadata tool to take job parameters and use parameters for set_metadata jobs within Trackster. affected #: 2 files diff -r a01497f68018ccc78b2a987b8514bae0e8cf70f1 -r cc2605facf6be23d0a84f81904650042374d398c lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py +++ b/lib/galaxy/tools/actions/metadata.py @@ -1,6 +1,7 @@ from __init__ import ToolAction from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper from galaxy.util.odict import odict +from galaxy.util.json import to_json_string import logging log = logging.getLogger( __name__ ) @@ -8,7 +9,7 @@ class SetMetadataToolAction( ToolAction ): """Tool action used for setting external metadata on an existing dataset""" - def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None ): + def execute( self, tool, trans, incoming = {}, set_output_hid = False, overwrite = True, history=None, job_params=None ): for name, value in incoming.iteritems(): if isinstance( value, trans.app.model.HistoryDatasetAssociation ): dataset = value @@ -30,6 +31,8 @@ job.tool_id = tool.id if trans.user: job.user_id = trans.user.id + if job_params: + job.params = to_json_string( job_params ) start_job_state = job.state #should be job.states.NEW try: # For backward compatibility, some tools may not have versions yet. diff -r a01497f68018ccc78b2a987b8514bae0e8cf70f1 -r cc2605facf6be23d0a84f81904650042374d398c lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -974,12 +974,15 @@ new_dataset.set_dataset_state( trans.app.model.Dataset.states.OK ) # Set metadata. + # TODO: set meta internally if dataset is small enough? if trans.app.config.set_metadata_externally: - trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':new_dataset }, overwrite=False ) + trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, + trans, incoming = { 'input1':new_dataset }, + overwrite=False, job_params={ "source" : "trackster" } ) else: message = 'Attributes updated' new_dataset.set_meta() - new_dataset.datatype.after_setting_metadata( new_dataset ) + new_dataset.datatype.after_setting_metadata( new_dataset ) trans.sa_session.flush() https://bitbucket.org/galaxy/galaxy-central/changeset/15bd01c59c24/ changeset: 15bd01c59c24 user: jgoecks date: 2012-03-28 16:59:03 summary: Merge affected #: 1 file diff -r cc2605facf6be23d0a84f81904650042374d398c -r 15bd01c59c24eae40026470459c5577cba063768 contrib/universe_merger.py --- /dev/null +++ b/contrib/universe_merger.py @@ -0,0 +1,87 @@ +#! /usr/bin/env python +''' +universe_merger.py + +Created by Anne Pajon on 31 Jan 2012 + +Copyright (c) 2012 Cancer Research UK - Cambridge Research Institute. + +This source file is licensed under the Academic Free License version +3.0 available at http://www.opensource.org/licenses/AFL-3.0. + +Permission is hereby granted to reproduce, translate, adapt, alter, +transform, modify, or arrange this source file (the "Original Work"); +to distribute or communicate copies of it under any license of your +choice that does not contradict the terms and conditions; to perform +or display the Original Work publicly. + +THE ORIGINAL WORK IS PROVIDED UNDER THIS LICENSE ON AN "AS IS" BASIS +AND WITHOUT WARRANTY, EITHER EXPRESS OR IMPLIED, INCLUDING, WITHOUT +LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY OR +FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY OF +THE ORIGINAL WORK IS WITH YOU. + +Script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample +''' +import ConfigParser +import sys +import optparse +import logging + +def main(): + # logging configuration + logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO) + + # get the options + parser = optparse.OptionParser() + parser.add_option("-s", "--sample", dest="sample", action="store", help="path to Galaxy universe_wsgi.ini.sample file") + parser.add_option("-c", "--config", dest="config", action="store", help="path to your own universe_wsgi.ini file") + parser.add_option("-o", "--output", dest="output", action="store", help="path to the new merged universe_wsgi.ini.new file") + (options, args) = parser.parse_args() + + for option in ['sample', 'config']: + if getattr(options, option) == None: + print "Please supply a --%s parameter.\n" % (option) + parser.print_help() + sys.exit() + + config_sample = ConfigParser.RawConfigParser() + config_sample.read(options.sample) + config_sample_content = open(options.sample, 'r').read() + + config = ConfigParser.RawConfigParser() + config.read(options.config) + + logging.info("Merging your own config file %s into the sample one %s." % (options.config, options.sample)) + logging.info("---------- DIFFERENCE ANALYSIS BEGIN ----------") + for section in config.sections(): + if not config_sample.has_section(section): + logging.warning("-MISSING- section [%s] not found in sample file. It will be ignored." % section) + else: + for (name, value) in config.items(section): + if not config_sample.has_option(section, name): + if not "#%s" % name in config_sample_content: + logging.warning("-MISSING- section [%s] option '%s' not found in sample file. It will be ignored." % (section, name)) + else: + logging.info("-notset- section [%s] option '%s' not set in sample file. It will be added." % (section, name)) + config_sample.set(section, name, value) + else: + if not config_sample.get(section, name) == value: + logging.info("- diff - section [%s] option '%s' has different value ('%s':'%s'). It will be modified." % (section, name, config_sample.get(section, name), value)) + config_sample.set(section, name, value) + logging.info("---------- DIFFERENCE ANALYSIS END ----------") + + if options.output: + outputfile = open(options.output, 'w') + config_sample.write(outputfile) + outputfile.close() + else: + #print "----------" + #config_sample.write(sys.stdout) + #print "----------" + logging.info("use -o OUTPUT to write the merged configuration into a file.") + + logging.info("read Galaxy universe_wsgi.ini.sample for detailed information.") + +if __name__ == '__main__': + main() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample contributed by Anne Pajon.
by Bitbucket 28 Mar '12

28 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4b6cc14f1bb9/ changeset: 4b6cc14f1bb9 user: greg date: 2012-03-28 16:58:19 summary: Add script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample contributed by Anne Pajon. affected #: 1 file diff -r a01497f68018ccc78b2a987b8514bae0e8cf70f1 -r 4b6cc14f1bb9bffda9859f2857909d8708b5d86f contrib/universe_merger.py --- /dev/null +++ b/contrib/universe_merger.py @@ -0,0 +1,87 @@ +#! /usr/bin/env python +''' +universe_merger.py + +Created by Anne Pajon on 31 Jan 2012 + +Copyright (c) 2012 Cancer Research UK - Cambridge Research Institute. + +This source file is licensed under the Academic Free License version +3.0 available at http://www.opensource.org/licenses/AFL-3.0. + +Permission is hereby granted to reproduce, translate, adapt, alter, +transform, modify, or arrange this source file (the "Original Work"); +to distribute or communicate copies of it under any license of your +choice that does not contradict the terms and conditions; to perform +or display the Original Work publicly. + +THE ORIGINAL WORK IS PROVIDED UNDER THIS LICENSE ON AN "AS IS" BASIS +AND WITHOUT WARRANTY, EITHER EXPRESS OR IMPLIED, INCLUDING, WITHOUT +LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY OR +FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY OF +THE ORIGINAL WORK IS WITH YOU. + +Script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample +''' +import ConfigParser +import sys +import optparse +import logging + +def main(): + # logging configuration + logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO) + + # get the options + parser = optparse.OptionParser() + parser.add_option("-s", "--sample", dest="sample", action="store", help="path to Galaxy universe_wsgi.ini.sample file") + parser.add_option("-c", "--config", dest="config", action="store", help="path to your own universe_wsgi.ini file") + parser.add_option("-o", "--output", dest="output", action="store", help="path to the new merged universe_wsgi.ini.new file") + (options, args) = parser.parse_args() + + for option in ['sample', 'config']: + if getattr(options, option) == None: + print "Please supply a --%s parameter.\n" % (option) + parser.print_help() + sys.exit() + + config_sample = ConfigParser.RawConfigParser() + config_sample.read(options.sample) + config_sample_content = open(options.sample, 'r').read() + + config = ConfigParser.RawConfigParser() + config.read(options.config) + + logging.info("Merging your own config file %s into the sample one %s." % (options.config, options.sample)) + logging.info("---------- DIFFERENCE ANALYSIS BEGIN ----------") + for section in config.sections(): + if not config_sample.has_section(section): + logging.warning("-MISSING- section [%s] not found in sample file. It will be ignored." % section) + else: + for (name, value) in config.items(section): + if not config_sample.has_option(section, name): + if not "#%s" % name in config_sample_content: + logging.warning("-MISSING- section [%s] option '%s' not found in sample file. It will be ignored." % (section, name)) + else: + logging.info("-notset- section [%s] option '%s' not set in sample file. It will be added." % (section, name)) + config_sample.set(section, name, value) + else: + if not config_sample.get(section, name) == value: + logging.info("- diff - section [%s] option '%s' has different value ('%s':'%s'). It will be modified." % (section, name, config_sample.get(section, name), value)) + config_sample.set(section, name, value) + logging.info("---------- DIFFERENCE ANALYSIS END ----------") + + if options.output: + outputfile = open(options.output, 'w') + config_sample.write(outputfile) + outputfile.close() + else: + #print "----------" + #config_sample.write(sys.stdout) + #print "----------" + logging.info("use -o OUTPUT to write the merged configuration into a file.") + + logging.info("read Galaxy universe_wsgi.ini.sample for detailed information.") + +if __name__ == '__main__': + main() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Have the cloud controller explicitly require boto.
by Bitbucket 28 Mar '12

28 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/a01497f68018/ changeset: a01497f68018 user: natefoo date: 2012-03-28 16:02:55 summary: Have the cloud controller explicitly require boto. affected #: 1 file diff -r 377dd3efe3beb7f8d8ef06306fcadac0aafd6365 -r a01497f68018ccc78b2a987b8514bae0e8cf70f1 lib/galaxy/web/controllers/cloud.py --- a/lib/galaxy/web/controllers/cloud.py +++ b/lib/galaxy/web/controllers/cloud.py @@ -6,10 +6,13 @@ """ -import boto import datetime import logging import time +from galaxy import eggs +import pkg_resources +pkg_resources.require('boto') +import boto from galaxy import web from galaxy.web.base.controller import BaseUIController from boto.ec2.regioninfo import RegionInfo Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add FreeBayes to tool_conf.xml.main.
by Bitbucket 27 Mar '12

27 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/377dd3efe3be/ changeset: 377dd3efe3be user: dan date: 2012-03-28 00:09:55 summary: Add FreeBayes to tool_conf.xml.main. affected #: 3 files diff -r 0282e24997db8e5b5a41a82b6e1904650af42934 -r 377dd3efe3beb7f8d8ef06306fcadac0aafd6365 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -208,6 +208,7 @@ <tool file="phenotype_association/lps.xml" /><tool file="phenotype_association/hilbertvis.xml" /><tool file="phenotype_association/freebayes.xml" /> + <tool file="variant_detection/freebayes.xml" /><tool file="phenotype_association/master2pg.xml" /><tool file="phenotype_association/vcf2pgSnp.xml" /><tool file="phenotype_association/dividePgSnpAlleles.xml" /> @@ -326,6 +327,9 @@ <tool file="indels/indel_sam2interval.xml" /><tool file="indels/indel_analysis.xml" /></section> + <section name="NGS: Variant Detection" id="variant_detection"> + <tool file="variant_detection/freebayes.xml" /> + </section><section name="NGS: Peak Calling" id="peak_calling"><tool file="peak_calling/macs_wrapper.xml" /><tool file="peak_calling/sicer_wrapper.xml" /> diff -r 0282e24997db8e5b5a41a82b6e1904650af42934 -r 377dd3efe3beb7f8d8ef06306fcadac0aafd6365 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -477,6 +477,7 @@ <tool file="phenotype_association/lps.xml" /><tool file="phenotype_association/hilbertvis.xml" /><tool file="phenotype_association/freebayes.xml" /> + <tool file="variant_detection/freebayes.xml" /><tool file="phenotype_association/master2pg.xml" /><tool file="phenotype_association/vcf2pgSnp.xml" /><tool file="phenotype_association/dividePgSnpAlleles.xml" /> diff -r 0282e24997db8e5b5a41a82b6e1904650af42934 -r 377dd3efe3beb7f8d8ef06306fcadac0aafd6365 tools/phenotype_association/freebayes.xml --- a/tools/phenotype_association/freebayes.xml +++ b/tools/phenotype_association/freebayes.xml @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="freebayes_wrapper" name="Call SNPS with Freebayes" version="0.5.0"> +<tool id="freebayes_wrapper" name="Call SNPS with Freebayes" version="0.5.0" hidden="True"><requirements><requirement type="package">freebayes</requirement></requirements> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Add FreeBayes to tool_conf.xml.main
by Bitbucket 27 Mar '12

27 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0282e24997db/ changeset: 0282e24997db user: dan date: 2012-03-27 23:54:12 summary: Add FreeBayes to tool_conf.xml.main affected #: 1 file diff -r 8d1b7e28fd6027d7ef3c69d17592d6d49cdbcc57 -r 0282e24997db8e5b5a41a82b6e1904650af42934 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -318,6 +318,9 @@ <tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> + <section name="NGS: Variant Detection" id="variant_detection"> + <tool file="variant_detection/freebayes.xml" /> + </section><section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /><tool file="indels/indel_sam2interval.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Basics for API access to tools: (a) enable tools, tool panel labels, and tool panel sections to be dictified; and (b) add RESTful UI controller tools. Once session-based authentication is enabled in API, controller will be moved to API.
by Bitbucket 27 Mar '12

27 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8d1b7e28fd60/ changeset: 8d1b7e28fd60 user: jgoecks date: 2012-03-27 19:03:21 summary: Basics for API access to tools: (a) enable tools, tool panel labels, and tool panel sections to be dictified; and (b) add RESTful UI controller tools. Once session-based authentication is enabled in API, controller will be moved to API. affected #: 2 files diff -r f6010ee7c7f8d5a021cba09bbfef937c28265c82 -r 8d1b7e28fd6027d7ef3c69d17592d6d49cdbcc57 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -485,6 +485,13 @@ self.id = elem.get( "id" ) self.version = elem.get( "version" ) or '' self.elems = odict() + + def to_dict( self ): + """ Return a dict that includes section's attributes. """ + section_elts = [] + for key, val in self.elems.items(): + section_elts.append( val.to_dict() ) + return { 'type': 'section', 'id': self.id, 'name': self.name, 'version': self.version, 'elems': section_elts } class ToolSectionLabel( object ): """ @@ -495,6 +502,10 @@ self.text = elem.get( "text" ) self.id = elem.get( "id" ) self.version = elem.get( "version" ) or '' + + def to_dict( self ): + """ Return a dict that includes label's attributes. """ + return { 'type': 'label', 'id': self.id, 'name': self.text, 'version': self.version } class DefaultToolState( object ): """ @@ -2238,6 +2249,11 @@ self.sa_session.add( new_data ) self.sa_session.flush() return primary_datasets + + def to_dict( self, **kwds ): + """ Return dict that includes tool's attributes. """ + return { 'type': 'tool', 'id': self.id, 'name': self.name, + 'version': self.version, 'description': self.description } class DataSourceTool( Tool ): """ diff -r f6010ee7c7f8d5a021cba09bbfef937c28265c82 -r 8d1b7e28fd6027d7ef3c69d17592d6d49cdbcc57 lib/galaxy/web/controllers/tools.py --- /dev/null +++ b/lib/galaxy/web/controllers/tools.py @@ -0,0 +1,32 @@ +from galaxy import config, tools, web, util +from galaxy.web.base.controller import BaseController, BaseUIController + +class ToolsController( BaseUIController ): + """ + RESTful controller for interactions with tools. Once session-based + authentication can be done with API controllers, this will be moved + to be part of the API. + """ + + @web.json + def index( self, trans, **kwds ): + """ + GET /api/tools: returns a list of tools defined by parameters + parameters: + in_panel - if true, tools are returned in panel structure, including sections and labels + """ + in_panel = util.string_as_bool( kwds.get( 'in_panel', 'True' ) ) + if in_panel: + panel_elts = [] + # Taken from tool_menu.mako: + for key, val in self.app.toolbox.tool_panel.items(): + panel_elts.append( val.to_dict() ) + rval = panel_elts + else: + tools = [] + for id, tool in self.app.toolbox.tools_by_id.items(): + tools.append( tool.to_dict() ) + rval = tools + + return rval + \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 27 Mar '12

27 Mar '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/70397647fad5/ changeset: 70397647fad5 user: jgoecks date: 2012-03-27 16:59:31 summary: Add backbone.js, underscore.js, and handlebars.js libraries in a new /libs directory and modify pack scripts accordingly. affected #: 8 files diff -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 -r 70397647fad54c50213e015aaedfed94e6b19eda static/scripts/libs/backbone.js --- /dev/null +++ b/static/scripts/libs/backbone.js @@ -0,0 +1,1431 @@ +// Backbone.js 0.9.2 + +// (c) 2010-2012 Jeremy Ashkenas, DocumentCloud Inc. +// Backbone may be freely distributed under the MIT license. +// For all details and documentation: +// http://backbonejs.org + +(function(){ + + // Initial Setup + // ------------- + + // Save a reference to the global object (`window` in the browser, `global` + // on the server). + var root = this; + + // Save the previous value of the `Backbone` variable, so that it can be + // restored later on, if `noConflict` is used. + var previousBackbone = root.Backbone; + + // Create a local reference to slice/splice. + var slice = Array.prototype.slice; + var splice = Array.prototype.splice; + + // The top-level namespace. All public Backbone classes and modules will + // be attached to this. Exported for both CommonJS and the browser. + var Backbone; + if (typeof exports !== 'undefined') { + Backbone = exports; + } else { + Backbone = root.Backbone = {}; + } + + // Current version of the library. Keep in sync with `package.json`. + Backbone.VERSION = '0.9.2'; + + // Require Underscore, if we're on the server, and it's not already present. + var _ = root._; + if (!_ && (typeof require !== 'undefined')) _ = require('underscore'); + + // For Backbone's purposes, jQuery, Zepto, or Ender owns the `$` variable. + var $ = root.jQuery || root.Zepto || root.ender; + + // Set the JavaScript library that will be used for DOM manipulation and + // Ajax calls (a.k.a. the `$` variable). By default Backbone will use: jQuery, + // Zepto, or Ender; but the `setDomLibrary()` method lets you inject an + // alternate JavaScript library (or a mock library for testing your views + // outside of a browser). + Backbone.setDomLibrary = function(lib) { + $ = lib; + }; + + // Runs Backbone.js in *noConflict* mode, returning the `Backbone` variable + // to its previous owner. Returns a reference to this Backbone object. + Backbone.noConflict = function() { + root.Backbone = previousBackbone; + return this; + }; + + // Turn on `emulateHTTP` to support legacy HTTP servers. Setting this option + // will fake `"PUT"` and `"DELETE"` requests via the `_method` parameter and + // set a `X-Http-Method-Override` header. + Backbone.emulateHTTP = false; + + // Turn on `emulateJSON` to support legacy servers that can't deal with direct + // `application/json` requests ... will encode the body as + // `application/x-www-form-urlencoded` instead and will send the model in a + // form param named `model`. + Backbone.emulateJSON = false; + + // Backbone.Events + // ----------------- + + // Regular expression used to split event strings + var eventSplitter = /\s+/; + + // A module that can be mixed in to *any object* in order to provide it with + // custom events. You may bind with `on` or remove with `off` callback functions + // to an event; trigger`-ing an event fires all callbacks in succession. + // + // var object = {}; + // _.extend(object, Backbone.Events); + // object.on('expand', function(){ alert('expanded'); }); + // object.trigger('expand'); + // + var Events = Backbone.Events = { + + // Bind one or more space separated events, `events`, to a `callback` + // function. Passing `"all"` will bind the callback to all events fired. + on: function(events, callback, context) { + + var calls, event, node, tail, list; + if (!callback) return this; + events = events.split(eventSplitter); + calls = this._callbacks || (this._callbacks = {}); + + // Create an immutable callback list, allowing traversal during + // modification. The tail is an empty object that will always be used + // as the next node. + while (event = events.shift()) { + list = calls[event]; + node = list ? list.tail : {}; + node.next = tail = {}; + node.context = context; + node.callback = callback; + calls[event] = {tail: tail, next: list ? list.next : node}; + } + + return this; + }, + + // Remove one or many callbacks. If `context` is null, removes all callbacks + // with that function. If `callback` is null, removes all callbacks for the + // event. If `events` is null, removes all bound callbacks for all events. + off: function(events, callback, context) { + var event, calls, node, tail, cb, ctx; + + // No events, or removing *all* events. + if (!(calls = this._callbacks)) return; + if (!(events || callback || context)) { + delete this._callbacks; + return this; + } + + // Loop through the listed events and contexts, splicing them out of the + // linked list of callbacks if appropriate. + events = events ? events.split(eventSplitter) : _.keys(calls); + while (event = events.shift()) { + node = calls[event]; + delete calls[event]; + if (!node || !(callback || context)) continue; + // Create a new list, omitting the indicated callbacks. + tail = node.tail; + while ((node = node.next) !== tail) { + cb = node.callback; + ctx = node.context; + if ((callback && cb !== callback) || (context && ctx !== context)) { + this.on(event, cb, ctx); + } + } + } + + return this; + }, + + // Trigger one or many events, firing all bound callbacks. Callbacks are + // passed the same arguments as `trigger` is, apart from the event name + // (unless you're listening on `"all"`, which will cause your callback to + // receive the true name of the event as the first argument). + trigger: function(events) { + var event, node, calls, tail, args, all, rest; + if (!(calls = this._callbacks)) return this; + all = calls.all; + events = events.split(eventSplitter); + rest = slice.call(arguments, 1); + + // For each event, walk through the linked list of callbacks twice, + // first to trigger the event, then to trigger any `"all"` callbacks. + while (event = events.shift()) { + if (node = calls[event]) { + tail = node.tail; + while ((node = node.next) !== tail) { + node.callback.apply(node.context || this, rest); + } + } + if (node = all) { + tail = node.tail; + args = [event].concat(rest); + while ((node = node.next) !== tail) { + node.callback.apply(node.context || this, args); + } + } + } + + return this; + } + + }; + + // Aliases for backwards compatibility. + Events.bind = Events.on; + Events.unbind = Events.off; + + // Backbone.Model + // -------------- + + // Create a new model, with defined attributes. A client id (`cid`) + // is automatically generated and assigned for you. + var Model = Backbone.Model = function(attributes, options) { + var defaults; + attributes || (attributes = {}); + if (options && options.parse) attributes = this.parse(attributes); + if (defaults = getValue(this, 'defaults')) { + attributes = _.extend({}, defaults, attributes); + } + if (options && options.collection) this.collection = options.collection; + this.attributes = {}; + this._escapedAttributes = {}; + this.cid = _.uniqueId('c'); + this.changed = {}; + this._silent = {}; + this._pending = {}; + this.set(attributes, {silent: true}); + // Reset change tracking. + this.changed = {}; + this._silent = {}; + this._pending = {}; + this._previousAttributes = _.clone(this.attributes); + this.initialize.apply(this, arguments); + }; + + // Attach all inheritable methods to the Model prototype. + _.extend(Model.prototype, Events, { + + // A hash of attributes whose current and previous value differ. + changed: null, + + // A hash of attributes that have silently changed since the last time + // `change` was called. Will become pending attributes on the next call. + _silent: null, + + // A hash of attributes that have changed since the last `'change'` event + // began. + _pending: null, + + // The default name for the JSON `id` attribute is `"id"`. MongoDB and + // CouchDB users may want to set this to `"_id"`. + idAttribute: 'id', + + // Initialize is an empty function by default. Override it with your own + // initialization logic. + initialize: function(){}, + + // Return a copy of the model's `attributes` object. + toJSON: function(options) { + return _.clone(this.attributes); + }, + + // Get the value of an attribute. + get: function(attr) { + return this.attributes[attr]; + }, + + // Get the HTML-escaped value of an attribute. + escape: function(attr) { + var html; + if (html = this._escapedAttributes[attr]) return html; + var val = this.get(attr); + return this._escapedAttributes[attr] = _.escape(val == null ? '' : '' + val); + }, + + // Returns `true` if the attribute contains a value that is not null + // or undefined. + has: function(attr) { + return this.get(attr) != null; + }, + + // Set a hash of model attributes on the object, firing `"change"` unless + // you choose to silence it. + set: function(key, value, options) { + var attrs, attr, val; + + // Handle both `"key", value` and `{key: value}` -style arguments. + if (_.isObject(key) || key == null) { + attrs = key; + options = value; + } else { + attrs = {}; + attrs[key] = value; + } + + // Extract attributes and options. + options || (options = {}); + if (!attrs) return this; + if (attrs instanceof Model) attrs = attrs.attributes; + if (options.unset) for (attr in attrs) attrs[attr] = void 0; + + // Run validation. + if (!this._validate(attrs, options)) return false; + + // Check for changes of `id`. + if (this.idAttribute in attrs) this.id = attrs[this.idAttribute]; + + var changes = options.changes = {}; + var now = this.attributes; + var escaped = this._escapedAttributes; + var prev = this._previousAttributes || {}; + + // For each `set` attribute... + for (attr in attrs) { + val = attrs[attr]; + + // If the new and current value differ, record the change. + if (!_.isEqual(now[attr], val) || (options.unset && _.has(now, attr))) { + delete escaped[attr]; + (options.silent ? this._silent : changes)[attr] = true; + } + + // Update or delete the current value. + options.unset ? delete now[attr] : now[attr] = val; + + // If the new and previous value differ, record the change. If not, + // then remove changes for this attribute. + if (!_.isEqual(prev[attr], val) || (_.has(now, attr) != _.has(prev, attr))) { + this.changed[attr] = val; + if (!options.silent) this._pending[attr] = true; + } else { + delete this.changed[attr]; + delete this._pending[attr]; + } + } + + // Fire the `"change"` events. + if (!options.silent) this.change(options); + return this; + }, + + // Remove an attribute from the model, firing `"change"` unless you choose + // to silence it. `unset` is a noop if the attribute doesn't exist. + unset: function(attr, options) { + (options || (options = {})).unset = true; + return this.set(attr, null, options); + }, + + // Clear all attributes on the model, firing `"change"` unless you choose + // to silence it. + clear: function(options) { + (options || (options = {})).unset = true; + return this.set(_.clone(this.attributes), options); + }, + + // Fetch the model from the server. If the server's representation of the + // model differs from its current attributes, they will be overriden, + // triggering a `"change"` event. + fetch: function(options) { + options = options ? _.clone(options) : {}; + var model = this; + var success = options.success; + options.success = function(resp, status, xhr) { + if (!model.set(model.parse(resp, xhr), options)) return false; + if (success) success(model, resp); + }; + options.error = Backbone.wrapError(options.error, model, options); + return (this.sync || Backbone.sync).call(this, 'read', this, options); + }, + + // Set a hash of model attributes, and sync the model to the server. + // If the server returns an attributes hash that differs, the model's + // state will be `set` again. + save: function(key, value, options) { + var attrs, current; + + // Handle both `("key", value)` and `({key: value})` -style calls. + if (_.isObject(key) || key == null) { + attrs = key; + options = value; + } else { + attrs = {}; + attrs[key] = value; + } + options = options ? _.clone(options) : {}; + + // If we're "wait"-ing to set changed attributes, validate early. + if (options.wait) { + if (!this._validate(attrs, options)) return false; + current = _.clone(this.attributes); + } + + // Regular saves `set` attributes before persisting to the server. + var silentOptions = _.extend({}, options, {silent: true}); + if (attrs && !this.set(attrs, options.wait ? silentOptions : options)) { + return false; + } + + // After a successful server-side save, the client is (optionally) + // updated with the server-side state. + var model = this; + var success = options.success; + options.success = function(resp, status, xhr) { + var serverAttrs = model.parse(resp, xhr); + if (options.wait) { + delete options.wait; + serverAttrs = _.extend(attrs || {}, serverAttrs); + } + if (!model.set(serverAttrs, options)) return false; + if (success) { + success(model, resp); + } else { + model.trigger('sync', model, resp, options); + } + }; + + // Finish configuring and sending the Ajax request. + options.error = Backbone.wrapError(options.error, model, options); + var method = this.isNew() ? 'create' : 'update'; + var xhr = (this.sync || Backbone.sync).call(this, method, this, options); + if (options.wait) this.set(current, silentOptions); + return xhr; + }, + + // Destroy this model on the server if it was already persisted. + // Optimistically removes the model from its collection, if it has one. + // If `wait: true` is passed, waits for the server to respond before removal. + destroy: function(options) { + options = options ? _.clone(options) : {}; + var model = this; + var success = options.success; + + var triggerDestroy = function() { + model.trigger('destroy', model, model.collection, options); + }; + + if (this.isNew()) { + triggerDestroy(); + return false; + } + + options.success = function(resp) { + if (options.wait) triggerDestroy(); + if (success) { + success(model, resp); + } else { + model.trigger('sync', model, resp, options); + } + }; + + options.error = Backbone.wrapError(options.error, model, options); + var xhr = (this.sync || Backbone.sync).call(this, 'delete', this, options); + if (!options.wait) triggerDestroy(); + return xhr; + }, + + // Default URL for the model's representation on the server -- if you're + // using Backbone's restful methods, override this to change the endpoint + // that will be called. + url: function() { + var base = getValue(this, 'urlRoot') || getValue(this.collection, 'url') || urlError(); + if (this.isNew()) return base; + return base + (base.charAt(base.length - 1) == '/' ? '' : '/') + encodeURIComponent(this.id); + }, + + // **parse** converts a response into the hash of attributes to be `set` on + // the model. The default implementation is just to pass the response along. + parse: function(resp, xhr) { + return resp; + }, + + // Create a new model with identical attributes to this one. + clone: function() { + return new this.constructor(this.attributes); + }, + + // A model is new if it has never been saved to the server, and lacks an id. + isNew: function() { + return this.id == null; + }, + + // Call this method to manually fire a `"change"` event for this model and + // a `"change:attribute"` event for each changed attribute. + // Calling this will cause all objects observing the model to update. + change: function(options) { + options || (options = {}); + var changing = this._changing; + this._changing = true; + + // Silent changes become pending changes. + for (var attr in this._silent) this._pending[attr] = true; + + // Silent changes are triggered. + var changes = _.extend({}, options.changes, this._silent); + this._silent = {}; + for (var attr in changes) { + this.trigger('change:' + attr, this, this.get(attr), options); + } + if (changing) return this; + + // Continue firing `"change"` events while there are pending changes. + while (!_.isEmpty(this._pending)) { + this._pending = {}; + this.trigger('change', this, options); + // Pending and silent changes still remain. + for (var attr in this.changed) { + if (this._pending[attr] || this._silent[attr]) continue; + delete this.changed[attr]; + } + this._previousAttributes = _.clone(this.attributes); + } + + this._changing = false; + return this; + }, + + // Determine if the model has changed since the last `"change"` event. + // If you specify an attribute name, determine if that attribute has changed. + hasChanged: function(attr) { + if (!arguments.length) return !_.isEmpty(this.changed); + return _.has(this.changed, attr); + }, + + // Return an object containing all the attributes that have changed, or + // false if there are no changed attributes. Useful for determining what + // parts of a view need to be updated and/or what attributes need to be + // persisted to the server. Unset attributes will be set to undefined. + // You can also pass an attributes object to diff against the model, + // determining if there *would be* a change. + changedAttributes: function(diff) { + if (!diff) return this.hasChanged() ? _.clone(this.changed) : false; + var val, changed = false, old = this._previousAttributes; + for (var attr in diff) { + if (_.isEqual(old[attr], (val = diff[attr]))) continue; + (changed || (changed = {}))[attr] = val; + } + return changed; + }, + + // Get the previous value of an attribute, recorded at the time the last + // `"change"` event was fired. + previous: function(attr) { + if (!arguments.length || !this._previousAttributes) return null; + return this._previousAttributes[attr]; + }, + + // Get all of the attributes of the model at the time of the previous + // `"change"` event. + previousAttributes: function() { + return _.clone(this._previousAttributes); + }, + + // Check if the model is currently in a valid state. It's only possible to + // get into an *invalid* state if you're using silent changes. + isValid: function() { + return !this.validate(this.attributes); + }, + + // Run validation against the next complete set of model attributes, + // returning `true` if all is well. If a specific `error` callback has + // been passed, call that instead of firing the general `"error"` event. + _validate: function(attrs, options) { + if (options.silent || !this.validate) return true; + attrs = _.extend({}, this.attributes, attrs); + var error = this.validate(attrs, options); + if (!error) return true; + if (options && options.error) { + options.error(this, error, options); + } else { + this.trigger('error', this, error, options); + } + return false; + } + + }); + + // Backbone.Collection + // ------------------- + + // Provides a standard collection class for our sets of models, ordered + // or unordered. If a `comparator` is specified, the Collection will maintain + // its models in sort order, as they're added and removed. + var Collection = Backbone.Collection = function(models, options) { + options || (options = {}); + if (options.model) this.model = options.model; + if (options.comparator) this.comparator = options.comparator; + this._reset(); + this.initialize.apply(this, arguments); + if (models) this.reset(models, {silent: true, parse: options.parse}); + }; + + // Define the Collection's inheritable methods. + _.extend(Collection.prototype, Events, { + + // The default model for a collection is just a **Backbone.Model**. + // This should be overridden in most cases. + model: Model, + + // Initialize is an empty function by default. Override it with your own + // initialization logic. + initialize: function(){}, + + // The JSON representation of a Collection is an array of the + // models' attributes. + toJSON: function(options) { + return this.map(function(model){ return model.toJSON(options); }); + }, + + // Add a model, or list of models to the set. Pass **silent** to avoid + // firing the `add` event for every new model. + add: function(models, options) { + var i, index, length, model, cid, id, cids = {}, ids = {}, dups = []; + options || (options = {}); + models = _.isArray(models) ? models.slice() : [models]; + + // Begin by turning bare objects into model references, and preventing + // invalid models or duplicate models from being added. + for (i = 0, length = models.length; i < length; i++) { + if (!(model = models[i] = this._prepareModel(models[i], options))) { + throw new Error("Can't add an invalid model to a collection"); + } + cid = model.cid; + id = model.id; + if (cids[cid] || this._byCid[cid] || ((id != null) && (ids[id] || this._byId[id]))) { + dups.push(i); + continue; + } + cids[cid] = ids[id] = model; + } + + // Remove duplicates. + i = dups.length; + while (i--) { + models.splice(dups[i], 1); + } + + // Listen to added models' events, and index models for lookup by + // `id` and by `cid`. + for (i = 0, length = models.length; i < length; i++) { + (model = models[i]).on('all', this._onModelEvent, this); + this._byCid[model.cid] = model; + if (model.id != null) this._byId[model.id] = model; + } + + // Insert models into the collection, re-sorting if needed, and triggering + // `add` events unless silenced. + this.length += length; + index = options.at != null ? options.at : this.models.length; + splice.apply(this.models, [index, 0].concat(models)); + if (this.comparator) this.sort({silent: true}); + if (options.silent) return this; + for (i = 0, length = this.models.length; i < length; i++) { + if (!cids[(model = this.models[i]).cid]) continue; + options.index = i; + model.trigger('add', model, this, options); + } + return this; + }, + + // Remove a model, or a list of models from the set. Pass silent to avoid + // firing the `remove` event for every model removed. + remove: function(models, options) { + var i, l, index, model; + options || (options = {}); + models = _.isArray(models) ? models.slice() : [models]; + for (i = 0, l = models.length; i < l; i++) { + model = this.getByCid(models[i]) || this.get(models[i]); + if (!model) continue; + delete this._byId[model.id]; + delete this._byCid[model.cid]; + index = this.indexOf(model); + this.models.splice(index, 1); + this.length--; + if (!options.silent) { + options.index = index; + model.trigger('remove', model, this, options); + } + this._removeReference(model); + } + return this; + }, + + // Add a model to the end of the collection. + push: function(model, options) { + model = this._prepareModel(model, options); + this.add(model, options); + return model; + }, + + // Remove a model from the end of the collection. + pop: function(options) { + var model = this.at(this.length - 1); + this.remove(model, options); + return model; + }, + + // Add a model to the beginning of the collection. + unshift: function(model, options) { + model = this._prepareModel(model, options); + this.add(model, _.extend({at: 0}, options)); + return model; + }, + + // Remove a model from the beginning of the collection. + shift: function(options) { + var model = this.at(0); + this.remove(model, options); + return model; + }, + + // Get a model from the set by id. + get: function(id) { + if (id == null) return void 0; + return this._byId[id.id != null ? id.id : id]; + }, + + // Get a model from the set by client id. + getByCid: function(cid) { + return cid && this._byCid[cid.cid || cid]; + }, + + // Get the model at the given index. + at: function(index) { + return this.models[index]; + }, + + // Return models with matching attributes. Useful for simple cases of `filter`. + where: function(attrs) { + if (_.isEmpty(attrs)) return []; + return this.filter(function(model) { + for (var key in attrs) { + if (attrs[key] !== model.get(key)) return false; + } + return true; + }); + }, + + // Force the collection to re-sort itself. You don't need to call this under + // normal circumstances, as the set will maintain sort order as each item + // is added. + sort: function(options) { + options || (options = {}); + if (!this.comparator) throw new Error('Cannot sort a set without a comparator'); + var boundComparator = _.bind(this.comparator, this); + if (this.comparator.length == 1) { + this.models = this.sortBy(boundComparator); + } else { + this.models.sort(boundComparator); + } + if (!options.silent) this.trigger('reset', this, options); + return this; + }, + + // Pluck an attribute from each model in the collection. + pluck: function(attr) { + return _.map(this.models, function(model){ return model.get(attr); }); + }, + + // When you have more items than you want to add or remove individually, + // you can reset the entire set with a new list of models, without firing + // any `add` or `remove` events. Fires `reset` when finished. + reset: function(models, options) { + models || (models = []); + options || (options = {}); + for (var i = 0, l = this.models.length; i < l; i++) { + this._removeReference(this.models[i]); + } + this._reset(); + this.add(models, _.extend({silent: true}, options)); + if (!options.silent) this.trigger('reset', this, options); + return this; + }, + + // Fetch the default set of models for this collection, resetting the + // collection when they arrive. If `add: true` is passed, appends the + // models to the collection instead of resetting. + fetch: function(options) { + options = options ? _.clone(options) : {}; + if (options.parse === undefined) options.parse = true; + var collection = this; + var success = options.success; + options.success = function(resp, status, xhr) { + collection[options.add ? 'add' : 'reset'](collection.parse(resp, xhr), options); + if (success) success(collection, resp); + }; + options.error = Backbone.wrapError(options.error, collection, options); + return (this.sync || Backbone.sync).call(this, 'read', this, options); + }, + + // Create a new instance of a model in this collection. Add the model to the + // collection immediately, unless `wait: true` is passed, in which case we + // wait for the server to agree. + create: function(model, options) { + var coll = this; + options = options ? _.clone(options) : {}; + model = this._prepareModel(model, options); + if (!model) return false; + if (!options.wait) coll.add(model, options); + var success = options.success; + options.success = function(nextModel, resp, xhr) { + if (options.wait) coll.add(nextModel, options); + if (success) { + success(nextModel, resp); + } else { + nextModel.trigger('sync', model, resp, options); + } + }; + model.save(null, options); + return model; + }, + + // **parse** converts a response into a list of models to be added to the + // collection. The default implementation is just to pass it through. + parse: function(resp, xhr) { + return resp; + }, + + // Proxy to _'s chain. Can't be proxied the same way the rest of the + // underscore methods are proxied because it relies on the underscore + // constructor. + chain: function () { + return _(this.models).chain(); + }, + + // Reset all internal state. Called when the collection is reset. + _reset: function(options) { + this.length = 0; + this.models = []; + this._byId = {}; + this._byCid = {}; + }, + + // Prepare a model or hash of attributes to be added to this collection. + _prepareModel: function(model, options) { + options || (options = {}); + if (!(model instanceof Model)) { + var attrs = model; + options.collection = this; + model = new this.model(attrs, options); + if (!model._validate(model.attributes, options)) model = false; + } else if (!model.collection) { + model.collection = this; + } + return model; + }, + + // Internal method to remove a model's ties to a collection. + _removeReference: function(model) { + if (this == model.collection) { + delete model.collection; + } + model.off('all', this._onModelEvent, this); + }, + + // Internal method called every time a model in the set fires an event. + // Sets need to update their indexes when models change ids. All other + // events simply proxy through. "add" and "remove" events that originate + // in other collections are ignored. + _onModelEvent: function(event, model, collection, options) { + if ((event == 'add' || event == 'remove') && collection != this) return; + if (event == 'destroy') { + this.remove(model, options); + } + if (model && event === 'change:' + model.idAttribute) { + delete this._byId[model.previous(model.idAttribute)]; + this._byId[model.id] = model; + } + this.trigger.apply(this, arguments); + } + + }); + + // Underscore methods that we want to implement on the Collection. + var methods = ['forEach', 'each', 'map', 'reduce', 'reduceRight', 'find', + 'detect', 'filter', 'select', 'reject', 'every', 'all', 'some', 'any', + 'include', 'contains', 'invoke', 'max', 'min', 'sortBy', 'sortedIndex', + 'toArray', 'size', 'first', 'initial', 'rest', 'last', 'without', 'indexOf', + 'shuffle', 'lastIndexOf', 'isEmpty', 'groupBy']; + + // Mix in each Underscore method as a proxy to `Collection#models`. + _.each(methods, function(method) { + Collection.prototype[method] = function() { + return _[method].apply(_, [this.models].concat(_.toArray(arguments))); + }; + }); + + // Backbone.Router + // ------------------- + + // Routers map faux-URLs to actions, and fire events when routes are + // matched. Creating a new one sets its `routes` hash, if not set statically. + var Router = Backbone.Router = function(options) { + options || (options = {}); + if (options.routes) this.routes = options.routes; + this._bindRoutes(); + this.initialize.apply(this, arguments); + }; + + // Cached regular expressions for matching named param parts and splatted + // parts of route strings. + var namedParam = /:\w+/g; + var splatParam = /\*\w+/g; + var escapeRegExp = /[-[\]{}()+?.,\\^$|#\s]/g; + + // Set up all inheritable **Backbone.Router** properties and methods. + _.extend(Router.prototype, Events, { + + // Initialize is an empty function by default. Override it with your own + // initialization logic. + initialize: function(){}, + + // Manually bind a single named route to a callback. For example: + // + // this.route('search/:query/p:num', 'search', function(query, num) { + // ... + // }); + // + route: function(route, name, callback) { + Backbone.history || (Backbone.history = new History); + if (!_.isRegExp(route)) route = this._routeToRegExp(route); + if (!callback) callback = this[name]; + Backbone.history.route(route, _.bind(function(fragment) { + var args = this._extractParameters(route, fragment); + callback && callback.apply(this, args); + this.trigger.apply(this, ['route:' + name].concat(args)); + Backbone.history.trigger('route', this, name, args); + }, this)); + return this; + }, + + // Simple proxy to `Backbone.history` to save a fragment into the history. + navigate: function(fragment, options) { + Backbone.history.navigate(fragment, options); + }, + + // Bind all defined routes to `Backbone.history`. We have to reverse the + // order of the routes here to support behavior where the most general + // routes can be defined at the bottom of the route map. + _bindRoutes: function() { + if (!this.routes) return; + var routes = []; + for (var route in this.routes) { + routes.unshift([route, this.routes[route]]); + } + for (var i = 0, l = routes.length; i < l; i++) { + this.route(routes[i][0], routes[i][1], this[routes[i][1]]); + } + }, + + // Convert a route string into a regular expression, suitable for matching + // against the current location hash. + _routeToRegExp: function(route) { + route = route.replace(escapeRegExp, '\\$&') + .replace(namedParam, '([^\/]+)') + .replace(splatParam, '(.*?)'); + return new RegExp('^' + route + '$'); + }, + + // Given a route, and a URL fragment that it matches, return the array of + // extracted parameters. + _extractParameters: function(route, fragment) { + return route.exec(fragment).slice(1); + } + + }); + + // Backbone.History + // ---------------- + + // Handles cross-browser history management, based on URL fragments. If the + // browser does not support `onhashchange`, falls back to polling. + var History = Backbone.History = function() { + this.handlers = []; + _.bindAll(this, 'checkUrl'); + }; + + // Cached regex for cleaning leading hashes and slashes . + var routeStripper = /^[#\/]/; + + // Cached regex for detecting MSIE. + var isExplorer = /msie [\w.]+/; + + // Has the history handling already been started? + History.started = false; + + // Set up all inheritable **Backbone.History** properties and methods. + _.extend(History.prototype, Events, { + + // The default interval to poll for hash changes, if necessary, is + // twenty times a second. + interval: 50, + + // Gets the true hash value. Cannot use location.hash directly due to bug + // in Firefox where location.hash will always be decoded. + getHash: function(windowOverride) { + var loc = windowOverride ? windowOverride.location : window.location; + var match = loc.href.match(/#(.*)$/); + return match ? match[1] : ''; + }, + + // Get the cross-browser normalized URL fragment, either from the URL, + // the hash, or the override. + getFragment: function(fragment, forcePushState) { + if (fragment == null) { + if (this._hasPushState || forcePushState) { + fragment = window.location.pathname; + var search = window.location.search; + if (search) fragment += search; + } else { + fragment = this.getHash(); + } + } + if (!fragment.indexOf(this.options.root)) fragment = fragment.substr(this.options.root.length); + return fragment.replace(routeStripper, ''); + }, + + // Start the hash change handling, returning `true` if the current URL matches + // an existing route, and `false` otherwise. + start: function(options) { + if (History.started) throw new Error("Backbone.history has already been started"); + History.started = true; + + // Figure out the initial configuration. Do we need an iframe? + // Is pushState desired ... is it available? + this.options = _.extend({}, {root: '/'}, this.options, options); + this._wantsHashChange = this.options.hashChange !== false; + this._wantsPushState = !!this.options.pushState; + this._hasPushState = !!(this.options.pushState && window.history && window.history.pushState); + var fragment = this.getFragment(); + var docMode = document.documentMode; + var oldIE = (isExplorer.exec(navigator.userAgent.toLowerCase()) && (!docMode || docMode <= 7)); + + if (oldIE) { + this.iframe = $('<iframe src="javascript:0" tabindex="-1" />').hide().appendTo('body')[0].contentWindow; + this.navigate(fragment); + } + + // Depending on whether we're using pushState or hashes, and whether + // 'onhashchange' is supported, determine how we check the URL state. + if (this._hasPushState) { + $(window).bind('popstate', this.checkUrl); + } else if (this._wantsHashChange && ('onhashchange' in window) && !oldIE) { + $(window).bind('hashchange', this.checkUrl); + } else if (this._wantsHashChange) { + this._checkUrlInterval = setInterval(this.checkUrl, this.interval); + } + + // Determine if we need to change the base url, for a pushState link + // opened by a non-pushState browser. + this.fragment = fragment; + var loc = window.location; + var atRoot = loc.pathname == this.options.root; + + // If we've started off with a route from a `pushState`-enabled browser, + // but we're currently in a browser that doesn't support it... + if (this._wantsHashChange && this._wantsPushState && !this._hasPushState && !atRoot) { + this.fragment = this.getFragment(null, true); + window.location.replace(this.options.root + '#' + this.fragment); + // Return immediately as browser will do redirect to new url + return true; + + // Or if we've started out with a hash-based route, but we're currently + // in a browser where it could be `pushState`-based instead... + } else if (this._wantsPushState && this._hasPushState && atRoot && loc.hash) { + this.fragment = this.getHash().replace(routeStripper, ''); + window.history.replaceState({}, document.title, loc.protocol + '//' + loc.host + this.options.root + this.fragment); + } + + if (!this.options.silent) { + return this.loadUrl(); + } + }, + + // Disable Backbone.history, perhaps temporarily. Not useful in a real app, + // but possibly useful for unit testing Routers. + stop: function() { + $(window).unbind('popstate', this.checkUrl).unbind('hashchange', this.checkUrl); + clearInterval(this._checkUrlInterval); + History.started = false; + }, + + // Add a route to be tested when the fragment changes. Routes added later + // may override previous routes. + route: function(route, callback) { + this.handlers.unshift({route: route, callback: callback}); + }, + + // Checks the current URL to see if it has changed, and if it has, + // calls `loadUrl`, normalizing across the hidden iframe. + checkUrl: function(e) { + var current = this.getFragment(); + if (current == this.fragment && this.iframe) current = this.getFragment(this.getHash(this.iframe)); + if (current == this.fragment) return false; + if (this.iframe) this.navigate(current); + this.loadUrl() || this.loadUrl(this.getHash()); + }, + + // Attempt to load the current URL fragment. If a route succeeds with a + // match, returns `true`. If no defined routes matches the fragment, + // returns `false`. + loadUrl: function(fragmentOverride) { + var fragment = this.fragment = this.getFragment(fragmentOverride); + var matched = _.any(this.handlers, function(handler) { + if (handler.route.test(fragment)) { + handler.callback(fragment); + return true; + } + }); + return matched; + }, + + // Save a fragment into the hash history, or replace the URL state if the + // 'replace' option is passed. You are responsible for properly URL-encoding + // the fragment in advance. + // + // The options object can contain `trigger: true` if you wish to have the + // route callback be fired (not usually desirable), or `replace: true`, if + // you wish to modify the current URL without adding an entry to the history. + navigate: function(fragment, options) { + if (!History.started) return false; + if (!options || options === true) options = {trigger: options}; + var frag = (fragment || '').replace(routeStripper, ''); + if (this.fragment == frag) return; + + // If pushState is available, we use it to set the fragment as a real URL. + if (this._hasPushState) { + if (frag.indexOf(this.options.root) != 0) frag = this.options.root + frag; + this.fragment = frag; + window.history[options.replace ? 'replaceState' : 'pushState']({}, document.title, frag); + + // If hash changes haven't been explicitly disabled, update the hash + // fragment to store history. + } else if (this._wantsHashChange) { + this.fragment = frag; + this._updateHash(window.location, frag, options.replace); + if (this.iframe && (frag != this.getFragment(this.getHash(this.iframe)))) { + // Opening and closing the iframe tricks IE7 and earlier to push a history entry on hash-tag change. + // When replace is true, we don't want this. + if(!options.replace) this.iframe.document.open().close(); + this._updateHash(this.iframe.location, frag, options.replace); + } + + // If you've told us that you explicitly don't want fallback hashchange- + // based history, then `navigate` becomes a page refresh. + } else { + window.location.assign(this.options.root + fragment); + } + if (options.trigger) this.loadUrl(fragment); + }, + + // Update the hash location, either replacing the current entry, or adding + // a new one to the browser history. + _updateHash: function(location, fragment, replace) { + if (replace) { + location.replace(location.toString().replace(/(javascript:|#).*$/, '') + '#' + fragment); + } else { + location.hash = fragment; + } + } + }); + + // Backbone.View + // ------------- + + // Creating a Backbone.View creates its initial element outside of the DOM, + // if an existing element is not provided... + var View = Backbone.View = function(options) { + this.cid = _.uniqueId('view'); + this._configure(options || {}); + this._ensureElement(); + this.initialize.apply(this, arguments); + this.delegateEvents(); + }; + + // Cached regex to split keys for `delegate`. + var delegateEventSplitter = /^(\S+)\s*(.*)$/; + + // List of view options to be merged as properties. + var viewOptions = ['model', 'collection', 'el', 'id', 'attributes', 'className', 'tagName']; + + // Set up all inheritable **Backbone.View** properties and methods. + _.extend(View.prototype, Events, { + + // The default `tagName` of a View's element is `"div"`. + tagName: 'div', + + // jQuery delegate for element lookup, scoped to DOM elements within the + // current view. This should be prefered to global lookups where possible. + $: function(selector) { + return this.$el.find(selector); + }, + + // Initialize is an empty function by default. Override it with your own + // initialization logic. + initialize: function(){}, + + // **render** is the core function that your view should override, in order + // to populate its element (`this.el`), with the appropriate HTML. The + // convention is for **render** to always return `this`. + render: function() { + return this; + }, + + // Remove this view from the DOM. Note that the view isn't present in the + // DOM by default, so calling this method may be a no-op. + remove: function() { + this.$el.remove(); + return this; + }, + + // For small amounts of DOM Elements, where a full-blown template isn't + // needed, use **make** to manufacture elements, one at a time. + // + // var el = this.make('li', {'class': 'row'}, this.model.escape('title')); + // + make: function(tagName, attributes, content) { + var el = document.createElement(tagName); + if (attributes) $(el).attr(attributes); + if (content) $(el).html(content); + return el; + }, + + // Change the view's element (`this.el` property), including event + // re-delegation. + setElement: function(element, delegate) { + if (this.$el) this.undelegateEvents(); + this.$el = (element instanceof $) ? element : $(element); + this.el = this.$el[0]; + if (delegate !== false) this.delegateEvents(); + return this; + }, + + // Set callbacks, where `this.events` is a hash of + // + // *{"event selector": "callback"}* + // + // { + // 'mousedown .title': 'edit', + // 'click .button': 'save' + // 'click .open': function(e) { ... } + // } + // + // pairs. Callbacks will be bound to the view, with `this` set properly. + // Uses event delegation for efficiency. + // Omitting the selector binds the event to `this.el`. + // This only works for delegate-able events: not `focus`, `blur`, and + // not `change`, `submit`, and `reset` in Internet Explorer. + delegateEvents: function(events) { + if (!(events || (events = getValue(this, 'events')))) return; + this.undelegateEvents(); + for (var key in events) { + var method = events[key]; + if (!_.isFunction(method)) method = this[events[key]]; + if (!method) throw new Error('Method "' + events[key] + '" does not exist'); + var match = key.match(delegateEventSplitter); + var eventName = match[1], selector = match[2]; + method = _.bind(method, this); + eventName += '.delegateEvents' + this.cid; + if (selector === '') { + this.$el.bind(eventName, method); + } else { + this.$el.delegate(selector, eventName, method); + } + } + }, + + // Clears all callbacks previously bound to the view with `delegateEvents`. + // You usually don't need to use this, but may wish to if you have multiple + // Backbone views attached to the same DOM element. + undelegateEvents: function() { + this.$el.unbind('.delegateEvents' + this.cid); + }, + + // Performs the initial configuration of a View with a set of options. + // Keys with special meaning *(model, collection, id, className)*, are + // attached directly to the view. + _configure: function(options) { + if (this.options) options = _.extend({}, this.options, options); + for (var i = 0, l = viewOptions.length; i < l; i++) { + var attr = viewOptions[i]; + if (options[attr]) this[attr] = options[attr]; + } + this.options = options; + }, + + // Ensure that the View has a DOM element to render into. + // If `this.el` is a string, pass it through `$()`, take the first + // matching element, and re-assign it to `el`. Otherwise, create + // an element from the `id`, `className` and `tagName` properties. + _ensureElement: function() { + if (!this.el) { + var attrs = getValue(this, 'attributes') || {}; + if (this.id) attrs.id = this.id; + if (this.className) attrs['class'] = this.className; + this.setElement(this.make(this.tagName, attrs), false); + } else { + this.setElement(this.el, false); + } + } + + }); + + // The self-propagating extend function that Backbone classes use. + var extend = function (protoProps, classProps) { + var child = inherits(this, protoProps, classProps); + child.extend = this.extend; + return child; + }; + + // Set up inheritance for the model, collection, and view. + Model.extend = Collection.extend = Router.extend = View.extend = extend; + + // Backbone.sync + // ------------- + + // Map from CRUD to HTTP for our default `Backbone.sync` implementation. + var methodMap = { + 'create': 'POST', + 'update': 'PUT', + 'delete': 'DELETE', + 'read': 'GET' + }; + + // Override this function to change the manner in which Backbone persists + // models to the server. You will be passed the type of request, and the + // model in question. By default, makes a RESTful Ajax request + // to the model's `url()`. Some possible customizations could be: + // + // * Use `setTimeout` to batch rapid-fire updates into a single request. + // * Send up the models as XML instead of JSON. + // * Persist models via WebSockets instead of Ajax. + // + // Turn on `Backbone.emulateHTTP` in order to send `PUT` and `DELETE` requests + // as `POST`, with a `_method` parameter containing the true HTTP method, + // as well as all requests with the body as `application/x-www-form-urlencoded` + // instead of `application/json` with the model in a param named `model`. + // Useful when interfacing with server-side languages like **PHP** that make + // it difficult to read the body of `PUT` requests. + Backbone.sync = function(method, model, options) { + var type = methodMap[method]; + + // Default options, unless specified. + options || (options = {}); + + // Default JSON-request options. + var params = {type: type, dataType: 'json'}; + + // Ensure that we have a URL. + if (!options.url) { + params.url = getValue(model, 'url') || urlError(); + } + + // Ensure that we have the appropriate request data. + if (!options.data && model && (method == 'create' || method == 'update')) { + params.contentType = 'application/json'; + params.data = JSON.stringify(model.toJSON()); + } + + // For older servers, emulate JSON by encoding the request into an HTML-form. + if (Backbone.emulateJSON) { + params.contentType = 'application/x-www-form-urlencoded'; + params.data = params.data ? {model: params.data} : {}; + } + + // For older servers, emulate HTTP by mimicking the HTTP method with `_method` + // And an `X-HTTP-Method-Override` header. + if (Backbone.emulateHTTP) { + if (type === 'PUT' || type === 'DELETE') { + if (Backbone.emulateJSON) params.data._method = type; + params.type = 'POST'; + params.beforeSend = function(xhr) { + xhr.setRequestHeader('X-HTTP-Method-Override', type); + }; + } + } + + // Don't process data on a non-GET request. + if (params.type !== 'GET' && !Backbone.emulateJSON) { + params.processData = false; + } + + // Make the request, allowing the user to override any Ajax options. + return $.ajax(_.extend(params, options)); + }; + + // Wrap an optional error callback with a fallback error event. + Backbone.wrapError = function(onError, originalModel, options) { + return function(model, resp) { + resp = model === originalModel ? resp : model; + if (onError) { + onError(originalModel, resp, options); + } else { + originalModel.trigger('error', originalModel, resp, options); + } + }; + }; + + // Helpers + // ------- + + // Shared empty constructor function to aid in prototype-chain creation. + var ctor = function(){}; + + // Helper function to correctly set up the prototype chain, for subclasses. + // Similar to `goog.inherits`, but uses a hash of prototype properties and + // class properties to be extended. + var inherits = function(parent, protoProps, staticProps) { + var child; + + // The constructor function for the new subclass is either defined by you + // (the "constructor" property in your `extend` definition), or defaulted + // by us to simply call the parent's constructor. + if (protoProps && protoProps.hasOwnProperty('constructor')) { + child = protoProps.constructor; + } else { + child = function(){ parent.apply(this, arguments); }; + } + + // Inherit class (static) properties from parent. + _.extend(child, parent); + + // Set the prototype chain to inherit from `parent`, without calling + // `parent`'s constructor function. + ctor.prototype = parent.prototype; + child.prototype = new ctor(); + + // Add prototype properties (instance properties) to the subclass, + // if supplied. + if (protoProps) _.extend(child.prototype, protoProps); + + // Add static properties to the constructor function, if supplied. + if (staticProps) _.extend(child, staticProps); + + // Correctly set child's `prototype.constructor`. + child.prototype.constructor = child; + + // Set a convenience property in case the parent's prototype is needed later. + child.__super__ = parent.prototype; + + return child; + }; + + // Helper function to get a value from a Backbone object as a property + // or as a function. + var getValue = function(object, prop) { + if (!(object && object[prop])) return null; + return _.isFunction(object[prop]) ? object[prop]() : object[prop]; + }; + + // Throw an error when a URL is needed, and none is supplied. + var urlError = function() { + throw new Error('A "url" property or function must be specified'); + }; + +}).call(this); diff -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 -r 70397647fad54c50213e015aaedfed94e6b19eda static/scripts/libs/handlebars-1.0.0.beta.6.js --- /dev/null +++ b/static/scripts/libs/handlebars-1.0.0.beta.6.js @@ -0,0 +1,1550 @@ +// lib/handlebars/base.js +var Handlebars = {}; + +Handlebars.VERSION = "1.0.beta.6"; + +Handlebars.helpers = {}; +Handlebars.partials = {}; + +Handlebars.registerHelper = function(name, fn, inverse) { + if(inverse) { fn.not = inverse; } + this.helpers[name] = fn; +}; + +Handlebars.registerPartial = function(name, str) { + this.partials[name] = str; +}; + +Handlebars.registerHelper('helperMissing', function(arg) { + if(arguments.length === 2) { + return undefined; + } else { + throw new Error("Could not find property '" + arg + "'"); + } +}); + +var toString = Object.prototype.toString, functionType = "[object Function]"; + +Handlebars.registerHelper('blockHelperMissing', function(context, options) { + var inverse = options.inverse || function() {}, fn = options.fn; + + + var ret = ""; + var type = toString.call(context); + + if(type === functionType) { context = context.call(this); } + + if(context === true) { + return fn(this); + } else if(context === false || context == null) { + return inverse(this); + } else if(type === "[object Array]") { + if(context.length > 0) { + for(var i=0, j=context.length; i<j; i++) { + ret = ret + fn(context[i]); + } + } else { + ret = inverse(this); + } + return ret; + } else { + return fn(context); + } +}); + +Handlebars.registerHelper('each', function(context, options) { + var fn = options.fn, inverse = options.inverse; + var ret = ""; + + if(context && context.length > 0) { + for(var i=0, j=context.length; i<j; i++) { + ret = ret + fn(context[i]); + } + } else { + ret = inverse(this); + } + return ret; +}); + +Handlebars.registerHelper('if', function(context, options) { + var type = toString.call(context); + if(type === functionType) { context = context.call(this); } + + if(!context || Handlebars.Utils.isEmpty(context)) { + return options.inverse(this); + } else { + return options.fn(this); + } +}); + +Handlebars.registerHelper('unless', function(context, options) { + var fn = options.fn, inverse = options.inverse; + options.fn = inverse; + options.inverse = fn; + + return Handlebars.helpers['if'].call(this, context, options); +}); + +Handlebars.registerHelper('with', function(context, options) { + return options.fn(context); +}); + +Handlebars.registerHelper('log', function(context) { + Handlebars.log(context); +}); +; +// lib/handlebars/compiler/parser.js +/* Jison generated parser */ +var handlebars = (function(){ + +var parser = {trace: function trace() { }, +yy: {}, +symbols_: {"error":2,"root":3,"program":4,"EOF":5,"statements":6,"simpleInverse":7,"statement":8,"openInverse":9,"closeBlock":10,"openBlock":11,"mustache":12,"partial":13,"CONTENT":14,"COMMENT":15,"OPEN_BLOCK":16,"inMustache":17,"CLOSE":18,"OPEN_INVERSE":19,"OPEN_ENDBLOCK":20,"path":21,"OPEN":22,"OPEN_UNESCAPED":23,"OPEN_PARTIAL":24,"params":25,"hash":26,"param":27,"STRING":28,"INTEGER":29,"BOOLEAN":30,"hashSegments":31,"hashSegment":32,"ID":33,"EQUALS":34,"pathSegments":35,"SEP":36,"$accept":0,"$end":1}, +terminals_: {2:"error",5:"EOF",14:"CONTENT",15:"COMMENT",16:"OPEN_BLOCK",18:"CLOSE",19:"OPEN_INVERSE",20:"OPEN_ENDBLOCK",22:"OPEN",23:"OPEN_UNESCAPED",24:"OPEN_PARTIAL",28:"STRING",29:"INTEGER",30:"BOOLEAN",33:"ID",34:"EQUALS",36:"SEP"}, +productions_: [0,[3,2],[4,3],[4,1],[4,0],[6,1],[6,2],[8,3],[8,3],[8,1],[8,1],[8,1],[8,1],[11,3],[9,3],[10,3],[12,3],[12,3],[13,3],[13,4],[7,2],[17,3],[17,2],[17,2],[17,1],[25,2],[25,1],[27,1],[27,1],[27,1],[27,1],[26,1],[31,2],[31,1],[32,3],[32,3],[32,3],[32,3],[21,1],[35,3],[35,1]], +performAction: function anonymous(yytext,yyleng,yylineno,yy,yystate,$$,_$) { + +var $0 = $$.length - 1; +switch (yystate) { +case 1: return $$[$0-1] +break; +case 2: this.$ = new yy.ProgramNode($$[$0-2], $$[$0]) +break; +case 3: this.$ = new yy.ProgramNode($$[$0]) +break; +case 4: this.$ = new yy.ProgramNode([]) +break; +case 5: this.$ = [$$[$0]] +break; +case 6: $$[$0-1].push($$[$0]); this.$ = $$[$0-1] +break; +case 7: this.$ = new yy.InverseNode($$[$0-2], $$[$0-1], $$[$0]) +break; +case 8: this.$ = new yy.BlockNode($$[$0-2], $$[$0-1], $$[$0]) +break; +case 9: this.$ = $$[$0] +break; +case 10: this.$ = $$[$0] +break; +case 11: this.$ = new yy.ContentNode($$[$0]) +break; +case 12: this.$ = new yy.CommentNode($$[$0]) +break; +case 13: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) +break; +case 14: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) +break; +case 15: this.$ = $$[$0-1] +break; +case 16: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1]) +break; +case 17: this.$ = new yy.MustacheNode($$[$0-1][0], $$[$0-1][1], true) +break; +case 18: this.$ = new yy.PartialNode($$[$0-1]) +break; +case 19: this.$ = new yy.PartialNode($$[$0-2], $$[$0-1]) +break; +case 20: +break; +case 21: this.$ = [[$$[$0-2]].concat($$[$0-1]), $$[$0]] +break; +case 22: this.$ = [[$$[$0-1]].concat($$[$0]), null] +break; +case 23: this.$ = [[$$[$0-1]], $$[$0]] +break; +case 24: this.$ = [[$$[$0]], null] +break; +case 25: $$[$0-1].push($$[$0]); this.$ = $$[$0-1]; +break; +case 26: this.$ = [$$[$0]] +break; +case 27: this.$ = $$[$0] +break; +case 28: this.$ = new yy.StringNode($$[$0]) +break; +case 29: this.$ = new yy.IntegerNode($$[$0]) +break; +case 30: this.$ = new yy.BooleanNode($$[$0]) +break; +case 31: this.$ = new yy.HashNode($$[$0]) +break; +case 32: $$[$0-1].push($$[$0]); this.$ = $$[$0-1] +break; +case 33: this.$ = [$$[$0]] +break; +case 34: this.$ = [$$[$0-2], $$[$0]] +break; +case 35: this.$ = [$$[$0-2], new yy.StringNode($$[$0])] +break; +case 36: this.$ = [$$[$0-2], new yy.IntegerNode($$[$0])] +break; +case 37: this.$ = [$$[$0-2], new yy.BooleanNode($$[$0])] +break; +case 38: this.$ = new yy.IdNode($$[$0]) +break; +case 39: $$[$0-2].push($$[$0]); this.$ = $$[$0-2]; +break; +case 40: this.$ = [$$[$0]] +break; +} +}, +table: [{3:1,4:2,5:[2,4],6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],22:[1,13],23:[1,14],24:[1,15]},{1:[3]},{5:[1,16]},{5:[2,3],7:17,8:18,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,19],20:[2,3],22:[1,13],23:[1,14],24:[1,15]},{5:[2,5],14:[2,5],15:[2,5],16:[2,5],19:[2,5],20:[2,5],22:[2,5],23:[2,5],24:[2,5]},{4:20,6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,4],22:[1,13],23:[1,14],24:[1,15]},{4:21,6:3,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,4],22:[1,13],23:[1,14],24:[1,15]},{5:[2,9],14:[2,9],15:[2,9],16:[2,9],19:[2,9],20:[2,9],22:[2,9],23:[2,9],24:[2,9]},{5:[2,10],14:[2,10],15:[2,10],16:[2,10],19:[2,10],20:[2,10],22:[2,10],23:[2,10],24:[2,10]},{5:[2,11],14:[2,11],15:[2,11],16:[2,11],19:[2,11],20:[2,11],22:[2,11],23:[2,11],24:[2,11]},{5:[2,12],14:[2,12],15:[2,12],16:[2,12],19:[2,12],20:[2,12],22:[2,12],23:[2,12],24:[2,12]},{17:22,21:23,33:[1,25],35:24},{17:26,21:23,33:[1,25],35:24},{17:27,21:23,33:[1,25],35:24},{17:28,21:23,33:[1,25],35:24},{21:29,33:[1,25],35:24},{1:[2,1]},{6:30,8:4,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],22:[1,13],23:[1,14],24:[1,15]},{5:[2,6],14:[2,6],15:[2,6],16:[2,6],19:[2,6],20:[2,6],22:[2,6],23:[2,6],24:[2,6]},{17:22,18:[1,31],21:23,33:[1,25],35:24},{10:32,20:[1,33]},{10:34,20:[1,33]},{18:[1,35]},{18:[2,24],21:40,25:36,26:37,27:38,28:[1,41],29:[1,42],30:[1,43],31:39,32:44,33:[1,45],35:24},{18:[2,38],28:[2,38],29:[2,38],30:[2,38],33:[2,38],36:[1,46]},{18:[2,40],28:[2,40],29:[2,40],30:[2,40],33:[2,40],36:[2,40]},{18:[1,47]},{18:[1,48]},{18:[1,49]},{18:[1,50],21:51,33:[1,25],35:24},{5:[2,2],8:18,9:5,11:6,12:7,13:8,14:[1,9],15:[1,10],16:[1,12],19:[1,11],20:[2,2],22:[1,13],23:[1,14],24:[1,15]},{14:[2,20],15:[2,20],16:[2,20],19:[2,20],22:[2,20],23:[2,20],24:[2,20]},{5:[2,7],14:[2,7],15:[2,7],16:[2,7],19:[2,7],20:[2,7],22:[2,7],23:[2,7],24:[2,7]},{21:52,33:[1,25],35:24},{5:[2,8],14:[2,8],15:[2,8],16:[2,8],19:[2,8],20:[2,8],22:[2,8],23:[2,8],24:[2,8]},{14:[2,14],15:[2,14],16:[2,14],19:[2,14],20:[2,14],22:[2,14],23:[2,14],24:[2,14]},{18:[2,22],21:40,26:53,27:54,28:[1,41],29:[1,42],30:[1,43],31:39,32:44,33:[1,45],35:24},{18:[2,23]},{18:[2,26],28:[2,26],29:[2,26],30:[2,26],33:[2,26]},{18:[2,31],32:55,33:[1,56]},{18:[2,27],28:[2,27],29:[2,27],30:[2,27],33:[2,27]},{18:[2,28],28:[2,28],29:[2,28],30:[2,28],33:[2,28]},{18:[2,29],28:[2,29],29:[2,29],30:[2,29],33:[2,29]},{18:[2,30],28:[2,30],29:[2,30],30:[2,30],33:[2,30]},{18:[2,33],33:[2,33]},{18:[2,40],28:[2,40],29:[2,40],30:[2,40],33:[2,40],34:[1,57],36:[2,40]},{33:[1,58]},{14:[2,13],15:[2,13],16:[2,13],19:[2,13],20:[2,13],22:[2,13],23:[2,13],24:[2,13]},{5:[2,16],14:[2,16],15:[2,16],16:[2,16],19:[2,16],20:[2,16],22:[2,16],23:[2,16],24:[2,16]},{5:[2,17],14:[2,17],15:[2,17],16:[2,17],19:[2,17],20:[2,17],22:[2,17],23:[2,17],24:[2,17]},{5:[2,18],14:[2,18],15:[2,18],16:[2,18],19:[2,18],20:[2,18],22:[2,18],23:[2,18],24:[2,18]},{18:[1,59]},{18:[1,60]},{18:[2,21]},{18:[2,25],28:[2,25],29:[2,25],30:[2,25],33:[2,25]},{18:[2,32],33:[2,32]},{34:[1,57]},{21:61,28:[1,62],29:[1,63],30:[1,64],33:[1,25],35:24},{18:[2,39],28:[2,39],29:[2,39],30:[2,39],33:[2,39],36:[2,39]},{5:[2,19],14:[2,19],15:[2,19],16:[2,19],19:[2,19],20:[2,19],22:[2,19],23:[2,19],24:[2,19]},{5:[2,15],14:[2,15],15:[2,15],16:[2,15],19:[2,15],20:[2,15],22:[2,15],23:[2,15],24:[2,15]},{18:[2,34],33:[2,34]},{18:[2,35],33:[2,35]},{18:[2,36],33:[2,36]},{18:[2,37],33:[2,37]}], +defaultActions: {16:[2,1],37:[2,23],53:[2,21]}, +parseError: function parseError(str, hash) { + throw new Error(str); +}, +parse: function parse(input) { + var self = this, stack = [0], vstack = [null], lstack = [], table = this.table, yytext = "", yylineno = 0, yyleng = 0, recovering = 0, TERROR = 2, EOF = 1; + this.lexer.setInput(input); + this.lexer.yy = this.yy; + this.yy.lexer = this.lexer; + if (typeof this.lexer.yylloc == "undefined") + this.lexer.yylloc = {}; + var yyloc = this.lexer.yylloc; + lstack.push(yyloc); + if (typeof this.yy.parseError === "function") + this.parseError = this.yy.parseError; + function popStack(n) { + stack.length = stack.length - 2 * n; + vstack.length = vstack.length - n; + lstack.length = lstack.length - n; + } + function lex() { + var token; + token = self.lexer.lex() || 1; + if (typeof token !== "number") { + token = self.symbols_[token] || token; + } + return token; + } + var symbol, preErrorSymbol, state, action, a, r, yyval = {}, p, len, newState, expected; + while (true) { + state = stack[stack.length - 1]; + if (this.defaultActions[state]) { + action = this.defaultActions[state]; + } else { + if (symbol == null) + symbol = lex(); + action = table[state] && table[state][symbol]; + } + if (typeof action === "undefined" || !action.length || !action[0]) { + if (!recovering) { + expected = []; + for (p in table[state]) + if (this.terminals_[p] && p > 2) { + expected.push("'" + this.terminals_[p] + "'"); + } + var errStr = ""; + if (this.lexer.showPosition) { + errStr = "Parse error on line " + (yylineno + 1) + ":\n" + this.lexer.showPosition() + "\nExpecting " + expected.join(", ") + ", got '" + this.terminals_[symbol] + "'"; + } else { + errStr = "Parse error on line " + (yylineno + 1) + ": Unexpected " + (symbol == 1?"end of input":"'" + (this.terminals_[symbol] || symbol) + "'"); + } + this.parseError(errStr, {text: this.lexer.match, token: this.terminals_[symbol] || symbol, line: this.lexer.yylineno, loc: yyloc, expected: expected}); + } + } + if (action[0] instanceof Array && action.length > 1) { + throw new Error("Parse Error: multiple actions possible at state: " + state + ", token: " + symbol); + } + switch (action[0]) { + case 1: + stack.push(symbol); + vstack.push(this.lexer.yytext); + lstack.push(this.lexer.yylloc); + stack.push(action[1]); + symbol = null; + if (!preErrorSymbol) { + yyleng = this.lexer.yyleng; + yytext = this.lexer.yytext; + yylineno = this.lexer.yylineno; + yyloc = this.lexer.yylloc; + if (recovering > 0) + recovering--; + } else { + symbol = preErrorSymbol; + preErrorSymbol = null; + } + break; + case 2: + len = this.productions_[action[1]][1]; + yyval.$ = vstack[vstack.length - len]; + yyval._$ = {first_line: lstack[lstack.length - (len || 1)].first_line, last_line: lstack[lstack.length - 1].last_line, first_column: lstack[lstack.length - (len || 1)].first_column, last_column: lstack[lstack.length - 1].last_column}; + r = this.performAction.call(yyval, yytext, yyleng, yylineno, this.yy, action[1], vstack, lstack); + if (typeof r !== "undefined") { + return r; + } + if (len) { + stack = stack.slice(0, -1 * len * 2); + vstack = vstack.slice(0, -1 * len); + lstack = lstack.slice(0, -1 * len); + } + stack.push(this.productions_[action[1]][0]); + vstack.push(yyval.$); + lstack.push(yyval._$); + newState = table[stack[stack.length - 2]][stack[stack.length - 1]]; + stack.push(newState); + break; + case 3: + return true; + } + } + return true; +} +};/* Jison generated lexer */ +var lexer = (function(){ + +var lexer = ({EOF:1, +parseError:function parseError(str, hash) { + if (this.yy.parseError) { + this.yy.parseError(str, hash); + } else { + throw new Error(str); + } + }, +setInput:function (input) { + this._input = input; + this._more = this._less = this.done = false; + this.yylineno = this.yyleng = 0; + this.yytext = this.matched = this.match = ''; + this.conditionStack = ['INITIAL']; + this.yylloc = {first_line:1,first_column:0,last_line:1,last_column:0}; + return this; + }, +input:function () { + var ch = this._input[0]; + this.yytext+=ch; + this.yyleng++; + this.match+=ch; + this.matched+=ch; + var lines = ch.match(/\n/); + if (lines) this.yylineno++; + this._input = this._input.slice(1); + return ch; + }, +unput:function (ch) { + this._input = ch + this._input; + return this; + }, +more:function () { + this._more = true; + return this; + }, +pastInput:function () { + var past = this.matched.substr(0, this.matched.length - this.match.length); + return (past.length > 20 ? '...':'') + past.substr(-20).replace(/\n/g, ""); + }, +upcomingInput:function () { + var next = this.match; + if (next.length < 20) { + next += this._input.substr(0, 20-next.length); + } + return (next.substr(0,20)+(next.length > 20 ? '...':'')).replace(/\n/g, ""); + }, +showPosition:function () { + var pre = this.pastInput(); + var c = new Array(pre.length + 1).join("-"); + return pre + this.upcomingInput() + "\n" + c+"^"; + }, +next:function () { + if (this.done) { + return this.EOF; + } + if (!this._input) this.done = true; + + var token, + match, + col, + lines; + if (!this._more) { + this.yytext = ''; + this.match = ''; + } + var rules = this._currentRules(); + for (var i=0;i < rules.length; i++) { + match = this._input.match(this.rules[rules[i]]); + if (match) { + lines = match[0].match(/\n.*/g); + if (lines) this.yylineno += lines.length; + this.yylloc = {first_line: this.yylloc.last_line, + last_line: this.yylineno+1, + first_column: this.yylloc.last_column, + last_column: lines ? lines[lines.length-1].length-1 : this.yylloc.last_column + match[0].length} + this.yytext += match[0]; + this.match += match[0]; + this.matches = match; + this.yyleng = this.yytext.length; + this._more = false; + this._input = this._input.slice(match[0].length); + this.matched += match[0]; + token = this.performAction.call(this, this.yy, this, rules[i],this.conditionStack[this.conditionStack.length-1]); + if (token) return token; + else return; + } + } + if (this._input === "") { + return this.EOF; + } else { + this.parseError('Lexical error on line '+(this.yylineno+1)+'. Unrecognized text.\n'+this.showPosition(), + {text: "", token: null, line: this.yylineno}); + } + }, +lex:function lex() { + var r = this.next(); + if (typeof r !== 'undefined') { + return r; + } else { + return this.lex(); + } + }, +begin:function begin(condition) { + this.conditionStack.push(condition); + }, +popState:function popState() { + return this.conditionStack.pop(); + }, +_currentRules:function _currentRules() { + return this.conditions[this.conditionStack[this.conditionStack.length-1]].rules; + }, +topState:function () { + return this.conditionStack[this.conditionStack.length-2]; + }, +pushState:function begin(condition) { + this.begin(condition); + }}); +lexer.performAction = function anonymous(yy,yy_,$avoiding_name_collisions,YY_START) { + +var YYSTATE=YY_START +switch($avoiding_name_collisions) { +case 0: + if(yy_.yytext.slice(-1) !== "\\") this.begin("mu"); + if(yy_.yytext.slice(-1) === "\\") yy_.yytext = yy_.yytext.substr(0,yy_.yyleng-1), this.begin("emu"); + if(yy_.yytext) return 14; + +break; +case 1: return 14; +break; +case 2: this.popState(); return 14; +break; +case 3: return 24; +break; +case 4: return 16; +break; +case 5: return 20; +break; +case 6: return 19; +break; +case 7: return 19; +break; +case 8: return 23; +break; +case 9: return 23; +break; +case 10: yy_.yytext = yy_.yytext.substr(3,yy_.yyleng-5); this.popState(); return 15; +break; +case 11: return 22; +break; +case 12: return 34; +break; +case 13: return 33; +break; +case 14: return 33; +break; +case 15: return 36; +break; +case 16: /*ignore whitespace*/ +break; +case 17: this.popState(); return 18; +break; +case 18: this.popState(); return 18; +break; +case 19: yy_.yytext = yy_.yytext.substr(1,yy_.yyleng-2).replace(/\\"/g,'"'); return 28; +break; +case 20: return 30; +break; +case 21: return 30; +break; +case 22: return 29; +break; +case 23: return 33; +break; +case 24: yy_.yytext = yy_.yytext.substr(1, yy_.yyleng-2); return 33; +break; +case 25: return 'INVALID'; +break; +case 26: return 5; +break; +} +}; +lexer.rules = [/^[^\x00]*?(?=(\{\{))/,/^[^\x00]+/,/^[^\x00]{2,}?(?=(\{\{))/,/^\{\{>/,/^\{\{#/,/^\{\{\//,/^\{\{\^/,/^\{\{\s*else\b/,/^\{\{\{/,/^\{\{&/,/^\{\{![\s\S]*?\}\}/,/^\{\{/,/^=/,/^\.(?=[} ])/,/^\.\./,/^[\/.]/,/^\s+/,/^\}\}\}/,/^\}\}/,/^"(\\["]|[^"])*"/,/^true(?=[}\s])/,/^false(?=[}\s])/,/^[0-9]+(?=[}\s])/,/^[a-zA-Z0-9_$-]+(?=[=}\s\/.])/,/^\[[^\]]*\]/,/^./,/^$/]; +lexer.conditions = {"mu":{"rules":[3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26],"inclusive":false},"emu":{"rules":[2],"inclusive":false},"INITIAL":{"rules":[0,1,26],"inclusive":true}};return lexer;})() +parser.lexer = lexer; +return parser; +})(); +if (typeof require !== 'undefined' && typeof exports !== 'undefined') { +exports.parser = handlebars; +exports.parse = function () { return handlebars.parse.apply(handlebars, arguments); } +exports.main = function commonjsMain(args) { + if (!args[1]) + throw new Error('Usage: '+args[0]+' FILE'); + if (typeof process !== 'undefined') { + var source = require('fs').readFileSync(require('path').join(process.cwd(), args[1]), "utf8"); + } else { + var cwd = require("file").path(require("file").cwd()); + var source = cwd.join(args[1]).read({charset: "utf-8"}); + } + return exports.parser.parse(source); +} +if (typeof module !== 'undefined' && require.main === module) { + exports.main(typeof process !== 'undefined' ? process.argv.slice(1) : require("system").args); +} +}; +; +// lib/handlebars/compiler/base.js +Handlebars.Parser = handlebars; + +Handlebars.parse = function(string) { + Handlebars.Parser.yy = Handlebars.AST; + return Handlebars.Parser.parse(string); +}; + +Handlebars.print = function(ast) { + return new Handlebars.PrintVisitor().accept(ast); +}; + +Handlebars.logger = { + DEBUG: 0, INFO: 1, WARN: 2, ERROR: 3, level: 3, + + // override in the host environment + log: function(level, str) {} +}; + +Handlebars.log = function(level, str) { Handlebars.logger.log(level, str); }; +; +// lib/handlebars/compiler/ast.js +(function() { + + Handlebars.AST = {}; + + Handlebars.AST.ProgramNode = function(statements, inverse) { + this.type = "program"; + this.statements = statements; + if(inverse) { this.inverse = new Handlebars.AST.ProgramNode(inverse); } + }; + + Handlebars.AST.MustacheNode = function(params, hash, unescaped) { + this.type = "mustache"; + this.id = params[0]; + this.params = params.slice(1); + this.hash = hash; + this.escaped = !unescaped; + }; + + Handlebars.AST.PartialNode = function(id, context) { + this.type = "partial"; + + // TODO: disallow complex IDs + + this.id = id; + this.context = context; + }; + + var verifyMatch = function(open, close) { + if(open.original !== close.original) { + throw new Handlebars.Exception(open.original + " doesn't match " + close.original); + } + }; + + Handlebars.AST.BlockNode = function(mustache, program, close) { + verifyMatch(mustache.id, close); + this.type = "block"; + this.mustache = mustache; + this.program = program; + }; + + Handlebars.AST.InverseNode = function(mustache, program, close) { + verifyMatch(mustache.id, close); + this.type = "inverse"; + this.mustache = mustache; + this.program = program; + }; + + Handlebars.AST.ContentNode = function(string) { + this.type = "content"; + this.string = string; + }; + + Handlebars.AST.HashNode = function(pairs) { + this.type = "hash"; + this.pairs = pairs; + }; + + Handlebars.AST.IdNode = function(parts) { + this.type = "ID"; + this.original = parts.join("."); + + var dig = [], depth = 0; + + for(var i=0,l=parts.length; i<l; i++) { + var part = parts[i]; + + if(part === "..") { depth++; } + else if(part === "." || part === "this") { this.isScoped = true; } + else { dig.push(part); } + } + + this.parts = dig; + this.string = dig.join('.'); + this.depth = depth; + this.isSimple = (dig.length === 1) && (depth === 0); + }; + + Handlebars.AST.StringNode = function(string) { + this.type = "STRING"; + this.string = string; + }; + + Handlebars.AST.IntegerNode = function(integer) { + this.type = "INTEGER"; + this.integer = integer; + }; + + Handlebars.AST.BooleanNode = function(bool) { + this.type = "BOOLEAN"; + this.bool = bool; + }; + + Handlebars.AST.CommentNode = function(comment) { + this.type = "comment"; + this.comment = comment; + }; + +})();; +// lib/handlebars/utils.js +Handlebars.Exception = function(message) { + var tmp = Error.prototype.constructor.apply(this, arguments); + + for (var p in tmp) { + if (tmp.hasOwnProperty(p)) { this[p] = tmp[p]; } + } + + this.message = tmp.message; +}; +Handlebars.Exception.prototype = new Error; + +// Build out our basic SafeString type +Handlebars.SafeString = function(string) { + this.string = string; +}; +Handlebars.SafeString.prototype.toString = function() { + return this.string.toString(); +}; + +(function() { + var escape = { + "<": "<", + ">": ">", + '"': """, + "'": "'", + "`": "`" + }; + + var badChars = /&(?!\w+;)|[<>"'`]/g; + var possible = /[&<>"'`]/; + + var escapeChar = function(chr) { + return escape[chr] || "&"; + }; + + Handlebars.Utils = { + escapeExpression: function(string) { + // don't escape SafeStrings, since they're already safe + if (string instanceof Handlebars.SafeString) { + return string.toString(); + } else if (string == null || string === false) { + return ""; + } + + if(!possible.test(string)) { return string; } + return string.replace(badChars, escapeChar); + }, + + isEmpty: function(value) { + if (typeof value === "undefined") { + return true; + } else if (value === null) { + return true; + } else if (value === false) { + return true; + } else if(Object.prototype.toString.call(value) === "[object Array]" && value.length === 0) { + return true; + } else { + return false; + } + } + }; +})();; +// lib/handlebars/compiler/compiler.js +Handlebars.Compiler = function() {}; +Handlebars.JavaScriptCompiler = function() {}; + +(function(Compiler, JavaScriptCompiler) { + Compiler.OPCODE_MAP = { + appendContent: 1, + getContext: 2, + lookupWithHelpers: 3, + lookup: 4, + append: 5, + invokeMustache: 6, + appendEscaped: 7, + pushString: 8, + truthyOrFallback: 9, + functionOrFallback: 10, + invokeProgram: 11, + invokePartial: 12, + push: 13, + assignToHash: 15, + pushStringParam: 16 + }; + + Compiler.MULTI_PARAM_OPCODES = { + appendContent: 1, + getContext: 1, + lookupWithHelpers: 2, + lookup: 1, + invokeMustache: 3, + pushString: 1, + truthyOrFallback: 1, + functionOrFallback: 1, + invokeProgram: 3, + invokePartial: 1, + push: 1, + assignToHash: 1, + pushStringParam: 1 + }; + + Compiler.DISASSEMBLE_MAP = {}; + + for(var prop in Compiler.OPCODE_MAP) { + var value = Compiler.OPCODE_MAP[prop]; + Compiler.DISASSEMBLE_MAP[value] = prop; + } + + Compiler.multiParamSize = function(code) { + return Compiler.MULTI_PARAM_OPCODES[Compiler.DISASSEMBLE_MAP[code]]; + }; + + Compiler.prototype = { + compiler: Compiler, + + disassemble: function() { + var opcodes = this.opcodes, opcode, nextCode; + var out = [], str, name, value; + + for(var i=0, l=opcodes.length; i<l; i++) { + opcode = opcodes[i]; + + if(opcode === 'DECLARE') { + name = opcodes[++i]; + value = opcodes[++i]; + out.push("DECLARE " + name + " = " + value); + } else { + str = Compiler.DISASSEMBLE_MAP[opcode]; + + var extraParams = Compiler.multiParamSize(opcode); + var codes = []; + + for(var j=0; j<extraParams; j++) { + nextCode = opcodes[++i]; + + if(typeof nextCode === "string") { + nextCode = "\"" + nextCode.replace("\n", "\\n") + "\""; + } + + codes.push(nextCode); + } + + str = str + " " + codes.join(" "); + + out.push(str); + } + } + + return out.join("\n"); + }, + + guid: 0, + + compile: function(program, options) { + this.children = []; + this.depths = {list: []}; + this.options = options; + + // These changes will propagate to the other compiler components + var knownHelpers = this.options.knownHelpers; + this.options.knownHelpers = { + 'helperMissing': true, + 'blockHelperMissing': true, + 'each': true, + 'if': true, + 'unless': true, + 'with': true, + 'log': true + }; + if (knownHelpers) { + for (var name in knownHelpers) { + this.options.knownHelpers[name] = knownHelpers[name]; + } + } + + return this.program(program); + }, + + accept: function(node) { + return this[node.type](node); + }, + + program: function(program) { + var statements = program.statements, statement; + this.opcodes = []; + + for(var i=0, l=statements.length; i<l; i++) { + statement = statements[i]; + this[statement.type](statement); + } + this.isSimple = l === 1; + + this.depths.list = this.depths.list.sort(function(a, b) { + return a - b; + }); + + return this; + }, + + compileProgram: function(program) { + var result = new this.compiler().compile(program, this.options); + var guid = this.guid++; + + this.usePartial = this.usePartial || result.usePartial; + + this.children[guid] = result; + + for(var i=0, l=result.depths.list.length; i<l; i++) { + depth = result.depths.list[i]; + + if(depth < 2) { continue; } + else { this.addDepth(depth - 1); } + } + + return guid; + }, + + block: function(block) { + var mustache = block.mustache; + var depth, child, inverse, inverseGuid; + + var params = this.setupStackForMustache(mustache); + + var programGuid = this.compileProgram(block.program); + + if(block.program.inverse) { + inverseGuid = this.compileProgram(block.program.inverse); + this.declare('inverse', inverseGuid); + } + + this.opcode('invokeProgram', programGuid, params.length, !!mustache.hash); + this.declare('inverse', null); + this.opcode('append'); + }, + + inverse: function(block) { + var params = this.setupStackForMustache(block.mustache); + + var programGuid = this.compileProgram(block.program); + + this.declare('inverse', programGuid); + + this.opcode('invokeProgram', null, params.length, !!block.mustache.hash); + this.declare('inverse', null); + this.opcode('append'); + }, + + hash: function(hash) { + var pairs = hash.pairs, pair, val; + + this.opcode('push', '{}'); + + for(var i=0, l=pairs.length; i<l; i++) { + pair = pairs[i]; + val = pair[1]; + + this.accept(val); + this.opcode('assignToHash', pair[0]); + } + }, + + partial: function(partial) { + var id = partial.id; + this.usePartial = true; + + if(partial.context) { + this.ID(partial.context); + } else { + this.opcode('push', 'depth0'); + } + + this.opcode('invokePartial', id.original); + this.opcode('append'); + }, + + content: function(content) { + this.opcode('appendContent', content.string); + }, + + mustache: function(mustache) { + var params = this.setupStackForMustache(mustache); + + this.opcode('invokeMustache', params.length, mustache.id.original, !!mustache.hash); + + if(mustache.escaped && !this.options.noEscape) { + this.opcode('appendEscaped'); + } else { + this.opcode('append'); + } + }, + + ID: function(id) { + this.addDepth(id.depth); + + this.opcode('getContext', id.depth); + + this.opcode('lookupWithHelpers', id.parts[0] || null, id.isScoped || false); + + for(var i=1, l=id.parts.length; i<l; i++) { + this.opcode('lookup', id.parts[i]); + } + }, + + STRING: function(string) { + this.opcode('pushString', string.string); + }, + + INTEGER: function(integer) { + this.opcode('push', integer.integer); + }, + + BOOLEAN: function(bool) { + this.opcode('push', bool.bool); + }, + + comment: function() {}, + + // HELPERS + pushParams: function(params) { + var i = params.length, param; + + while(i--) { + param = params[i]; + + if(this.options.stringParams) { + if(param.depth) { + this.addDepth(param.depth); + } + + this.opcode('getContext', param.depth || 0); + this.opcode('pushStringParam', param.string); + } else { + this[param.type](param); + } + } + }, + + opcode: function(name, val1, val2, val3) { + this.opcodes.push(Compiler.OPCODE_MAP[name]); + if(val1 !== undefined) { this.opcodes.push(val1); } + if(val2 !== undefined) { this.opcodes.push(val2); } + if(val3 !== undefined) { this.opcodes.push(val3); } + }, + + declare: function(name, value) { + this.opcodes.push('DECLARE'); + this.opcodes.push(name); + this.opcodes.push(value); + }, + + addDepth: function(depth) { + if(depth === 0) { return; } + + if(!this.depths[depth]) { + this.depths[depth] = true; + this.depths.list.push(depth); + } + }, + + setupStackForMustache: function(mustache) { + var params = mustache.params; + + this.pushParams(params); + + if(mustache.hash) { + this.hash(mustache.hash); + } + + this.ID(mustache.id); + + return params; + } + }; + + JavaScriptCompiler.prototype = { + // PUBLIC API: You can override these methods in a subclass to provide + // alternative compiled forms for name lookup and buffering semantics + nameLookup: function(parent, name, type) { + if (/^[0-9]+$/.test(name)) { + return parent + "[" + name + "]"; + } else if (JavaScriptCompiler.isValidJavaScriptVariableName(name)) { + return parent + "." + name; + } + else { + return parent + "['" + name + "']"; + } + }, + + appendToBuffer: function(string) { + if (this.environment.isSimple) { + return "return " + string + ";"; + } else { + return "buffer += " + string + ";"; + } + }, + + initializeBuffer: function() { + return this.quotedString(""); + }, + + namespace: "Handlebars", + // END PUBLIC API + + compile: function(environment, options, context, asObject) { + this.environment = environment; + this.options = options || {}; + + this.name = this.environment.name; + this.isChild = !!context; + this.context = context || { + programs: [], + aliases: { self: 'this' }, + registers: {list: []} + }; + + this.preamble(); + + this.stackSlot = 0; + this.stackVars = []; + + this.compileChildren(environment, options); + + var opcodes = environment.opcodes, opcode; + + this.i = 0; + + for(l=opcodes.length; this.i<l; this.i++) { + opcode = this.nextOpcode(0); + + if(opcode[0] === 'DECLARE') { + this.i = this.i + 2; + this[opcode[1]] = opcode[2]; + } else { + this.i = this.i + opcode[1].length; + this[opcode[0]].apply(this, opcode[1]); + } + } + + return this.createFunctionContext(asObject); + }, + + nextOpcode: function(n) { + var opcodes = this.environment.opcodes, opcode = opcodes[this.i + n], name, val; + var extraParams, codes; + + if(opcode === 'DECLARE') { + name = opcodes[this.i + 1]; + val = opcodes[this.i + 2]; + return ['DECLARE', name, val]; + } else { + name = Compiler.DISASSEMBLE_MAP[opcode]; + + extraParams = Compiler.multiParamSize(opcode); + codes = []; + + for(var j=0; j<extraParams; j++) { + codes.push(opcodes[this.i + j + 1 + n]); + } + + return [name, codes]; + } + }, + + eat: function(opcode) { + this.i = this.i + opcode.length; + }, + + preamble: function() { + var out = []; + + // this register will disambiguate helper lookup from finding a function in + // a context. This is necessary for mustache compatibility, which requires + // that context functions in blocks are evaluated by blockHelperMissing, and + // then proceed as if the resulting value was provided to blockHelperMissing. + this.useRegister('foundHelper'); + + if (!this.isChild) { + var namespace = this.namespace; + var copies = "helpers = helpers || " + namespace + ".helpers;"; + if(this.environment.usePartial) { copies = copies + " partials = partials || " + namespace + ".partials;"; } + out.push(copies); + } else { + out.push(''); + } + + if (!this.environment.isSimple) { + out.push(", buffer = " + this.initializeBuffer()); + } else { + out.push(""); + } + + // track the last context pushed into place to allow skipping the + // getContext opcode when it would be a noop + this.lastContext = 0; + this.source = out; + }, + + createFunctionContext: function(asObject) { + var locals = this.stackVars; + if (!this.isChild) { + locals = locals.concat(this.context.registers.list); + } + + if(locals.length > 0) { + this.source[1] = this.source[1] + ", " + locals.join(", "); + } + + // Generate minimizer alias mappings + if (!this.isChild) { + var aliases = [] + for (var alias in this.context.aliases) { + this.source[1] = this.source[1] + ', ' + alias + '=' + this.context.aliases[alias]; + } + } + + if (this.source[1]) { + this.source[1] = "var " + this.source[1].substring(2) + ";"; + } + + // Merge children + if (!this.isChild) { + this.source[1] += '\n' + this.context.programs.join('\n') + '\n'; + } + + if (!this.environment.isSimple) { + this.source.push("return buffer;"); + } + + var params = this.isChild ? ["depth0", "data"] : ["Handlebars", "depth0", "helpers", "partials", "data"]; + + for(var i=0, l=this.environment.depths.list.length; i<l; i++) { + params.push("depth" + this.environment.depths.list[i]); + } + + if (asObject) { + params.push(this.source.join("\n ")); + + return Function.apply(this, params); + } else { + var functionSource = 'function ' + (this.name || '') + '(' + params.join(',') + ') {\n ' + this.source.join("\n ") + '}'; + Handlebars.log(Handlebars.logger.DEBUG, functionSource + "\n\n"); + return functionSource; + } + }, + + appendContent: function(content) { + this.source.push(this.appendToBuffer(this.quotedString(content))); + }, + + append: function() { + var local = this.popStack(); + this.source.push("if(" + local + " || " + local + " === 0) { " + this.appendToBuffer(local) + " }"); + if (this.environment.isSimple) { + this.source.push("else { " + this.appendToBuffer("''") + " }"); + } + }, + + appendEscaped: function() { + var opcode = this.nextOpcode(1), extra = ""; + this.context.aliases.escapeExpression = 'this.escapeExpression'; + + if(opcode[0] === 'appendContent') { + extra = " + " + this.quotedString(opcode[1][0]); + this.eat(opcode); + } + + this.source.push(this.appendToBuffer("escapeExpression(" + this.popStack() + ")" + extra)); + }, + + getContext: function(depth) { + if(this.lastContext !== depth) { + this.lastContext = depth; + } + }, + + lookupWithHelpers: function(name, isScoped) { + if(name) { + var topStack = this.nextStack(); + + this.usingKnownHelper = false; + + var toPush; + if (!isScoped && this.options.knownHelpers[name]) { + toPush = topStack + " = " + this.nameLookup('helpers', name, 'helper'); + this.usingKnownHelper = true; + } else if (isScoped || this.options.knownHelpersOnly) { + toPush = topStack + " = " + this.nameLookup('depth' + this.lastContext, name, 'context'); + } else { + this.register('foundHelper', this.nameLookup('helpers', name, 'helper')); + toPush = topStack + " = foundHelper || " + this.nameLookup('depth' + this.lastContext, name, 'context'); + } + + toPush += ';'; + this.source.push(toPush); + } else { + this.pushStack('depth' + this.lastContext); + } + }, + + lookup: function(name) { + var topStack = this.topStack(); + this.source.push(topStack + " = (" + topStack + " === null || " + topStack + " === undefined || " + topStack + " === false ? " + + topStack + " : " + this.nameLookup(topStack, name, 'context') + ");"); + }, + + pushStringParam: function(string) { + this.pushStack('depth' + this.lastContext); + this.pushString(string); + }, + + pushString: function(string) { + this.pushStack(this.quotedString(string)); + }, + + push: function(name) { + this.pushStack(name); + }, + + invokeMustache: function(paramSize, original, hasHash) { + this.populateParams(paramSize, this.quotedString(original), "{}", null, hasHash, function(nextStack, helperMissingString, id) { + if (!this.usingKnownHelper) { + this.context.aliases.helperMissing = 'helpers.helperMissing'; + this.context.aliases.undef = 'void 0'; + this.source.push("else if(" + id + "=== undef) { " + nextStack + " = helperMissing.call(" + helperMissingString + "); }"); + if (nextStack !== id) { + this.source.push("else { " + nextStack + " = " + id + "; }"); + } + } + }); + }, + + invokeProgram: function(guid, paramSize, hasHash) { + var inverse = this.programExpression(this.inverse); + var mainProgram = this.programExpression(guid); + + this.populateParams(paramSize, null, mainProgram, inverse, hasHash, function(nextStack, helperMissingString, id) { + if (!this.usingKnownHelper) { + this.context.aliases.blockHelperMissing = 'helpers.blockHelperMissing'; + this.source.push("else { " + nextStack + " = blockHelperMissing.call(" + helperMissingString + "); }"); + } + }); + }, + + populateParams: function(paramSize, helperId, program, inverse, hasHash, fn) { + var needsRegister = hasHash || this.options.stringParams || inverse || this.options.data; + var id = this.popStack(), nextStack; + var params = [], param, stringParam, stringOptions; + + if (needsRegister) { + this.register('tmp1', program); + stringOptions = 'tmp1'; + } else { + stringOptions = '{ hash: {} }'; + } + + if (needsRegister) { + var hash = (hasHash ? this.popStack() : '{}'); + this.source.push('tmp1.hash = ' + hash + ';'); + } + + if(this.options.stringParams) { + this.source.push('tmp1.contexts = [];'); + } + + for(var i=0; i<paramSize; i++) { + param = this.popStack(); + params.push(param); + + if(this.options.stringParams) { + this.source.push('tmp1.contexts.push(' + this.popStack() + ');'); + } + } + + if(inverse) { + this.source.push('tmp1.fn = tmp1;'); + this.source.push('tmp1.inverse = ' + inverse + ';'); + } + + if(this.options.data) { + this.source.push('tmp1.data = data;'); + } + + params.push(stringOptions); + + this.populateCall(params, id, helperId || id, fn, program !== '{}'); + }, + + populateCall: function(params, id, helperId, fn, program) { + var paramString = ["depth0"].concat(params).join(", "); + var helperMissingString = ["depth0"].concat(helperId).concat(params).join(", "); + + var nextStack = this.nextStack(); + + if (this.usingKnownHelper) { + this.source.push(nextStack + " = " + id + ".call(" + paramString + ");"); + } else { + this.context.aliases.functionType = '"function"'; + var condition = program ? "foundHelper && " : "" + this.source.push("if(" + condition + "typeof " + id + " === functionType) { " + nextStack + " = " + id + ".call(" + paramString + "); }"); + } + fn.call(this, nextStack, helperMissingString, id); + this.usingKnownHelper = false; + }, + + invokePartial: function(context) { + params = [this.nameLookup('partials', context, 'partial'), "'" + context + "'", this.popStack(), "helpers", "partials"]; + + if (this.options.data) { + params.push("data"); + } + + this.pushStack("self.invokePartial(" + params.join(", ") + ");"); + }, + + assignToHash: function(key) { + var value = this.popStack(); + var hash = this.topStack(); + + this.source.push(hash + "['" + key + "'] = " + value + ";"); + }, + + // HELPERS + + compiler: JavaScriptCompiler, + + compileChildren: function(environment, options) { + var children = environment.children, child, compiler; + + for(var i=0, l=children.length; i<l; i++) { + child = children[i]; + compiler = new this.compiler(); + + this.context.programs.push(''); // Placeholder to prevent name conflicts for nested children + var index = this.context.programs.length; + child.index = index; + child.name = 'program' + index; + this.context.programs[index] = compiler.compile(child, options, this.context); + } + }, + + programExpression: function(guid) { + if(guid == null) { return "self.noop"; } + + var child = this.environment.children[guid], + depths = child.depths.list; + var programParams = [child.index, child.name, "data"]; + + for(var i=0, l = depths.length; i<l; i++) { + depth = depths[i]; + + if(depth === 1) { programParams.push("depth0"); } + else { programParams.push("depth" + (depth - 1)); } + } + + if(depths.length === 0) { + return "self.program(" + programParams.join(", ") + ")"; + } else { + programParams.shift(); + return "self.programWithDepth(" + programParams.join(", ") + ")"; + } + }, + + register: function(name, val) { + this.useRegister(name); + this.source.push(name + " = " + val + ";"); + }, + + useRegister: function(name) { + if(!this.context.registers[name]) { + this.context.registers[name] = true; + this.context.registers.list.push(name); + } + }, + + pushStack: function(item) { + this.source.push(this.nextStack() + " = " + item + ";"); + return "stack" + this.stackSlot; + }, + + nextStack: function() { + this.stackSlot++; + if(this.stackSlot > this.stackVars.length) { this.stackVars.push("stack" + this.stackSlot); } + return "stack" + this.stackSlot; + }, + + popStack: function() { + return "stack" + this.stackSlot--; + }, + + topStack: function() { + return "stack" + this.stackSlot; + }, + + quotedString: function(str) { + return '"' + str + .replace(/\\/g, '\\\\') + .replace(/"/g, '\\"') + .replace(/\n/g, '\\n') + .replace(/\r/g, '\\r') + '"'; + } + }; + + var reservedWords = ( + "break else new var" + + " case finally return void" + + " catch for switch while" + + " continue function this with" + + " default if throw" + + " delete in try" + + " do instanceof typeof" + + " abstract enum int short" + + " boolean export interface static" + + " byte extends long super" + + " char final native synchronized" + + " class float package throws" + + " const goto private transient" + + " debugger implements protected volatile" + + " double import public let yield" + ).split(" "); + + var compilerWords = JavaScriptCompiler.RESERVED_WORDS = {}; + + for(var i=0, l=reservedWords.length; i<l; i++) { + compilerWords[reservedWords[i]] = true; + } + + JavaScriptCompiler.isValidJavaScriptVariableName = function(name) { + if(!JavaScriptCompiler.RESERVED_WORDS[name] && /^[a-zA-Z_$][0-9a-zA-Z_$]+$/.test(name)) { + return true; + } + return false; + } + +})(Handlebars.Compiler, Handlebars.JavaScriptCompiler); + +Handlebars.precompile = function(string, options) { + options = options || {}; + + var ast = Handlebars.parse(string); + var environment = new Handlebars.Compiler().compile(ast, options); + return new Handlebars.JavaScriptCompiler().compile(environment, options); +}; + +Handlebars.compile = function(string, options) { + options = options || {}; + + var compiled; + function compile() { + var ast = Handlebars.parse(string); + var environment = new Handlebars.Compiler().compile(ast, options); + var templateSpec = new Handlebars.JavaScriptCompiler().compile(environment, options, undefined, true); + return Handlebars.template(templateSpec); + } + + // Template is only compiled on first use and cached after that point. + return function(context, options) { + if (!compiled) { + compiled = compile(); + } + return compiled.call(this, context, options); + }; +}; +; +// lib/handlebars/runtime.js +Handlebars.VM = { + template: function(templateSpec) { + // Just add water + var container = { + escapeExpression: Handlebars.Utils.escapeExpression, + invokePartial: Handlebars.VM.invokePartial, + programs: [], + program: function(i, fn, data) { + var programWrapper = this.programs[i]; + if(data) { + return Handlebars.VM.program(fn, data); + } else if(programWrapper) { + return programWrapper; + } else { + programWrapper = this.programs[i] = Handlebars.VM.program(fn); + return programWrapper; + } + }, + programWithDepth: Handlebars.VM.programWithDepth, + noop: Handlebars.VM.noop + }; + + return function(context, options) { + options = options || {}; + return templateSpec.call(container, Handlebars, context, options.helpers, options.partials, options.data); + }; + }, + + programWithDepth: function(fn, data, $depth) { + var args = Array.prototype.slice.call(arguments, 2); + + return function(context, options) { + options = options || {}; + + return fn.apply(this, [context, options.data || data].concat(args)); + }; + }, + program: function(fn, data) { + return function(context, options) { + options = options || {}; + + return fn(context, options.data || data); + }; + }, + noop: function() { return ""; }, + invokePartial: function(partial, name, context, helpers, partials, data) { + options = { helpers: helpers, partials: partials, data: data }; + + if(partial === undefined) { + throw new Handlebars.Exception("The partial " + name + " could not be found"); + } else if(partial instanceof Function) { + return partial(context, options); + } else if (!Handlebars.compile) { + throw new Handlebars.Exception("The partial " + name + " could not be compiled when running in runtime-only mode"); + } else { + partials[name] = Handlebars.compile(partial); + return partials[name](context, options); + } + } +}; + +Handlebars.template = Handlebars.VM.template; +; diff -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 -r 70397647fad54c50213e015aaedfed94e6b19eda static/scripts/libs/underscore.js --- /dev/null +++ b/static/scripts/libs/underscore.js @@ -0,0 +1,999 @@ +// Underscore.js 1.3.1 +// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc. +// Underscore is freely distributable under the MIT license. +// Portions of Underscore are inspired or borrowed from Prototype, +// Oliver Steele's Functional, and John Resig's Micro-Templating. +// For all details and documentation: +// http://documentcloud.github.com/underscore + +(function() { + + // Baseline setup + // -------------- + + // Establish the root object, `window` in the browser, or `global` on the server. + var root = this; + + // Save the previous value of the `_` variable. + var previousUnderscore = root._; + + // Establish the object that gets returned to break out of a loop iteration. + var breaker = {}; + + // Save bytes in the minified (but not gzipped) version: + var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype; + + // Create quick reference variables for speed access to core prototypes. + var slice = ArrayProto.slice, + unshift = ArrayProto.unshift, + toString = ObjProto.toString, + hasOwnProperty = ObjProto.hasOwnProperty; + + // All **ECMAScript 5** native function implementations that we hope to use + // are declared here. + var + nativeForEach = ArrayProto.forEach, + nativeMap = ArrayProto.map, + nativeReduce = ArrayProto.reduce, + nativeReduceRight = ArrayProto.reduceRight, + nativeFilter = ArrayProto.filter, + nativeEvery = ArrayProto.every, + nativeSome = ArrayProto.some, + nativeIndexOf = ArrayProto.indexOf, + nativeLastIndexOf = ArrayProto.lastIndexOf, + nativeIsArray = Array.isArray, + nativeKeys = Object.keys, + nativeBind = FuncProto.bind; + + // Create a safe reference to the Underscore object for use below. + var _ = function(obj) { return new wrapper(obj); }; + + // Export the Underscore object for **Node.js**, with + // backwards-compatibility for the old `require()` API. If we're in + // the browser, add `_` as a global object via a string identifier, + // for Closure Compiler "advanced" mode. + if (typeof exports !== 'undefined') { + if (typeof module !== 'undefined' && module.exports) { + exports = module.exports = _; + } + exports._ = _; + } else { + root['_'] = _; + } + + // Current version. + _.VERSION = '1.3.1'; + + // Collection Functions + // -------------------- + + // The cornerstone, an `each` implementation, aka `forEach`. + // Handles objects with the built-in `forEach`, arrays, and raw objects. + // Delegates to **ECMAScript 5**'s native `forEach` if available. + var each = _.each = _.forEach = function(obj, iterator, context) { + if (obj == null) return; + if (nativeForEach && obj.forEach === nativeForEach) { + obj.forEach(iterator, context); + } else if (obj.length === +obj.length) { + for (var i = 0, l = obj.length; i < l; i++) { + if (i in obj && iterator.call(context, obj[i], i, obj) === breaker) return; + } + } else { + for (var key in obj) { + if (_.has(obj, key)) { + if (iterator.call(context, obj[key], key, obj) === breaker) return; + } + } + } + }; + + // Return the results of applying the iterator to each element. + // Delegates to **ECMAScript 5**'s native `map` if available. + _.map = _.collect = function(obj, iterator, context) { + var results = []; + if (obj == null) return results; + if (nativeMap && obj.map === nativeMap) return obj.map(iterator, context); + each(obj, function(value, index, list) { + results[results.length] = iterator.call(context, value, index, list); + }); + if (obj.length === +obj.length) results.length = obj.length; + return results; + }; + + // **Reduce** builds up a single result from a list of values, aka `inject`, + // or `foldl`. Delegates to **ECMAScript 5**'s native `reduce` if available. + _.reduce = _.foldl = _.inject = function(obj, iterator, memo, context) { + var initial = arguments.length > 2; + if (obj == null) obj = []; + if (nativeReduce && obj.reduce === nativeReduce) { + if (context) iterator = _.bind(iterator, context); + return initial ? obj.reduce(iterator, memo) : obj.reduce(iterator); + } + each(obj, function(value, index, list) { + if (!initial) { + memo = value; + initial = true; + } else { + memo = iterator.call(context, memo, value, index, list); + } + }); + if (!initial) throw new TypeError('Reduce of empty array with no initial value'); + return memo; + }; + + // The right-associative version of reduce, also known as `foldr`. + // Delegates to **ECMAScript 5**'s native `reduceRight` if available. + _.reduceRight = _.foldr = function(obj, iterator, memo, context) { + var initial = arguments.length > 2; + if (obj == null) obj = []; + if (nativeReduceRight && obj.reduceRight === nativeReduceRight) { + if (context) iterator = _.bind(iterator, context); + return initial ? obj.reduceRight(iterator, memo) : obj.reduceRight(iterator); + } + var reversed = _.toArray(obj).reverse(); + if (context && !initial) iterator = _.bind(iterator, context); + return initial ? _.reduce(reversed, iterator, memo, context) : _.reduce(reversed, iterator); + }; + + // Return the first value which passes a truth test. Aliased as `detect`. + _.find = _.detect = function(obj, iterator, context) { + var result; + any(obj, function(value, index, list) { + if (iterator.call(context, value, index, list)) { + result = value; + return true; + } + }); + return result; + }; + + // Return all the elements that pass a truth test. + // Delegates to **ECMAScript 5**'s native `filter` if available. + // Aliased as `select`. + _.filter = _.select = function(obj, iterator, context) { + var results = []; + if (obj == null) return results; + if (nativeFilter && obj.filter === nativeFilter) return obj.filter(iterator, context); + each(obj, function(value, index, list) { + if (iterator.call(context, value, index, list)) results[results.length] = value; + }); + return results; + }; + + // Return all the elements for which a truth test fails. + _.reject = function(obj, iterator, context) { + var results = []; + if (obj == null) return results; + each(obj, function(value, index, list) { + if (!iterator.call(context, value, index, list)) results[results.length] = value; + }); + return results; + }; + + // Determine whether all of the elements match a truth test. + // Delegates to **ECMAScript 5**'s native `every` if available. + // Aliased as `all`. + _.every = _.all = function(obj, iterator, context) { + var result = true; + if (obj == null) return result; + if (nativeEvery && obj.every === nativeEvery) return obj.every(iterator, context); + each(obj, function(value, index, list) { + if (!(result = result && iterator.call(context, value, index, list))) return breaker; + }); + return result; + }; + + // Determine if at least one element in the object matches a truth test. + // Delegates to **ECMAScript 5**'s native `some` if available. + // Aliased as `any`. + var any = _.some = _.any = function(obj, iterator, context) { + iterator || (iterator = _.identity); + var result = false; + if (obj == null) return result; + if (nativeSome && obj.some === nativeSome) return obj.some(iterator, context); + each(obj, function(value, index, list) { + if (result || (result = iterator.call(context, value, index, list))) return breaker; + }); + return !!result; + }; + + // Determine if a given value is included in the array or object using `===`. + // Aliased as `contains`. + _.include = _.contains = function(obj, target) { + var found = false; + if (obj == null) return found; + if (nativeIndexOf && obj.indexOf === nativeIndexOf) return obj.indexOf(target) != -1; + found = any(obj, function(value) { + return value === target; + }); + return found; + }; + + // Invoke a method (with arguments) on every item in a collection. + _.invoke = function(obj, method) { + var args = slice.call(arguments, 2); + return _.map(obj, function(value) { + return (_.isFunction(method) ? method || value : value[method]).apply(value, args); + }); + }; + + // Convenience version of a common use case of `map`: fetching a property. + _.pluck = function(obj, key) { + return _.map(obj, function(value){ return value[key]; }); + }; + + // Return the maximum element or (element-based computation). + _.max = function(obj, iterator, context) { + if (!iterator && _.isArray(obj)) return Math.max.apply(Math, obj); + if (!iterator && _.isEmpty(obj)) return -Infinity; + var result = {computed : -Infinity}; + each(obj, function(value, index, list) { + var computed = iterator ? iterator.call(context, value, index, list) : value; + computed >= result.computed && (result = {value : value, computed : computed}); + }); + return result.value; + }; + + // Return the minimum element (or element-based computation). + _.min = function(obj, iterator, context) { + if (!iterator && _.isArray(obj)) return Math.min.apply(Math, obj); + if (!iterator && _.isEmpty(obj)) return Infinity; + var result = {computed : Infinity}; + each(obj, function(value, index, list) { + var computed = iterator ? iterator.call(context, value, index, list) : value; + computed < result.computed && (result = {value : value, computed : computed}); + }); + return result.value; + }; + + // Shuffle an array. + _.shuffle = function(obj) { + var shuffled = [], rand; + each(obj, function(value, index, list) { + if (index == 0) { + shuffled[0] = value; + } else { + rand = Math.floor(Math.random() * (index + 1)); + shuffled[index] = shuffled[rand]; + shuffled[rand] = value; + } + }); + return shuffled; + }; + + // Sort the object's values by a criterion produced by an iterator. + _.sortBy = function(obj, iterator, context) { + return _.pluck(_.map(obj, function(value, index, list) { + return { + value : value, + criteria : iterator.call(context, value, index, list) + }; + }).sort(function(left, right) { + var a = left.criteria, b = right.criteria; + return a < b ? -1 : a > b ? 1 : 0; + }), 'value'); + }; + + // Groups the object's values by a criterion. Pass either a string attribute + // to group by, or a function that returns the criterion. + _.groupBy = function(obj, val) { + var result = {}; + var iterator = _.isFunction(val) ? val : function(obj) { return obj[val]; }; + each(obj, function(value, index) { + var key = iterator(value, index); + (result[key] || (result[key] = [])).push(value); + }); + return result; + }; + + // Use a comparator function to figure out at what index an object should + // be inserted so as to maintain order. Uses binary search. + _.sortedIndex = function(array, obj, iterator) { + iterator || (iterator = _.identity); + var low = 0, high = array.length; + while (low < high) { + var mid = (low + high) >> 1; + iterator(array[mid]) < iterator(obj) ? low = mid + 1 : high = mid; + } + return low; + }; + + // Safely convert anything iterable into a real, live array. + _.toArray = function(iterable) { + if (!iterable) return []; + if (iterable.toArray) return iterable.toArray(); + if (_.isArray(iterable)) return slice.call(iterable); + if (_.isArguments(iterable)) return slice.call(iterable); + return _.values(iterable); + }; + + // Return the number of elements in an object. + _.size = function(obj) { + return _.toArray(obj).length; + }; + + // Array Functions + // --------------- + + // Get the first element of an array. Passing **n** will return the first N + // values in the array. Aliased as `head`. The **guard** check allows it to work + // with `_.map`. + _.first = _.head = function(array, n, guard) { + return (n != null) && !guard ? slice.call(array, 0, n) : array[0]; + }; + + // Returns everything but the last entry of the array. Especcialy useful on + // the arguments object. Passing **n** will return all the values in + // the array, excluding the last N. The **guard** check allows it to work with + // `_.map`. + _.initial = function(array, n, guard) { + return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n)); + }; + + // Get the last element of an array. Passing **n** will return the last N + // values in the array. The **guard** check allows it to work with `_.map`. + _.last = function(array, n, guard) { + if ((n != null) && !guard) { + return slice.call(array, Math.max(array.length - n, 0)); + } else { + return array[array.length - 1]; + } + }; + + // Returns everything but the first entry of the array. Aliased as `tail`. + // Especially useful on the arguments object. Passing an **index** will return + // the rest of the values in the array from that index onward. The **guard** + // check allows it to work with `_.map`. + _.rest = _.tail = function(array, index, guard) { + return slice.call(array, (index == null) || guard ? 1 : index); + }; + + // Trim out all falsy values from an array. + _.compact = function(array) { + return _.filter(array, function(value){ return !!value; }); + }; + + // Return a completely flattened version of an array. + _.flatten = function(array, shallow) { + return _.reduce(array, function(memo, value) { + if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value)); + memo[memo.length] = value; + return memo; + }, []); + }; + + // Return a version of the array that does not contain the specified value(s). + _.without = function(array) { + return _.difference(array, slice.call(arguments, 1)); + }; + + // Produce a duplicate-free version of the array. If the array has already + // been sorted, you have the option of using a faster algorithm. + // Aliased as `unique`. + _.uniq = _.unique = function(array, isSorted, iterator) { + var initial = iterator ? _.map(array, iterator) : array; + var result = []; + _.reduce(initial, function(memo, el, i) { + if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) { + memo[memo.length] = el; + result[result.length] = array[i]; + } + return memo; + }, []); + return result; + }; + + // Produce an array that contains the union: each distinct element from all of + // the passed-in arrays. + _.union = function() { + return _.uniq(_.flatten(arguments, true)); + }; + + // Produce an array that contains every item shared between all the + // passed-in arrays. (Aliased as "intersect" for back-compat.) + _.intersection = _.intersect = function(array) { + var rest = slice.call(arguments, 1); + return _.filter(_.uniq(array), function(item) { + return _.every(rest, function(other) { + return _.indexOf(other, item) >= 0; + }); + }); + }; + + // Take the difference between one array and a number of other arrays. + // Only the elements present in just the first array will remain. + _.difference = function(array) { + var rest = _.flatten(slice.call(arguments, 1)); + return _.filter(array, function(value){ return !_.include(rest, value); }); + }; + + // Zip together multiple lists into a single array -- elements that share + // an index go together. + _.zip = function() { + var args = slice.call(arguments); + var length = _.max(_.pluck(args, 'length')); + var results = new Array(length); + for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i); + return results; + }; + + // If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**), + // we need this function. Return the position of the first occurrence of an + // item in an array, or -1 if the item is not included in the array. + // Delegates to **ECMAScript 5**'s native `indexOf` if available. + // If the array is large and already in sort order, pass `true` + // for **isSorted** to use binary search. + _.indexOf = function(array, item, isSorted) { + if (array == null) return -1; + var i, l; + if (isSorted) { + i = _.sortedIndex(array, item); + return array[i] === item ? i : -1; + } + if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item); + for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i; + return -1; + }; + + // Delegates to **ECMAScript 5**'s native `lastIndexOf` if available. + _.lastIndexOf = function(array, item) { + if (array == null) return -1; + if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item); + var i = array.length; + while (i--) if (i in array && array[i] === item) return i; + return -1; + }; + + // Generate an integer Array containing an arithmetic progression. A port of + // the native Python `range()` function. See + // [the Python documentation](http://docs.python.org/library/functions.html#range). + _.range = function(start, stop, step) { + if (arguments.length <= 1) { + stop = start || 0; + start = 0; + } + step = arguments[2] || 1; + + var len = Math.max(Math.ceil((stop - start) / step), 0); + var idx = 0; + var range = new Array(len); + + while(idx < len) { + range[idx++] = start; + start += step; + } + + return range; + }; + + // Function (ahem) Functions + // ------------------ + + // Reusable constructor function for prototype setting. + var ctor = function(){}; + + // Create a function bound to a given object (assigning `this`, and arguments, + // optionally). Binding with arguments is also known as `curry`. + // Delegates to **ECMAScript 5**'s native `Function.bind` if available. + // We check for `func.bind` first, to fail fast when `func` is undefined. + _.bind = function bind(func, context) { + var bound, args; + if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1)); + if (!_.isFunction(func)) throw new TypeError; + args = slice.call(arguments, 2); + return bound = function() { + if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments))); + ctor.prototype = func.prototype; + var self = new ctor; + var result = func.apply(self, args.concat(slice.call(arguments))); + if (Object(result) === result) return result; + return self; + }; + }; + + // Bind all of an object's methods to that object. Useful for ensuring that + // all callbacks defined on an object belong to it. + _.bindAll = function(obj) { + var funcs = slice.call(arguments, 1); + if (funcs.length == 0) funcs = _.functions(obj); + each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); }); + return obj; + }; + + // Memoize an expensive function by storing its results. + _.memoize = function(func, hasher) { + var memo = {}; + hasher || (hasher = _.identity); + return function() { + var key = hasher.apply(this, arguments); + return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments)); + }; + }; + + // Delays a function for the given number of milliseconds, and then calls + // it with the arguments supplied. + _.delay = function(func, wait) { + var args = slice.call(arguments, 2); + return setTimeout(function(){ return func.apply(func, args); }, wait); + }; + + // Defers a function, scheduling it to run after the current call stack has + // cleared. + _.defer = function(func) { + return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1))); + }; + + // Returns a function, that, when invoked, will only be triggered at most once + // during a given window of time. + _.throttle = function(func, wait) { + var context, args, timeout, throttling, more; + var whenDone = _.debounce(function(){ more = throttling = false; }, wait); + return function() { + context = this; args = arguments; + var later = function() { + timeout = null; + if (more) func.apply(context, args); + whenDone(); + }; + if (!timeout) timeout = setTimeout(later, wait); + if (throttling) { + more = true; + } else { + func.apply(context, args); + } + whenDone(); + throttling = true; + }; + }; + + // Returns a function, that, as long as it continues to be invoked, will not + // be triggered. The function will be called after it stops being called for + // N milliseconds. + _.debounce = function(func, wait) { + var timeout; + return function() { + var context = this, args = arguments; + var later = function() { + timeout = null; + func.apply(context, args); + }; + clearTimeout(timeout); + timeout = setTimeout(later, wait); + }; + }; + + // Returns a function that will be executed at most one time, no matter how + // often you call it. Useful for lazy initialization. + _.once = function(func) { + var ran = false, memo; + return function() { + if (ran) return memo; + ran = true; + return memo = func.apply(this, arguments); + }; + }; + + // Returns the first function passed as an argument to the second, + // allowing you to adjust arguments, run code before and after, and + // conditionally execute the original function. + _.wrap = function(func, wrapper) { + return function() { + var args = [func].concat(slice.call(arguments, 0)); + return wrapper.apply(this, args); + }; + }; + + // Returns a function that is the composition of a list of functions, each + // consuming the return value of the function that follows. + _.compose = function() { + var funcs = arguments; + return function() { + var args = arguments; + for (var i = funcs.length - 1; i >= 0; i--) { + args = [funcs[i].apply(this, args)]; + } + return args[0]; + }; + }; + + // Returns a function that will only be executed after being called N times. + _.after = function(times, func) { + if (times <= 0) return func(); + return function() { + if (--times < 1) { return func.apply(this, arguments); } + }; + }; + + // Object Functions + // ---------------- + + // Retrieve the names of an object's properties. + // Delegates to **ECMAScript 5**'s native `Object.keys` + _.keys = nativeKeys || function(obj) { + if (obj !== Object(obj)) throw new TypeError('Invalid object'); + var keys = []; + for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key; + return keys; + }; + + // Retrieve the values of an object's properties. + _.values = function(obj) { + return _.map(obj, _.identity); + }; + + // Return a sorted list of the function names available on the object. + // Aliased as `methods` + _.functions = _.methods = function(obj) { + var names = []; + for (var key in obj) { + if (_.isFunction(obj[key])) names.push(key); + } + return names.sort(); + }; + + // Extend a given object with all the properties in passed-in object(s). + _.extend = function(obj) { + each(slice.call(arguments, 1), function(source) { + for (var prop in source) { + obj[prop] = source[prop]; + } + }); + return obj; + }; + + // Fill in a given object with default properties. + _.defaults = function(obj) { + each(slice.call(arguments, 1), function(source) { + for (var prop in source) { + if (obj[prop] == null) obj[prop] = source[prop]; + } + }); + return obj; + }; + + // Create a (shallow-cloned) duplicate of an object. + _.clone = function(obj) { + if (!_.isObject(obj)) return obj; + return _.isArray(obj) ? obj.slice() : _.extend({}, obj); + }; + + // Invokes interceptor with the obj, and then returns obj. + // The primary purpose of this method is to "tap into" a method chain, in + // order to perform operations on intermediate results within the chain. + _.tap = function(obj, interceptor) { + interceptor(obj); + return obj; + }; + + // Internal recursive comparison function. + function eq(a, b, stack) { + // Identical objects are equal. `0 === -0`, but they aren't identical. + // See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal. + if (a === b) return a !== 0 || 1 / a == 1 / b; + // A strict comparison is necessary because `null == undefined`. + if (a == null || b == null) return a === b; + // Unwrap any wrapped objects. + if (a._chain) a = a._wrapped; + if (b._chain) b = b._wrapped; + // Invoke a custom `isEqual` method if one is provided. + if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b); + if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a); + // Compare `[[Class]]` names. + var className = toString.call(a); + if (className != toString.call(b)) return false; + switch (className) { + // Strings, numbers, dates, and booleans are compared by value. + case '[object String]': + // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is + // equivalent to `new String("5")`. + return a == String(b); + case '[object Number]': + // `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for + // other numeric values. + return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b); + case '[object Date]': + case '[object Boolean]': + // Coerce dates and booleans to numeric primitive values. Dates are compared by their + // millisecond representations. Note that invalid dates with millisecond representations + // of `NaN` are not equivalent. + return +a == +b; + // RegExps are compared by their source patterns and flags. + case '[object RegExp]': + return a.source == b.source && + a.global == b.global && + a.multiline == b.multiline && + a.ignoreCase == b.ignoreCase; + } + if (typeof a != 'object' || typeof b != 'object') return false; + // Assume equality for cyclic structures. The algorithm for detecting cyclic + // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`. + var length = stack.length; + while (length--) { + // Linear search. Performance is inversely proportional to the number of + // unique nested structures. + if (stack[length] == a) return true; + } + // Add the first object to the stack of traversed objects. + stack.push(a); + var size = 0, result = true; + // Recursively compare objects and arrays. + if (className == '[object Array]') { + // Compare array lengths to determine if a deep comparison is necessary. + size = a.length; + result = size == b.length; + if (result) { + // Deep compare the contents, ignoring non-numeric properties. + while (size--) { + // Ensure commutative equality for sparse arrays. + if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break; + } + } + } else { + // Objects with different constructors are not equivalent. + if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false; + // Deep compare objects. + for (var key in a) { + if (_.has(a, key)) { + // Count the expected number of properties. + size++; + // Deep compare each member. + if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break; + } + } + // Ensure that both objects contain the same number of properties. + if (result) { + for (key in b) { + if (_.has(b, key) && !(size--)) break; + } + result = !size; + } + } + // Remove the first object from the stack of traversed objects. + stack.pop(); + return result; + } + + // Perform a deep comparison to check if two objects are equal. + _.isEqual = function(a, b) { + return eq(a, b, []); + }; + + // Is a given array, string, or object empty? + // An "empty" object has no enumerable own-properties. + _.isEmpty = function(obj) { + if (_.isArray(obj) || _.isString(obj)) return obj.length === 0; + for (var key in obj) if (_.has(obj, key)) return false; + return true; + }; + + // Is a given value a DOM element? + _.isElement = function(obj) { + return !!(obj && obj.nodeType == 1); + }; + + // Is a given value an array? + // Delegates to ECMA5's native Array.isArray + _.isArray = nativeIsArray || function(obj) { + return toString.call(obj) == '[object Array]'; + }; + + // Is a given variable an object? + _.isObject = function(obj) { + return obj === Object(obj); + }; + + // Is a given variable an arguments object? + _.isArguments = function(obj) { + return toString.call(obj) == '[object Arguments]'; + }; + if (!_.isArguments(arguments)) { + _.isArguments = function(obj) { + return !!(obj && _.has(obj, 'callee')); + }; + } + + // Is a given value a function? + _.isFunction = function(obj) { + return toString.call(obj) == '[object Function]'; + }; + + // Is a given value a string? + _.isString = function(obj) { + return toString.call(obj) == '[object String]'; + }; + + // Is a given value a number? + _.isNumber = function(obj) { + return toString.call(obj) == '[object Number]'; + }; + + // Is the given value `NaN`? + _.isNaN = function(obj) { + // `NaN` is the only value for which `===` is not reflexive. + return obj !== obj; + }; + + // Is a given value a boolean? + _.isBoolean = function(obj) { + return obj === true || obj === false || toString.call(obj) == '[object Boolean]'; + }; + + // Is a given value a date? + _.isDate = function(obj) { + return toString.call(obj) == '[object Date]'; + }; + + // Is the given value a regular expression? + _.isRegExp = function(obj) { + return toString.call(obj) == '[object RegExp]'; + }; + + // Is a given value equal to null? + _.isNull = function(obj) { + return obj === null; + }; + + // Is a given variable undefined? + _.isUndefined = function(obj) { + return obj === void 0; + }; + + // Has own property? + _.has = function(obj, key) { + return hasOwnProperty.call(obj, key); + }; + + // Utility Functions + // ----------------- + + // Run Underscore.js in *noConflict* mode, returning the `_` variable to its + // previous owner. Returns a reference to the Underscore object. + _.noConflict = function() { + root._ = previousUnderscore; + return this; + }; + + // Keep the identity function around for default iterators. + _.identity = function(value) { + return value; + }; + + // Run a function **n** times. + _.times = function (n, iterator, context) { + for (var i = 0; i < n; i++) iterator.call(context, i); + }; + + // Escape a string for HTML interpolation. + _.escape = function(string) { + return (''+string).replace(/&/g, '&').replace(/</g, '<').replace(/>/g, '>').replace(/"/g, '"').replace(/'/g, ''').replace(/\//g,'/'); + }; + + // Add your own custom functions to the Underscore object, ensuring that + // they're correctly added to the OOP wrapper as well. + _.mixin = function(obj) { + each(_.functions(obj), function(name){ + addToWrapper(name, _[name] = obj[name]); + }); + }; + + // Generate a unique integer id (unique within the entire client session). + // Useful for temporary DOM ids. + var idCounter = 0; + _.uniqueId = function(prefix) { + var id = idCounter++; + return prefix ? prefix + id : id; + }; + + // By default, Underscore uses ERB-style template delimiters, change the + // following template settings to use alternative delimiters. + _.templateSettings = { + evaluate : /<%([\s\S]+?)%>/g, + interpolate : /<%=([\s\S]+?)%>/g, + escape : /<%-([\s\S]+?)%>/g + }; + + // When customizing `templateSettings`, if you don't want to define an + // interpolation, evaluation or escaping regex, we need one that is + // guaranteed not to match. + var noMatch = /.^/; + + // Within an interpolation, evaluation, or escaping, remove HTML escaping + // that had been previously added. + var unescape = function(code) { + return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'"); + }; + + // JavaScript micro-templating, similar to John Resig's implementation. + // Underscore templating handles arbitrary delimiters, preserves whitespace, + // and correctly escapes quotes within interpolated code. + _.template = function(str, data) { + var c = _.templateSettings; + var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' + + 'with(obj||{}){__p.push(\'' + + str.replace(/\\/g, '\\\\') + .replace(/'/g, "\\'") + .replace(c.escape || noMatch, function(match, code) { + return "',_.escape(" + unescape(code) + "),'"; + }) + .replace(c.interpolate || noMatch, function(match, code) { + return "'," + unescape(code) + ",'"; + }) + .replace(c.evaluate || noMatch, function(match, code) { + return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('"; + }) + .replace(/\r/g, '\\r') + .replace(/\n/g, '\\n') + .replace(/\t/g, '\\t') + + "');}return __p.join('');"; + var func = new Function('obj', '_', tmpl); + if (data) return func(data, _); + return function(data) { + return func.call(this, data, _); + }; + }; + + // Add a "chain" function, which will delegate to the wrapper. + _.chain = function(obj) { + return _(obj).chain(); + }; + + // The OOP Wrapper + // --------------- + + // If Underscore is called as a function, it returns a wrapped object that + // can be used OO-style. This wrapper holds altered versions of all the + // underscore functions. Wrapped objects may be chained. + var wrapper = function(obj) { this._wrapped = obj; }; + + // Expose `wrapper.prototype` as `_.prototype` + _.prototype = wrapper.prototype; + + // Helper function to continue chaining intermediate results. + var result = function(obj, chain) { + return chain ? _(obj).chain() : obj; + }; + + // A method to easily add functions to the OOP wrapper. + var addToWrapper = function(name, func) { + wrapper.prototype[name] = function() { + var args = slice.call(arguments); + unshift.call(args, this._wrapped); + return result(func.apply(_, args), this._chain); + }; + }; + + // Add all of the Underscore functions to the wrapper object. + _.mixin(_); + + // Add all mutator Array functions to the wrapper. + each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) { + var method = ArrayProto[name]; + wrapper.prototype[name] = function() { + var wrapped = this._wrapped; + method.apply(wrapped, arguments); + var length = wrapped.length; + if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0]; + return result(wrapped, this._chain); + }; + }); + + // Add all accessor Array functions to the wrapper. + each(['concat', 'join', 'slice'], function(name) { + var method = ArrayProto[name]; + wrapper.prototype[name] = function() { + return result(method.apply(this._wrapped, arguments), this._chain); + }; + }); + + // Start chaining a wrapped Underscore object. + wrapper.prototype.chain = function() { + this._chain = true; + return this; + }; + + // Extracts the result from a wrapped and chained object. + wrapper.prototype.value = function() { + return this._wrapped; + }; + +}).call(this); diff -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 -r 70397647fad54c50213e015aaedfed94e6b19eda static/scripts/pack_scripts.py --- a/static/scripts/pack_scripts.py +++ b/static/scripts/pack_scripts.py @@ -20,6 +20,7 @@ to_pack = sys.argv[1:] else: to_pack = glob( "*.js" ) + to_pack.extend( glob( "libs/*.js" ) ) for fname in to_pack: d = dict( fname=fname ) diff -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 -r 70397647fad54c50213e015aaedfed94e6b19eda static/scripts/packed/libs/backbone.js --- /dev/null +++ b/static/scripts/packed/libs/backbone.js @@ -0,0 +1,1 @@ +(function(){var q=this;var o=q.Backbone;var p=Array.prototype.slice;var y=Array.prototype.splice;var c;if(typeof exports!=="undefined"){c=exports}else{c=q.Backbone={}}c.VERSION="0.9.2";var A=q._;if(!A&&(typeof require!=="undefined")){A=require("underscore")}var g=q.jQuery||q.Zepto||q.ender;c.setDomLibrary=function(C){g=C};c.noConflict=function(){q.Backbone=o;return this};c.emulateHTTP=false;c.emulateJSON=false;var a=/\s+/;var n=c.Events={on:function(F,J,E){var D,H,G,C,I;if(!J){return this}F=F.split(a);D=this._callbacks||(this._callbacks={});while(H=F.shift()){I=D[H];G=I?I.tail:{};G.next=C={};G.context=E;G.callback=J;D[H]={tail:C,next:I?I.next:G}}return this},off:function(J,H,D){var C,K,E,G,F,I;if(!(K=this._callbacks)){return}if(!(J||H||D)){delete this._callbacks;return this}J=J?J.split(a):A.keys(K);while(C=J.shift()){E=K[C];delete K[C];if(!E||!(H||D)){continue}G=E.tail;while((E=E.next)!==G){F=E.callback;I=E.context;if((H&&F!==H)||(D&&I!==D)){this.on(C,F,I)}}}return this},trigger:function(F){var J,I,E,D,C,H,G;if(!(E=this._callbacks)){return this}H=E.all;F=F.split(a);G=p.call(arguments,1);while(J=F.shift()){if(I=E[J]){D=I.tail;while((I=I.next)!==D){I.callback.apply(I.context||this,G)}}if(I=H){D=I.tail;C=[J].concat(G);while((I=I.next)!==D){I.callback.apply(I.context||this,C)}}}return this}};n.bind=n.on;n.unbind=n.off;var k=c.Model=function(C,D){var 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C=d(this,"urlRoot")||d(this.collection,"url")||t();if(this.isNew()){return C}return C+(C.charAt(C.length-1)=="/"?"":"/")+encodeURIComponent(this.id)},parse:function(D,C){return D},clone:function(){return new this.constructor(this.attributes)},isNew:function(){return this.id==null},change:function(D){D||(D={});var F=this._changing;this._changing=true;for(var C in this._silent){this._pending[C]=true}var E=A.extend({},D.changes,this._silent);this._silent={};for(var C in E){this.trigger("change:"+C,this,this.get(C),D)}if(F){return this}while(!A.isEmpty(this._pending)){this._pending={};this.trigger("change",this,D);for(var C in this.changed){if(this._pending[C]||this._silent[C]){continue}delete this.changed[C]}this._previousAttributes=A.clone(this.attributes)}this._changing=false;return this},hasChanged:function(C){if(!arguments.length){return !A.isEmpty(this.changed)}return A.has(this.changed,C)},changedAttributes:function(E){if(!E){return this.hasChanged()?A.clone(this.changed):false}var 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22:this.$=[[i[h-1]].concat(i[h]),null];break;case 23:this.$=[[i[h-1]],i[h]];break;case 24:this.$=[[i[h]],null];break;case 25:i[h-1].push(i[h]);this.$=i[h-1];break;case 26:this.$=[i[h]];break;case 27:this.$=i[h];break;case 28:this.$=new n.StringNode(i[h]);break;case 29:this.$=new n.IntegerNode(i[h]);break;case 30:this.$=new n.BooleanNode(i[h]);break;case 31:this.$=new n.HashNode(i[h]);break;case 32:i[h-1].push(i[h]);this.$=i[h-1];break;case 33:this.$=[i[h]];break;case 34:this.$=[i[h-2],i[h]];break;case 35:this.$=[i[h-2],new n.StringNode(i[h])];break;case 36:this.$=[i[h-2],new n.IntegerNode(i[h])];break;case 37:this.$=[i[h-2],new n.BooleanNode(i[h])];break;case 38:this.$=new n.IdNode(i[h]);break;case 39:i[h-2].push(i[h]);this.$=i[h-2];break;case 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d(h,g){throw new Error(h)},parse:function e(o){var x=this,l=[0],G=[null],s=[],H=this.table,h="",q=0,E=0,j=0,n=2,u=1;this.lexer.setInput(o);this.lexer.yy=this.yy;this.yy.lexer=this.lexer;if(typeof this.lexer.yylloc=="undefined"){this.lexer.yylloc={}}var i=this.lexer.yylloc;s.push(i);if(typeof this.yy.parseError==="function"){this.parseError=this.yy.parseError}function w(p){l.length=l.length-2*p;G.length=G.length-p;s.length=s.length-p}function v(){var p;p=x.lexer.lex()||1;if(typeof p!=="number"){p=x.symbols_[p]||p}return p}var D,z,k,C,I,t,B={},y,F,g,m;while(true){k=l[l.length-1];if(this.defaultActions[k]){C=this.defaultActions[k]}else{if(D==null){D=v()}C=H[k]&&H[k][D]}if(typeof C==="undefined"||!C.length||!C[0]){if(!j){m=[];for(y in H[k]){if(this.terminals_[y]&&y>2){m.push("'"+this.terminals_[y]+"'")}}var A="";if(this.lexer.showPosition){A="Parse error on line "+(q+1)+":\n"+this.lexer.showPosition()+"\nExpecting "+m.join(", ")+", got '"+this.terminals_[D]+"'"}else{A="Parse error on line "+(q+1)+": Unexpected "+(D==1?"end of input":"'"+(this.terminals_[D]||D)+"'")}this.parseError(A,{text:this.lexer.match,token:this.terminals_[D]||D,line:this.lexer.yylineno,loc:i,expected:m})}}if(C[0] instanceof Array&&C.length>1){throw new Error("Parse Error: multiple actions possible at state: "+k+", token: "+D)}switch(C[0]){case 1:l.push(D);G.push(this.lexer.yytext);s.push(this.lexer.yylloc);l.push(C[1]);D=null;if(!z){E=this.lexer.yyleng;h=this.lexer.yytext;q=this.lexer.yylineno;i=this.lexer.yylloc;if(j>0){j--}}else{D=z;z=null}break;case 2:F=this.productions_[C[1]][1];B.$=G[G.length-F];B._$={first_line:s[s.length-(F||1)].first_line,last_line:s[s.length-1].last_line,first_column:s[s.length-(F||1)].first_column,last_column:s[s.length-1].last_column};t=this.performAction.call(B,h,E,q,this.yy,C[1],G,s);if(typeof t!=="undefined"){return t}if(F){l=l.slice(0,-1*F*2);G=G.slice(0,-1*F);s=s.slice(0,-1*F)}l.push(this.productions_[C[1]][0]);G.push(B.$);s.push(B._$);g=H[l[l.length-2]][l[l.length-1]];l.push(g);break;case 3:return true}}return true}};var a=(function(){var j=({EOF:1,parseError:function l(o,n){if(this.yy.parseError){this.yy.parseError(o,n)}else{throw new Error(o)}},setInput:function(n){this._input=n;this._more=this._less=this.done=false;this.yylineno=this.yyleng=0;this.yytext=this.matched=this.match="";this.conditionStack=["INITIAL"];this.yylloc={first_line:1,first_column:0,last_line:1,last_column:0};return this},input:function(){var o=this._input[0];this.yytext+=o;this.yyleng++;this.match+=o;this.matched+=o;var n=o.match(/\n/);if(n){this.yylineno++}this._input=this._input.slice(1);return o},unput:function(n){this._input=n+this._input;return this},more:function(){this._more=true;return this},pastInput:function(){var n=this.matched.substr(0,this.matched.length-this.match.length);return(n.length>20?"...":"")+n.substr(-20).replace(/\n/g,"")},upcomingInput:function(){var n=this.match;if(n.length<20){n+=this._input.substr(0,20-n.length)}return(n.substr(0,20)+(n.length>20?"...":"")).replace(/\n/g,"")},showPosition:function(){var n=this.pastInput();var o=new Array(n.length+1).join("-");return n+this.upcomingInput()+"\n"+o+"^"},next:function(){if(this.done){return this.EOF}if(!this._input){this.done=true}var r,p,o,n;if(!this._more){this.yytext="";this.match=""}var s=this._currentRules();for(var q=0;q<s.length;q++){p=this._input.match(this.rules[s[q]]);if(p){n=p[0].match(/\n.*/g);if(n){this.yylineno+=n.length}this.yylloc={first_line:this.yylloc.last_line,last_line:this.yylineno+1,first_column:this.yylloc.last_column,last_column:n?n[n.length-1].length-1:this.yylloc.last_column+p[0].length};this.yytext+=p[0];this.match+=p[0];this.matches=p;this.yyleng=this.yytext.length;this._more=false;this._input=this._input.slice(p[0].length);this.matched+=p[0];r=this.performAction.call(this,this.yy,this,s[q],this.conditionStack[this.conditionStack.length-1]);if(r){return r}else{return}}}if(this._input===""){return this.EOF}else{this.parseError("Lexical error on line "+(this.yylineno+1)+". Unrecognized text.\n"+this.showPosition(),{text:"",token:null,line:this.yylineno})}},lex:function g(){var n=this.next();if(typeof n!=="undefined"){return n}else{return this.lex()}},begin:function h(n){this.conditionStack.push(n)},popState:function m(){return this.conditionStack.pop()},_currentRules:function k(){return this.conditions[this.conditionStack[this.conditionStack.length-1]].rules},topState:function(){return this.conditionStack[this.conditionStack.length-2]},pushState:function h(n){this.begin(n)}});j.performAction=function i(r,o,q,n){var p=n;switch(q){case 0:if(o.yytext.slice(-1)!=="\\"){this.begin("mu")}if(o.yytext.slice(-1)==="\\"){o.yytext=o.yytext.substr(0,o.yyleng-1),this.begin("emu")}if(o.yytext){return 14}break;case 1:return 14;break;case 2:this.popState();return 14;break;case 3:return 24;break;case 4:return 16;break;case 5:return 20;break;case 6:return 19;break;case 7:return 19;break;case 8:return 23;break;case 9:return 23;break;case 10:o.yytext=o.yytext.substr(3,o.yyleng-5);this.popState();return 15;break;case 11:return 22;break;case 12:return 34;break;case 13:return 33;break;case 14:return 33;break;case 15:return 36;break;case 16:break;case 17:this.popState();return 18;break;case 18:this.popState();return 18;break;case 19:o.yytext=o.yytext.substr(1,o.yyleng-2).replace(/\\"/g,'"');return 28;break;case 20:return 30;break;case 21:return 30;break;case 22:return 29;break;case 23:return 33;break;case 24:o.yytext=o.yytext.substr(1,o.yyleng-2);return 33;break;case 25:return"INVALID";break;case 26:return 5;break}};j.rules=[/^[^\x00]*?(?=(\{\{))/,/^[^\x00]+/,/^[^\x00]{2,}?(?=(\{\{))/,/^\{\{>/,/^\{\{#/,/^\{\{\//,/^\{\{\^/,/^\{\{\s*else\b/,/^\{\{\{/,/^\{\{&/,/^\{\{![\s\S]*?\}\}/,/^\{\{/,/^=/,/^\.(?=[} ])/,/^\.\./,/^[\/.]/,/^\s+/,/^\}\}\}/,/^\}\}/,/^"(\\["]|[^"])*"/,/^true(?=[}\s])/,/^false(?=[}\s])/,/^[0-9]+(?=[}\s])/,/^[a-zA-Z0-9_$-]+(?=[=}\s\/.])/,/^\[[^\]]*\]/,/^./,/^$/];j.conditions={mu:{rules:[3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26],inclusive:false},emu:{rules:[2],inclusive:false},INITIAL:{rules:[0,1,26],inclusive:true}};return j})();f.lexer=a;return f})();if(typeof require!=="undefined"&&typeof exports!=="undefined"){exports.parser=handlebars;exports.parse=function(){return handlebars.parse.apply(handlebars,arguments)};exports.main=function commonjsMain(a){if(!a[1]){throw new Error("Usage: "+a[0]+" FILE")}if(typeof process!=="undefined"){var c=require("fs").readFileSync(require("path").join(process.cwd(),a[1]),"utf8")}else{var b=require("file").path(require("file").cwd());var c=b.join(a[1]).read({charset:"utf-8"})}return exports.parser.parse(c)};if(typeof module!=="undefined"&&require.main===module){exports.main(typeof process!=="undefined"?process.argv.slice(1):require("system").args)}}Handlebars.Parser=handlebars;Handlebars.parse=function(a){Handlebars.Parser.yy=Handlebars.AST;return Handlebars.Parser.parse(a)};Handlebars.print=function(a){return new Handlebars.PrintVisitor().accept(a)};Handlebars.logger={DEBUG:0,INFO:1,WARN:2,ERROR:3,level:3,log:function(b,a){}};Handlebars.log=function(b,a){Handlebars.logger.log(b,a)};(function(){Handlebars.AST={};Handlebars.AST.ProgramNode=function(c,b){this.type="program";this.statements=c;if(b){this.inverse=new Handlebars.AST.ProgramNode(b)}};Handlebars.AST.MustacheNode=function(d,c,b){this.type="mustache";this.id=d[0];this.params=d.slice(1);this.hash=c;this.escaped=!b};Handlebars.AST.PartialNode=function(c,b){this.type="partial";this.id=c;this.context=b};var a=function(b,c){if(b.original!==c.original){throw new Handlebars.Exception(b.original+" doesn't match "+c.original)}};Handlebars.AST.BlockNode=function(c,b,d){a(c.id,d);this.type="block";this.mustache=c;this.program=b};Handlebars.AST.InverseNode=function(c,b,d){a(c.id,d);this.type="inverse";this.mustache=c;this.program=b};Handlebars.AST.ContentNode=function(b){this.type="content";this.string=b};Handlebars.AST.HashNode=function(b){this.type="hash";this.pairs=b};Handlebars.AST.IdNode=function(f){this.type="ID";this.original=f.join(".");var d=[],g=0;for(var e=0,b=f.length;e<b;e++){var c=f[e];if(c===".."){g++}else{if(c==="."||c==="this"){this.isScoped=true}else{d.push(c)}}}this.parts=d;this.string=d.join(".");this.depth=g;this.isSimple=(d.length===1)&&(g===0)};Handlebars.AST.StringNode=function(b){this.type="STRING";this.string=b};Handlebars.AST.IntegerNode=function(b){this.type="INTEGER";this.integer=b};Handlebars.AST.BooleanNode=function(b){this.type="BOOLEAN";this.bool=b};Handlebars.AST.CommentNode=function(b){this.type="comment";this.comment=b}})();Handlebars.Exception=function(b){var a=Error.prototype.constructor.apply(this,arguments);for(var c in a){if(a.hasOwnProperty(c)){this[c]=a[c]}}this.message=a.message};Handlebars.Exception.prototype=new Error;Handlebars.SafeString=function(a){this.string=a};Handlebars.SafeString.prototype.toString=function(){return this.string.toString()};(function(){var c={"<":"<",">":">",'"':""","'":"'","`":"`"};var d=/&(?!\w+;)|[<>"'`]/g;var b=/[&<>"'`]/;var a=function(e){return c[e]||"&"};Handlebars.Utils={escapeExpression:function(e){if(e instanceof Handlebars.SafeString){return e.toString()}else{if(e==null||e===false){return""}}if(!b.test(e)){return e}return e.replace(d,a)},isEmpty:function(e){if(typeof e==="undefined"){return true}else{if(e===null){return true}else{if(e===false){return true}else{if(Object.prototype.toString.call(e)==="[object Array]"&&e.length===0){return true}else{return false}}}}}}})();Handlebars.Compiler=function(){};Handlebars.JavaScriptCompiler=function(){};(function(f,e){f.OPCODE_MAP={appendContent:1,getContext:2,lookupWithHelpers:3,lookup:4,append:5,invokeMustache:6,appendEscaped:7,pushString:8,truthyOrFallback:9,functionOrFallback:10,invokeProgram:11,invokePartial:12,push:13,assignToHash:15,pushStringParam:16};f.MULTI_PARAM_OPCODES={appendContent:1,getContext:1,lookupWithHelpers:2,lookup:1,invokeMustache:3,pushString:1,truthyOrFallback:1,functionOrFallback:1,invokeProgram:3,invokePartial:1,push:1,assignToHash:1,pushStringParam:1};f.DISASSEMBLE_MAP={};for(var h in f.OPCODE_MAP){var g=f.OPCODE_MAP[h];f.DISASSEMBLE_MAP[g]=h}f.multiParamSize=function(i){return f.MULTI_PARAM_OPCODES[f.DISASSEMBLE_MAP[i]]};f.prototype={compiler:f,disassemble:function(){var t=this.opcodes,r,n;var q=[],v,m,w;for(var s=0,o=t.length;s<o;s++){r=t[s];if(r==="DECLARE"){m=t[++s];w=t[++s];q.push("DECLARE "+m+" = "+w)}else{v=f.DISASSEMBLE_MAP[r];var u=f.multiParamSize(r);var k=[];for(var p=0;p<u;p++){n=t[++s];if(typeof n==="string"){n='"'+n.replace("\n","\\n")+'"'}k.push(n)}v=v+" "+k.join(" ");q.push(v)}}return q.join("\n")},guid:0,compile:function(i,k){this.children=[];this.depths={list:[]};this.options=k;var l=this.options.knownHelpers;this.options.knownHelpers={helperMissing:true,blockHelperMissing:true,each:true,"if":true,unless:true,"with":true,log:true};if(l){for(var j in l){this.options.knownHelpers[j]=l[j]}}return this.program(i)},accept:function(i){return this[i.type](i)},program:function(m){var k=m.statements,o;this.opcodes=[];for(var n=0,j=k.length;n<j;n++){o=k[n];this[o.type](o)}this.isSimple=j===1;this.depths.list=this.depths.list.sort(function(l,i){return l-i});return this},compileProgram:function(m){var j=new this.compiler().compile(m,this.options);var n=this.guid++;this.usePartial=this.usePartial||j.usePartial;this.children[n]=j;for(var o=0,k=j.depths.list.length;o<k;o++){depth=j.depths.list[o];if(depth<2){continue}else{this.addDepth(depth-1)}}return n},block:function(o){var l=o.mustache;var n,p,j,k;var m=this.setupStackForMustache(l);var i=this.compileProgram(o.program);if(o.program.inverse){k=this.compileProgram(o.program.inverse);this.declare("inverse",k)}this.opcode("invokeProgram",i,m.length,!!l.hash);this.declare("inverse",null);this.opcode("append")},inverse:function(k){var j=this.setupStackForMustache(k.mustache);var i=this.compileProgram(k.program);this.declare("inverse",i);this.opcode("invokeProgram",null,j.length,!!k.mustache.hash);this.declare("inverse",null);this.opcode("append")},hash:function(n){var m=n.pairs,p,o;this.opcode("push","{}");for(var k=0,j=m.length;k<j;k++){p=m[k];o=p[1];this.accept(o);this.opcode("assignToHash",p[0])}},partial:function(i){var 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false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.tiles_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.tiles_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data 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style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(af){var ac=false;if(!this.applies_to(af)){return ac}var ad=af[this.index];if(!(ad instanceof Array)){ad=[ad]}for(var ae=0;ae<ad.length;ae++){var ag=ad[ae];if(ag<this.min){this.min=Math.floor(ag);ac=true}if(ag>this.max){this.max=Math.ceil(ag);ac=true}}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. 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Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.tiles_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.tiles_div.text(V);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.after_show_tile(ae)},after_show_tile:function(ac){},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={resize:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,ac,{content_div:ac.top_labeltrack,resize:false},{});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false)};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){af.content_div.css("height","0px");return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}return new b(af,ad,ag,ae,ak)}this.content_div.css("height","0px")},after_show_tile:function(ac){if(ac){this.content_div.css("height","12px")}}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};p(j.prototype,q.prototype,K.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},after_show_tile:function(ac){this.max_height_px=Math.max(this.max_height_px,ac.html_elt.height());ac.html_elt.parent().children().css("height",this.max_height_px+"px");var ad=this.max_height_px;if(this.visible_height_px!==0){ad=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ad+"px")},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,U){var p=e("class").extend,s=e("slotting"),J=e("painters");var ab=function(ac,ad){this.document=ac;this.default_font=ad!==undefined?ad:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ab.prototype,{load_pattern:function(ac,ag){var ad=this.patterns,ae=this.dummy_context,af=new Image();af.src=image_path+ag;af.onload=function(){ad[ac]=ae.createPattern(af,"repeat")}},get_pattern:function(ac){return this.patterns[ac]},new_canvas:function(){var ac=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(ac)}ac.manager=this;return ac}});var n={};var l=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this);var at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}var aj;for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};U.moveable=m;var aa=16,D=9,A=20,x=100,G=12000,R=400,I=5000,u=100,o="There was an error in indexing this dataset. ",H="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",t="Preparing data. This is very fast for a small dataset but can take a long time for a large dataset. If visualization is saved and closed, preparation will continue in the background.",v="Tool cannot be rerun: ",a="Loading data...",V="Ready for display",O=10,F=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var c=function(ac){this.num_elements=ac;this.clear()};p(c.prototype,{get:function(ad){var ac=this.key_ary.indexOf(ad);if(ac!==-1){if(this.obj_cache[ad].stale){this.key_ary.splice(ac,1);delete this.obj_cache[ad]}else{this.move_key_to_end(ad,ac)}}return this.obj_cache[ad]},set:function(ad,ae){if(!this.obj_cache[ad]){if(this.key_ary.length>=this.num_elements){var ac=this.key_ary.shift();delete this.obj_cache[ac]}this.key_ary.push(ad)}this.obj_cache[ad]=ae;return ae},move_key_to_end:function(ad,ac){this.key_ary.splice(ac,1);this.key_ary.push(ad)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var P=function(ad,ac){c.call(this,ad);this.track=ac};p(P.prototype,c.prototype,{load_data:function(al,ag,aj,ad,ai){var ak=this.track.view.chrom,af={chrom:ak,low:al,high:ag,mode:aj,resolution:ad,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(af,ai);if(this.track.filters_manager){var am=[];var ac=this.track.filters_manager.filters;for(var ah=0;ah<ac.length;ah++){am.push(ac[ah].name)}af.filter_cols=JSON.stringify(am)}var ae=this;return $.getJSON(this.track.data_url,af,function(an){ae.set_data(al,ag,an)})},get_data:function(ak,ae,ai,ad,ah){var al=this.get(ak,ae);if(al&&(is_deferred(al)||this.track.data_and_mode_compatible(al,ai))){return al}var am,aj,ac,ag,ai,al;for(var af=0;af<this.key_ary.length;af++){am=this.key_ary[af];aj=this.split_key(am);ac=aj[0];ag=aj[1];if(ak>=ac&&ae<=ag){var al=this.obj_cache[am];if(is_deferred(al)||(this.track.data_and_mode_compatible(al,ai)&&this.track.can_subset(al))){this.move_key_to_end(am,af);return al}}}al=this.load_data(ak,ae,ai,ad,ah);this.set_data(ak,ae,al);return al},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(ak,af,aj,ae,ai,ag){var al=this.get(ak,af);if(!(al&&this.track.data_and_mode_compatible(al,aj))){console.log("ERROR: no current data for: ",this.track,ak,af,aj,ae,ai);return}al.stale=true;var ad=ak;if(ag===this.DEEP_DATA_REQ){$.extend(ai,{start_val:al.data.length+1})}else{if(ag===this.BROAD_DATA_REQ){ad=(al.max_high?al.max_high:al.data[al.data.length-1][2])+1}}var ac=this,ah=this.load_data(ad,af,aj,ae,ai);new_data_available=$.Deferred();this.set_data(ak,af,new_data_available);$.when(ah).then(function(am){if(am.data){am.data=al.data.concat(am.data);if(am.max_low){am.max_low=al.max_low}if(am.message){am.message=am.message.replace(/[0-9]+/,am.data.length)}}ac.set_data(ak,af,am);new_data_available.resolve(am)});return new_data_available},get:function(ac,ad){return c.prototype.get.call(this,this.gen_key(ac,ad))},set_data:function(ad,ae,ac){return this.set(this.gen_key(ad,ae),ac)},gen_key:function(ac,ae){var ad=ac+"_"+ae;return ad},split_key:function(ac){return ac.split("_")}});var E=function(ad,ac,ae){P.call(this,ad,ac,ae)};p(E.prototype,P.prototype,c.prototype,{get:P.prototype.get,load_data:function(ac,af,ag,ad,ae){if(ad>1){return{data:null}}return P.prototype.load_data.call(this,ac,af,ag,ad,ae)}});var q=function(ad,ac,af){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tipsy").remove();ac.remove()}}];p(q.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},update_icons:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tipsy({gravity:"s"}).click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var w=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(w.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=object_from_template(ae[ac],this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false}});var N=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});w.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new X(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new X(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(N.prototype,q.prototype,w.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},q.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof h){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(var al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof d){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(var al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(var ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new S({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new h(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){w.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(w.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=function(ac){p(ac,{obj_type:"View"});w.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.init();this.canvas_manager=new ab(this.container.get(0).ownerDocument);this.reset()};p(Z.prototype,w.prototype,{init:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new Y(this,{content_div:this.top_labeltrack}));this.add_label_track(new Y(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ac.resize_window()});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ac,ad){this.location_span.text(commatize(ac)+" - "+commatize(ad));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ad))},load_chroms:function(ae){ae.num=u;ae.dbkey=this.dbkey;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){alert("Invalid chromosome: "+ae.chrom);return}if(ag.reference){ac.add_label_track(new y(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+u+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+u+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){if(!ah||ah==="None"){return}var ae=this;if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-u});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+u});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(ae){var ac=this;var ad=ac.high-ac.low;if(ac.low-ae<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ad}else{if(ac.high-ae>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ad}else{ac.high-=ae;ac.low-=ae}}ac.request_redraw()},add_drawable:function(ac){w.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){w.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,ad){var ai=this,ag=(ad?[ad]:ai.drawables),ae;var ad;for(var ah=0;ah<ag.length;ah++){ad=ag[ah];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ah][1]=ac;ai.tracks_to_be_redrawn[ah][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}this.update_location(this.low,this.high);if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tipsy").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var r=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new f(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new L(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);var ak=this;ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=JSON.stringify(ae)});return ac},get_param_values:function(){var ad=[];var ac={};this.parent_div.find(":input").each(function(){var ae=$(this).attr("name"),af=$(this).val();if(ae){ad[ad.length]=af}});return ad},run_on_dataset:function(){var ac=this;ac.run({dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ad={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ad.chrom,ad.low,ad.high),ac;if(ah.container===view){var ag=new N(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var ai=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});ai.init_for_tool_data();ai.change_mode(ah.mode);ai.set_filters_manager(ah.filters_manager.copy(ai));ai.update_icons();ac.add_drawable(ai);ai.tiles_div.text("Starting job.");this.update_params();this.run(ad,ai,function(aj){ai.dataset_id=aj.dataset_id;ai.tiles_div.text("Running job.");ai.init()})},run:function(ad,ae,af){$.extend(ad,this.get_param_values_dict());var ac=function(){$.getJSON(rerun_tool_url,ad,function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(H)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(v+ag.message)}else{if(ag==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ac,2000)}else{af(ag)}}}})};ac()}});var L=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(L.prototype,{update_value:function(){this.value=$(this.html).val()}});var f=function(ae,ad,ag,ah,af,ac){L.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(f.prototype,L.prototype,{update_value:function(){L.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var g=function(ac){this.manager=null;this.name=ac.name;this.index=ac.index;this.tool_id=ac.tool_id;this.tool_exp_name=ac.tool_exp_name};p(g.prototype,{to_dict:function(){return{name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name}}});var S=function(al){g.call(this,al);this.low=("low" in al?al.low:-Number.MAX_VALUE);this.high=("high" in al?al.high:Number.MAX_VALUE);this.min=("min" in al?al.min:Number.MAX_VALUE);this.max=("max" in al?al.max:-Number.MAX_VALUE);this.container=null;this.slider=null;this.slider_label=null;var ah=function(am,an,ao){am.click(function(){var au=an.text(),ar=parseFloat(ao.slider("option","max")),aq=(ar<=1?4:ar<=1000000?ar.toString().length:6),at=false,ap=$(this).parents(".slider-row");ap.addClass("input");if(ao.slider("option","values")){aq=2*aq+1;at=true}an.text("");$("<input type='text'/>").attr("size",aq).attr("maxlength",aq).attr("value",au).appendTo(an).focus().select().click(function(av){av.stopPropagation()}).blur(function(){$(this).remove();an.text(au);ap.removeClass("input")}).keyup(function(az){if(az.keyCode===27){$(this).trigger("blur")}else{if(az.keyCode===13){var ax=ao.slider("option","min"),av=ao.slider("option","max"),ay=function(aA){return(isNaN(aA)||aA>av||aA<ax)},aw=$(this).val();if(!at){aw=parseFloat(aw);if(ay(aw)){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}else{aw=aw.split("-");aw=[parseFloat(aw[0]),parseFloat(aw[1])];if(ay(aw[0])||ay(aw[1])){alert("Parameter value must be in the range ["+ax+"-"+av+"]");return $(this)}}ao.slider((at?"values":"value"),aw);ap.removeClass("input")}}})})};var ad=this;ad.parent_div=$("<div/>").addClass("filter-row slider-row");var ac=$("<div/>").addClass("elt-label").appendTo(ad.parent_div),aj=$("<span/>").addClass("slider-name").text(ad.name+" ").appendTo(ac),ae=$("<span/>").text(this.low+"-"+this.high),af=$("<span/>").addClass("slider-value").appendTo(ac).append("[").append(ae).append("]");ad.values_span=ae;var ai=$("<div/>").addClass("slider").appendTo(ad.parent_div);ad.control_element=$("<div/>").attr("id",ad.name+"-filter-control").appendTo(ai);var ag=[0,0];ad.control_element.slider({range:true,min:this.min,max:this.max,step:this.get_slider_step(this.min,this.max),values:[this.low,this.high],slide:function(am,an){ad.slide(am,an)},change:function(am,an){ad.control_element.slider("option","slide").call(ad.control_element,am,an)}});ad.slider=ad.control_element;ad.slider_label=ae;ah(af,ae,ad.control_element);var ak=$("<div/>").addClass("display-controls").appendTo(ad.parent_div);this.transparency_icon=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ad.manager.alpha_filter!==ad){ad.manager.alpha_filter=ad;ad.manager.parent_div.find(".layer-transparent").removeClass("active").hide();ad.transparency_icon.addClass("active").show()}else{ad.manager.alpha_filter=null;ad.transparency_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();this.height_icon=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ad.manager.height_filter!==ad){ad.manager.height_filter=ad;ad.manager.parent_div.find(".arrow-resize-090").removeClass("active").hide();ad.height_icon.addClass("active").show()}else{ad.manager.height_filter=null;ad.height_icon.removeClass("active")}ad.manager.track.request_draw(true,true)}).appendTo(ak).hide();ad.parent_div.hover(function(){ad.transparency_icon.show();ad.height_icon.show()},function(){if(ad.manager.alpha_filter!==ad){ad.transparency_icon.hide()}if(ad.manager.height_filter!==ad){ad.height_icon.hide()}});$("<div style='clear: both;'/>").appendTo(ad.parent_div)};p(S.prototype,{to_dict:function(){var ac=g.prototype.to_dict.call(this);return p(ac,{type:"number",min:this.min,max:this.max,low:this.low,high:this.high})},copy:function(){return new S({name:this.name,index:this.index,tool_id:this.tool_id,tool_exp_name:this.tool_exp_name})},get_slider_step:function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)},slide:function(ad,ae){var ac=ae.values;this.values_span.text(ac[0]+"-"+ac[1]);this.low=ac[0];this.high=ac[1];this.manager.track.request_draw(true,true)},applies_to:function(ac){if(ac.length>this.index){return true}return false},_keep_val:function(ac){return(isNaN(ac)||(ac>=this.low&&ac<=this.high))},keep:function(ad){if(!this.applies_to(ad)){return true}var af=this;var ag=ad[this.index];if(ag instanceof Array){var ae=true;for(var ac=0;ac<ag.length;ac++){if(!this._keep_val(ag[ac])){ae=false;break}}return ae}else{return this._keep_val(ad[this.index])}},update_attrs:function(af){var ac=false;if(!this.applies_to(af)){return ac}var ad=af[this.index];if(!(ad instanceof Array)){ad=[ad]}for(var ae=0;ae<ad.length;ae++){var ag=ad[ae];if(ag<this.min){this.min=Math.floor(ag);ac=true}if(ag>this.max){this.max=Math.ceil(ag);ac=true}}return ac},update_ui_elt:function(){if(this.min!==this.max){this.parent_div.show()}else{this.parent_div.hide()}var ad=this.slider.slider("option","min"),ac=this.slider.slider("option","max");if(this.min<ad||this.max>ac){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",this.get_slider_step(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var X=function(ae,ak){this.track=ae;this.alpha_filter=null;this.height_filter=null;this.filters=[];this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(am){am.stopPropagation()}).click(function(am){am.stopPropagation()}).bind("dblclick",function(am){am.stopPropagation()}).bind("keydown",function(am){am.stopPropagation()});if(ak&&"filters" in ak){var ac=("alpha_filter" in ak?ak.alpha_filter:null),af=("height_filter" in ak?ak.height_filter:null),ah=ak.filters,ad;for(var ai=0;ai<ah.length;ai++){if(ah[ai].type==="number"){ad=new S(ah[ai]);this.add_filter(ad);if(ad.name===ac){this.alpha_filter=ad;ad.transparency_icon.addClass("active").show()}if(ad.name===af){this.height_filter=ad;ad.height_icon.addClass("active").show()}}else{console.log("ERROR: unsupported filter: ",name,type)}}if("visible" in ak&&ak.visible){this.parent_div.show()}}if(this.filters.length!==0){var al=$("<div/>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(al);var ag=this;aj.click(function(){ag.run_on_dataset()})}};p(X.prototype,{show:function(){this.parent_div.show()},hide:function(){this.parent_div.hide()},toggle:function(){this.parent_div.toggle()},visible:function(){return this.parent_div.is(":visible")},to_dict:function(){var af={},ae=[],ad;for(var ac=0;ac<this.filters.length;ac++){ad=this.filters[ac];ae.push(ad.to_dict())}af.filters=ae;af.alpha_filter=(this.alpha_filter?this.alpha_filter.name:null);af.height_filter=(this.height_filter?this.height_filter.name:null);af.visible=this.parent_div.is(":visible");return af},copy:function(ad){var ae=new X(ad);for(var ac=0;ac<this.filters.length;ac++){ae.add_filter(this.filters[ac].copy())}return ae},add_filter:function(ac){ac.manager=this;this.parent_div.append(ac.parent_div);this.filters.push(ac)},remove_all:function(){this.filters=[];this.parent_div.children().remove()},init_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.update_ui_elt()}},clear_filters:function(){for(var ac=0;ac<this.filters.length;ac++){var ad=this.filters[ac];ad.slider.slider("option","values",[ad.min,ad.max])}this.alpha_filter=null;this.height_filter=null;this.parent_div.find(".icon-button").hide()},run_on_dataset:function(){var ak=function(ao,am,an){if(!(am in ao)){ao[am]=an}return ao[am]};var ae={},ac,ad,af;for(var ag=0;ag<this.filters.length;ag++){ac=this.filters[ag];if(ac.tool_id){if(ac.min!==ac.low){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" >= "+ac.low}if(ac.max!==ac.high){ad=ak(ae,ac.tool_id,[]);ad[ad.length]=ac.tool_exp_name+" <= "+ac.high}}}var ai=[];for(var al in ae){ai[ai.length]=[al,ae[al]]}var aj=ai.length;(function ah(at,ap){var an=ap[0],ao=an[0],ar=an[1],aq="("+ar.join(") and (")+")",am={cond:aq,input:at,target_dataset_id:at,tool_id:ao},ap=ap.slice(1);$.getJSON(run_tool_url,am,function(au){if(au.error){show_modal("Filter Dataset","Error running tool "+ao,{Close:hide_modal})}else{if(ap.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ah(au.dataset_id,ap)}}})})(this.track.dataset_id,ai)}});var z=function(ac,ad){J.Scaler.call(this,ad);this.filter=ac};z.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var C=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};p(C.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(aj,ag){for(var an=0;an<aj.length;an++){ae=aj[an];if(ae.hidden){continue}var ah="param_"+an;var ar=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ah).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ah).attr("name",ah).attr("checked",ar))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ah).val(ar).click(function(){$(this).select()}))}else{if(ae.type==="select"){var ap=$("<select />").attr("id",ah);for(var al=0;al<ae.options.length;al++){$("<option/>").text(ae.options[al].label).attr("value",ae.options[al].value).appendTo(ap)}ap.val(ar);av.append(ap)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ao=$("<input />").attr("id",ah).attr("name",ah).val(ar).css("float","left").appendTo(au).click(function(ax){$(".tipsy").hide();var aw=$(this).siblings(".tipsy");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),am=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tipsy({gravity:"s"}),aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").appendTo(au).hide(),ai=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(aq),at=$("<div/>").appendTo(ai),ak=$.farbtastic(at,{width:100,height:100,callback:ao,color:ar});au.append($("<div/>").css("clear","both"));(function(aw){am.click(function(){aw.setColor(get_random_color())})})(ak)}else{av.append($("<input />").attr("id",ah).attr("name",ah).val(ar))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,af,ae,ad,ag){this.track=ac;this.index=af;var ah=this.track._get_tile_bounds(af,ae);this.low=ah[0];this.high=ah[1];this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad);this.data=ag;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ac,af,ae,ad,ag,ah){b.call(this,ac,af,ae,ad,ag);this.max_val=ah};p(k.prototype,b.prototype);var M=function(af,ak,ag,ae,ai,ao,aj,ap,ad,am){b.call(this,af,ak,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(ap){this.has_icons=true;var al=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:A-1,width:ae.width}).prependTo(this.html_elt);var an=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ah.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){al.stale=true;af.data_manager.get_more_data(al.low,al.high,af.mode,al.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};p(M.prototype,b.prototype);M.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var i=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.data_url=("data_url" in ae?ae.data_url:default_data_url);this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:I);this.dataset_check_url=converted_datasets_state_url;this.data_manager=("data_manager" in ae?ae.data_manager:new P(F,this));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof Y){return"LabelTrack"}else{if(this instanceof y){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Q){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred();$.getJSON(converted_datasets_state_url,{hda_ldda:ad.hda_ldda,dataset_id:ad.dataset_id,chrom:ad.view.chrom},function(ae){if(!ae||ae==="error"||ae.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ae.message){var af=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ae.message+"</pre>",{Close:hide_modal})});ad.tiles_div.append(af)}}else{if(ae==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(H)}else{if(ae==="no data"||(ae.data!==undefined&&(ae.data===null||ae.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(B)}else{if(ae==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(t);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ae.status==="data"){if(ae.valid_chroms){ad.valid_chroms=ae.valid_chroms;ad.update_icons()}ad.tiles_div.text(V);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){}});var K=function(ae,ad,af){i.call(this,ae,ad,af);var ac=this,ae=ac.view;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new X(this,("filters" in af?af.filters:null));this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new c(O);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(K.prototype,q.prototype,i.prototype,{action_icons_def:i.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tipsy").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();p(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show()}else{ac.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ad,ae,ac){return ad+"_"+ae+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=Math.pow(RESOLUTION,Math.ceil(Math.log((view.max_high-view.max_low)/R)/Math.log(RESOLUTION)));ap=ae/(view.max_high-view.max_low)}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*R)),ak=true,ao=[],ai=function(aq){return(aq&&"track" in aq)};while((ac*R*ag)<ah){var am=this.draw_helper(ad,ae,ac,ag,this.tiles_div,ap);if(ai(am)){ao.push(am)}else{ak=false}ac+=1}if(!an){this.tiles_div.children(".remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ao,ae,ap,an)}},postdraw_actions:function(af,ag,ai,ac){var ae=this;var ah=false;for(var ad=0;ad<af.length;ad++){if(af[ad].has_icons){ah=true;break}}if(ah){for(var ad=0;ad<af.length;ad++){tile=af[ad];if(!tile.has_icons){tile.html_elt.css("padding-top",A)}}}},draw_helper:function(ac,ao,au,ar,ah,ai,ap){var an=this,ax=this._gen_tile_cache_key(ao,ai,au),af=this._get_tile_bounds(au,ar),av=af[0],ad=af[1];if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get(ax));if(aw){an.show_tile(aw,ah,ai);return aw}var al=true;var at=an.data_manager.get_data(av,ad,an.mode,ar,an.data_url_extra_params);if(is_deferred(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(av,ad,an.mode,ar,view.reference_track.data_url_extra_params);if(is_deferred(aj)){al=false}}if(al){p(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),af=an._get_tile_bounds(au,ar),av=af[0],ad=af[1],ao=Math.ceil((ad-av)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ao);ae.width=ao;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var aw=an.draw_tile(at,aq,ak,ar,au,ai,aj);if(aw!==undefined){an.tile_cache.set(ax,aw);an.show_tile(aw,ah,ai)}return aw}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ae,ah,ag,ad,ai,af){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ag,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var af=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){af-=this.left_offset}ac.css({position:"absolute",top:0,left:af,height:""});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ag.append(ac)}ad.after_show_tile(ae)},after_show_tile:function(ac){},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*R*ad),ag=Math.ceil(R*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return[af,ae]},tool_region_and_parameters_str:function(ae,ac,af){var ad=this,ag=(ae!==undefined&&ac!==undefined&&af!==undefined?ae+":"+ac+"-"+af:"all");return" - region=["+ag+"], parameters=["+ad.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ad=this;var ac=function(){if(ad.data_manager.size()===0){setTimeout(ac,300)}else{ad.data_url=default_data_url;ad.data_query_wait=I;ad.dataset_state_url=converted_datasets_state_url;$.getJSON(ad.dataset_state_url,{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},function(ae){})}};ac()}}});var Y=function(ad,ac){var ae={resize:false};i.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(Y.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var h=function(ad,ac,ag){K.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=object_from_template(af);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,K.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tipsy").remove();ac.show_group()}}].concat(K.prototype.action_icons_def),to_dict:w.prototype.to_dict,add_drawable:w.prototype.add_drawable,unpack_drawables:w.prototype.unpack_drawables,change_mode:function(ac){K.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ad,ar,ay,av,aj,al,at){var aq=this,aC=this._gen_tile_cache_key(ar,al,ay),ah=this._get_tile_bounds(ay,av),az=ah[0],ae=ah[1];if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get(aC));if(aB){aq.show_tile(aB,aj,al);return aB}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(az,ae,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(az,ae,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}ak.push(am)}if(ao){p(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ah=aq._get_tile_bounds(ay,av),az=ah[0],ae=ah[1],aA=0,ar=Math.ceil((ae-az)*al)+this.left_offset,ap=0,af=[];var ac=0;for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);aA=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(var ax=0;ax<this.drawables.length;ax++,aA+=2){aq=this.drawables[ax];aw=ak[aA];am=ak[aA+1];aB=aq.draw_tile(aw,au,af[ax],av,ay,al,am)}this.tile_cache.set(aC,aB);this.show_tile(aB,aj,al);return aB}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new N(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof j){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){K.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ah,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var y=function(ac){K.call(this,ac,{content_div:ac.top_labeltrack,resize:false},{});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ac.dbkey};this.data_manager=new E(F,this,false);this.hide_contents()};p(y.prototype,q.prototype,K.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(ak,al,ah,ag,ad,am){var af=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){this.hide_contents();return}var ae=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ai=0,aj=ak.length;ai<aj;ai++){var ac=Math.floor(ai*am);al.fillText(ak[ai],ac,10)}this.show_contents();return new b(af,ad,ag,ae,ak)}this.hide_contents()}});var j=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";K.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};p(j.prototype,q.prototype,K.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.data_url,{stats:true,chrom:ac.view.chrom,low:null,high:null,hda_ldda:ac.hda_ldda,dataset_id:ac.dataset_id},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min;var ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".tipsy").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(am,ak,ah,af,ad,al){var ae=ak.canvas,ac=this._get_tile_bounds(ad,af),ag=ac[0],aj=ac[1],ai=new J.LinePainter(am.data,ag,aj,this.prefs,ah);ai.draw(ak,ae.width,ae.height,al);return new b(this,ad,af,ae,am.data)},can_subset:function(ac){return false},});var d=function(ae,ad,af){var ac=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];K.call(this,ae,ad,af);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.tile_cache.clear();ac.set_painter_from_config();ac.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=af.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,K.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=J.ArcLinkedFeaturePainter}else{this.painter=J.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},after_show_tile:function(ac){this.max_height_px=Math.max(this.max_height_px,ac.html_elt.height());ac.html_elt.parent().children().css("height",this.max_height_px+"px");var ad=this.max_height_px;if(this.visible_height_px!==0){ad=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ad+"px")},postdraw_actions:function(ar,am,ah,ag){K.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(al.mode==="Histogram"){var ad=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof k){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".tipsy").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof M){var ap=true;for(var ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (s.FeatureSlotter)(ag,af,x,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_summary_tree_data:function(ag,aj,ae,ar){if(ar>ae-aj){ar=ae-aj}var an=Math.floor((ae-aj)/ar),aq=[],af=0;var ah=0,ai=0,am,ap=0,ak=[],ao,al;var ad=function(av,au,aw,at){av[0]=au+aw*at;av[1]=au+(aw+1)*at};while(ap<ar&&ah!==ag.length){var ac=false;for(;ap<ar&&!ac;ap++){ad(ak,aj,ap,an);for(ai=ah;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ac=true;break}}if(ac){break}}data_start_index=ai;aq[aq.length]=ao=[ak[0],0];for(;ai<ag.length;ai++){am=ag[ai].slice(1,3);if(is_overlap(am,ak)){ao[1]++}else{break}}if(ao[1]>af){af=ao[1]}ap++}return{max:af,delta:an,data:aq}},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>G){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Histogram"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(an,ar,ap,at,ax,aj,ae){var aq=this,ad=ar.canvas,ag=this._get_tile_bounds(ax,at),aA=ag[0],ac=ag[1],aF=25,af=this.left_offset;if(ap==="summary_tree"||ap==="Histogram"){if(an.dataset_type!=="summary_tree"){var ak=this.get_summary_tree_data(an.data,aA,ac,200);if(an.max){ak.max=an.max}an=ak}var aC=new J.SummaryTreePainter(an,aA,ac,this.prefs);aC.draw(ar,ad.width,ad.height,aj);return new k(aq,ax,at,ad,an.data,an.max)}var ai=[],ao=this.slotters[aj].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var au=0,aw=an.data.length;au<aw;au++){var ah=an.data[au];var av=false;var am;for(var az=0,aE=al.length;az<aE;az++){am=al[az];am.update_attrs(ah);if(!am.keep(ah)){av=true;break}}if(!av){ai.push(ah);if(!(ah[0] in ao)){all_slotted=false}}}}var aD=(this.filters_manager.alpha_filter?new z(this.filters_manager.alpha_filter):null);var aB=(this.filters_manager.height_filter?new z(this.filters_manager.height_filter):null);var aC=new (this.painter)(ai,aA,ac,this.prefs,ap,aD,aB,ae);var ay=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){ay=aC.draw(ar,ad.width,ad.height,aj,ao);ay.translation=-af}return new M(aq,ax,at,ad,an.data,aj,ap,an.message,all_slotted,ay)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message){return false}return true},});var Q=function(ad,ac,ae){d.call(this,ad,ac,ae);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter};p(Q.prototype,q.prototype,K.prototype,d.prototype);var T=function(ae,ad,ag){d.call(this,ae,ad,ag);var af=get_random_color(),ac=get_random_color([af,"#ffffff"]);this.config=new C({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=J.ReadPainter;this.update_icons()};p(T.prototype,q.prototype,K.prototype,d.prototype);U.View=Z;U.DrawableGroup=N;U.LineTrack=j;U.FeatureTrack=d;U.ReadTrack=T;U.VcfTrack=Q;U.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode==="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length===1&&D==="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences){if(this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}else{continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai==="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/a9ad7d60fc48/ changeset: a9ad7d60fc48 user: jgoecks date: 2012-03-27 17:06:28 summary: Add CSS build artifacts to .hgignore affected #: 1 file diff -r 70397647fad54c50213e015aaedfed94e6b19eda -r a9ad7d60fc48fe4da3174753a3497ba0f555d6f2 .hgignore --- a/.hgignore +++ b/.hgignore @@ -64,8 +64,12 @@ # Jars tool-data/shared/jars/ +# CSS build artifacts. +*/variables.less +static/june_2007_style/blue/base_sprites.less + # Misc *.orig .DS_Store *.rej -*~ +*~ \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/changeset/f6010ee7c7f8/ changeset: f6010ee7c7f8 user: jgoecks date: 2012-03-27 17:06:56 summary: Merge. affected #: 1 file diff -r a9ad7d60fc48fe4da3174753a3497ba0f555d6f2 -r f6010ee7c7f8d5a021cba09bbfef937c28265c82 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -997,16 +997,24 @@ """ repo = hg.repository( get_configured_ui(), repository.repo_path ) options = [] + changeset_tups = [] refresh_on_change_values = [] for repository_metadata in repository.downloadable_revisions: changeset_revision = repository_metadata.changeset_revision - revision_label = get_revision_label( trans, repository, changeset_revision ) - options.append( ( revision_label, changeset_revision ) ) + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + rev = '-1' + label = "-1:%s" % changeset_revision + changeset_tups.append( ( rev, label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, - # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time, - # screwing up the order. - sorted_options = sorted( options ) + # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. + for changeset_tup in sorted( changeset_tups ): + # Display the latest revision first. + options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) ) if add_id_to_name: name = 'changeset_revision_%d' % repository.id else: @@ -1014,7 +1022,7 @@ select_field = SelectField( name=name, refresh_on_change=True, refresh_on_change_values=refresh_on_change_values ) - for option_tup in sorted_options: + for option_tup in options: selected = selected_value and option_tup[1] == selected_value select_field.add_option( option_tup[0], option_tup[1], selected=selected ) return select_field Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Missed the copyright - removed from the distribution.
by Bitbucket 27 Mar '12

27 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/241353a85198/ changeset: 241353a85198 user: greg date: 2012-03-27 16:53:45 summary: Missed the copyright - removed from the distribution. affected #: 1 file diff -r 28641bb419101ca7d83f9d1ca92b134866155cf2 -r 241353a8519857a4db755a7cad8227f825b98d4e contrib/universe_merger.py --- a/contrib/universe_merger.py +++ /dev/null @@ -1,71 +0,0 @@ -#! /usr/bin/env python -''' -universe_merger.py - -Created by Anne Pajon on 31 Jan 2012 -Copyright (c) 2012 Cancer Research UK - Cambridge Research Institute. All rights reserved. - -Script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample -''' -import ConfigParser -import sys -import optparse -import logging - -def main(): - # logging configuration - logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO) - - # get the options - parser = optparse.OptionParser() - parser.add_option("-s", "--sample", dest="sample", action="store", help="the path to the Galaxy universe_wsgi.ini.sample file") - parser.add_option("-c", "--config", dest="config", action="store", help="the path to your own universe_wsgi.ini.cri file") - parser.add_option("-o", "--output", dest="output", action="store", help="the path to the new merged universe_wsgi.ini file") - (options, args) = parser.parse_args() - - for option in ['sample', 'config']: - if getattr(options, option) == None: - print "Please supply a --%s parameter.\n" % (option) - parser.print_help() - sys.exit() - - config_sample = ConfigParser.RawConfigParser() - config_sample.read(options.sample) - config_sample_content = open(options.sample, 'r').read() - - config = ConfigParser.RawConfigParser() - config.read(options.config) - - logging.info("Merging your own config file %s into the sample one %s." % (options.config, options.sample)) - logging.info("---------- DIFFERENCE ANALYSIS BEGIN ----------") - for section in config.sections(): - if not config_sample.has_section(section): - logging.warning("-MISSING- section [%s] not found in sample file. It will be ignored." % section) - else: - for (name, value) in config.items(section): - if not config_sample.has_option(section, name): - if not "#%s" % name in config_sample_content: - logging.warning("-MISSING- section [%s] option '%s' not found in sample file. It will be ignored." % (section, name)) - else: - logging.info("-notset- section [%s] option '%s' not set in sample file. It will be added." % (section, name)) - config_sample.set(section, name, value) - else: - if not config_sample.get(section, name) == value: - logging.info("- diff - section [%s] option '%s' has different value ('%s':'%s'). It will be modified." % (section, name, config_sample.get(section, name), value)) - config_sample.set(section, name, value) - logging.info("---------- DIFFERENCE ANALYSIS END ----------") - - if options.output: - outputfile = open(options.output, 'w') - config_sample.write(outputfile) - outputfile.close() - else: - #print "----------" - #config_sample.write(sys.stdout) - #print "----------" - logging.info("use -o OUTPUT to write the merged configuration into a file.") - - logging.info("read Galaxy universe_wsgi.ini.sample for detailed information.") - -if __name__ == '__main__': - main() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample contributed by Anne Pajon.
by Bitbucket 27 Mar '12

27 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/28641bb41910/ changeset: 28641bb41910 user: greg date: 2012-03-27 16:19:04 summary: Add script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample contributed by Anne Pajon. affected #: 1 file diff -r 7dc0e48e9105f19a564263c54684d51bee8ac16e -r 28641bb419101ca7d83f9d1ca92b134866155cf2 contrib/universe_merger.py --- /dev/null +++ b/contrib/universe_merger.py @@ -0,0 +1,71 @@ +#! /usr/bin/env python +''' +universe_merger.py + +Created by Anne Pajon on 31 Jan 2012 +Copyright (c) 2012 Cancer Research UK - Cambridge Research Institute. All rights reserved. + +Script for merging specific local Galaxy config universe_wsgi.ini.cri with default Galaxy universe_wsgi.ini.sample +''' +import ConfigParser +import sys +import optparse +import logging + +def main(): + # logging configuration + logging.basicConfig(format='%(levelname)s: %(message)s', level=logging.INFO) + + # get the options + parser = optparse.OptionParser() + parser.add_option("-s", "--sample", dest="sample", action="store", help="the path to the Galaxy universe_wsgi.ini.sample file") + parser.add_option("-c", "--config", dest="config", action="store", help="the path to your own universe_wsgi.ini.cri file") + parser.add_option("-o", "--output", dest="output", action="store", help="the path to the new merged universe_wsgi.ini file") + (options, args) = parser.parse_args() + + for option in ['sample', 'config']: + if getattr(options, option) == None: + print "Please supply a --%s parameter.\n" % (option) + parser.print_help() + sys.exit() + + config_sample = ConfigParser.RawConfigParser() + config_sample.read(options.sample) + config_sample_content = open(options.sample, 'r').read() + + config = ConfigParser.RawConfigParser() + config.read(options.config) + + logging.info("Merging your own config file %s into the sample one %s." % (options.config, options.sample)) + logging.info("---------- DIFFERENCE ANALYSIS BEGIN ----------") + for section in config.sections(): + if not config_sample.has_section(section): + logging.warning("-MISSING- section [%s] not found in sample file. It will be ignored." % section) + else: + for (name, value) in config.items(section): + if not config_sample.has_option(section, name): + if not "#%s" % name in config_sample_content: + logging.warning("-MISSING- section [%s] option '%s' not found in sample file. It will be ignored." % (section, name)) + else: + logging.info("-notset- section [%s] option '%s' not set in sample file. It will be added." % (section, name)) + config_sample.set(section, name, value) + else: + if not config_sample.get(section, name) == value: + logging.info("- diff - section [%s] option '%s' has different value ('%s':'%s'). It will be modified." % (section, name, config_sample.get(section, name), value)) + config_sample.set(section, name, value) + logging.info("---------- DIFFERENCE ANALYSIS END ----------") + + if options.output: + outputfile = open(options.output, 'w') + config_sample.write(outputfile) + outputfile.close() + else: + #print "----------" + #config_sample.write(sys.stdout) + #print "----------" + logging.info("use -o OUTPUT to write the merged configuration into a file.") + + logging.info("read Galaxy universe_wsgi.ini.sample for detailed information.") + +if __name__ == '__main__': + main() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for tool shed changeset revision select field generation.
by Bitbucket 27 Mar '12

27 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7dc0e48e9105/ changeset: 7dc0e48e9105 user: greg date: 2012-03-27 15:45:18 summary: Fixes for tool shed changeset revision select field generation. affected #: 1 file diff -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 -r 7dc0e48e9105f19a564263c54684d51bee8ac16e lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -997,16 +997,24 @@ """ repo = hg.repository( get_configured_ui(), repository.repo_path ) options = [] + changeset_tups = [] refresh_on_change_values = [] for repository_metadata in repository.downloadable_revisions: changeset_revision = repository_metadata.changeset_revision - revision_label = get_revision_label( trans, repository, changeset_revision ) - options.append( ( revision_label, changeset_revision ) ) + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + rev = '-1' + label = "-1:%s" % changeset_revision + changeset_tups.append( ( rev, label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, - # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time, - # screwing up the order. - sorted_options = sorted( options ) + # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. + for changeset_tup in sorted( changeset_tups ): + # Display the latest revision first. + options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) ) if add_id_to_name: name = 'changeset_revision_%d' % repository.id else: @@ -1014,7 +1022,7 @@ select_field = SelectField( name=name, refresh_on_change=True, refresh_on_change_values=refresh_on_change_values ) - for option_tup in sorted_options: + for option_tup in options: selected = selected_value and option_tup[1] == selected_value select_field.add_option( option_tup[0], option_tup[1], selected=selected ) return select_field Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove duplicate hr style; this reinstates dashed lines between sections in help text.
by Bitbucket 27 Mar '12

27 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cb5ff5b1bd67/ changeset: cb5ff5b1bd67 user: jgoecks date: 2012-03-27 14:49:44 summary: Remove duplicate hr style; this reinstates dashed lines between sections in help text. affected #: 2 files diff -r 8aa5dfcbbb0815cb2b41eb381ff0202bff4bb517 -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 static/june_2007_style/base.less --- a/static/june_2007_style/base.less +++ b/static/june_2007_style/base.less @@ -1616,13 +1616,6 @@ margin-left: 10px; } -hr -{ - border: none; - height: 0px; - margin-top: 0px; -} - div.toolSectionPad { margin: 0; diff -r 8aa5dfcbbb0815cb2b41eb381ff0202bff4bb517 -r cb5ff5b1bd67ca6333d808beefab24beedfeed94 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -734,7 +734,6 @@ pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} body.toolMenuPage{background:white;color:#303030;background:#dfe5f9;margin:5px;margin-right:10px;margin-left:10px;} -hr{border:none;height:0px;margin-top:0px;} div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} div.toolSectionTitle{font-weight:bold;} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for ordering the options of the select list displaying change sets for a tool shed repository.
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8aa5dfcbbb08/ changeset: 8aa5dfcbbb08 user: greg date: 2012-03-26 21:43:27 summary: Fix for ordering the options of the select list displaying change sets for a tool shed repository. affected #: 1 file diff -r 29f8601357203ad282f3848b2fa2c144ef6980f2 -r 8aa5dfcbbb0815cb2b41eb381ff0202bff4bb517 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1003,6 +1003,10 @@ revision_label = get_revision_label( trans, repository, changeset_revision ) options.append( ( revision_label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) + # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, + # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time, + # screwing up the order. + sorted_options = sorted( options ) if add_id_to_name: name = 'changeset_revision_%d' % repository.id else: @@ -1010,7 +1014,7 @@ select_field = SelectField( name=name, refresh_on_change=True, refresh_on_change_values=refresh_on_change_values ) - for option_tup in options: + for option_tup in sorted_options: selected = selected_value and option_tup[1] == selected_value select_field.add_option( option_tup[0], option_tup[1], selected=selected ) return select_field Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: allow limiting the number of data lines used to determine column data types while still counting all data lines
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/29f860135720/ changeset: 29f860135720 user: richard_burhans date: 2012-03-26 19:55:05 summary: allow limiting the number of data lines used to determine column data types while still counting all data lines affected #: 1 file diff -r 6b8535e5b03001cc25e55f05b391fafacbf56b8e -r 29f8601357203ad282f3848b2fa2c144ef6980f2 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -26,7 +26,7 @@ def init_meta( self, dataset, copy_from=None ): data.Text.init_meta( self, dataset, copy_from=copy_from ) - def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = 100000, **kwd ): + def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = 100000, max_guess_type_data_lines = None, **kwd ): """ Tries to determine the number of columns as well as those columns that contain numerical values in the dataset. A skip parameter is @@ -116,13 +116,14 @@ comment_lines += 1 else: data_lines += 1 - fields = line.split( '\t' ) - for field_count, field in enumerate( fields ): - if field_count >= len( column_types ): #found a previously unknown column, we append None - column_types.append( None ) - column_type = guess_column_type( field ) - if type_overrules_type( column_type, column_types[field_count] ): - column_types[field_count] = column_type + if max_guess_type_data_lines is None or data_lines <= max_guess_type_data_lines: + fields = line.split( '\t' ) + for field_count, field in enumerate( fields ): + if field_count >= len( column_types ): #found a previously unknown column, we append None + column_types.append( None ) + column_type = guess_column_type( field ) + if type_overrules_type( column_type, column_types[field_count] ): + column_types[field_count] = column_type if i == 0 and requested_skip is None: # This is our first line, people seem to like to upload files that have a header line, but do not # start with '#' (i.e. all column types would then most likely be detected as str). We will assume Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Don't create the default path for installing tools from the tool shed until the time of installation, at which time the admin whll have over-ridden the default if they wanted to.
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6b8535e5b030/ changeset: 6b8535e5b030 user: greg date: 2012-03-26 19:27:17 summary: Don't create the default path for installing tools from the tool shed until the time of installation, at which time the admin whll have over-ridden the default if they wanted to. affected #: 1 file diff -r ba51ed3cf08491362d42e2d02dbb91d73a0f1dd3 -r 6b8535e5b03001cc25e55f05b391fafacbf56b8e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -238,16 +238,6 @@ return default def check( self ): paths_to_check = [ self.root, self.tool_path, self.tool_data_path, self.template_path ] - # Look for any tool shed configs and retrieve the tool_path attribute from the <toolbox> tag. - tool_configs = self.tool_configs - if self.migrated_tools_config not in tool_configs: - tool_configs.append( self.migrated_tools_config ) - for config_filename in tool_configs: - tree = parse_xml( config_filename ) - root = tree.getroot() - tool_path = root.get( 'tool_path' ) - if tool_path not in [ None, False ]: - paths_to_check.append( resolve_path( tool_path, self.root ) ) # Check that required directories exist for path in paths_to_check: if path not in [ None, False ] and not os.path.isdir( path ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Refactor changeset 164eef0d7693 to use less templates.
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ba51ed3cf084/ changeset: ba51ed3cf084 user: jgoecks date: 2012-03-26 18:34:15 summary: Refactor changeset 164eef0d7693 to use less templates. affected #: 2 files diff -r c401bfbbdcc70d50491e87c91fe18d5fb8fa18f7 -r ba51ed3cf08491362d42e2d02dbb91d73a0f1dd3 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -9,12 +9,12 @@ sub{bottom:-0.25em;} img{max-width:100%;height:auto;border:0;-ms-interpolation-mode:bicubic;} button,input,select,textarea{margin:0;font-size:100%;vertical-align:middle;} +input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex;} button,input{*overflow:visible;line-height:normal;} button::-moz-focus-inner,input::-moz-focus-inner{padding:0;border:0;} button,input[type="button"],input[type="reset"],input[type="submit"]{cursor:pointer;-webkit-appearance:button;} input[type="search"]{-webkit-appearance:textfield;-webkit-box-sizing:content-box;-moz-box-sizing:content-box;box-sizing:content-box;} input[type="search"]::-webkit-search-decoration,input[type="search"]::-webkit-search-cancel-button{-webkit-appearance:none;} -input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex;} textarea{overflow:auto;vertical-align:top;} body{margin:0;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:12px;line-height:16px;color:#111111;background-color:#ffffff;} a{color:#303030;text-decoration:none;} @@ -225,7 +225,7 @@ .navbar-form .radio,.navbar-form .checkbox{margin-top:5px;} .navbar-form input[type="image"],.navbar-form input[type="checkbox"],.navbar-form input[type="radio"]{margin-top:3px;} .navbar-search{position:relative;float:left;margin-top:6px;margin-bottom:0;}.navbar-search .search-query{padding:4px 9px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-size:13px;font-weight:normal;line-height:1;color:#ffffff;color:rgba(255, 255, 255, 0.75);background:#666;background:rgba(255, 255, 255, 0.3);border:1px solid #111;-webkit-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1),0 1px 0px rgba(255, 255, 255, 0.15);-moz-box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1),0 1px 0px rgba(255, 255, 255, 0.15);box-shadow:inset 0 1px 2px rgba(0, 0, 0, 0.1),0 1px 0px rgba(255, 255, 255, 0.15);-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none;}.navbar-search .search-query :-moz-placeholder{color:#eeeeee;} -.navbar-search .search-query::-webkit-input-placeholder{color:#eeeeee;} +.navbar-search .search-query ::-webkit-input-placeholder{color:#eeeeee;} .navbar-search .search-query:hover{color:#ffffff;background-color:#999999;background-color:rgba(255, 255, 255, 0.5);} .navbar-search .search-query:focus,.navbar-search .search-query.focused{padding:5px 10px;color:#333333;text-shadow:0 1px 0 #ffffff;background-color:#ffffff;border:0;-webkit-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 0 3px rgba(0, 0, 0, 0.15);box-shadow:0 0 3px rgba(0, 0, 0, 0.15);outline:0;} .navbar-fixed-top{position:fixed;top:0;right:0;left:0;z-index:1030;} diff -r c401bfbbdcc70d50491e87c91fe18d5fb8fa18f7 -r ba51ed3cf08491362d42e2d02dbb91d73a0f1dd3 static/june_2007_style/bootstrap/reset.less --- a/static/june_2007_style/bootstrap/reset.less +++ b/static/june_2007_style/bootstrap/reset.less @@ -93,6 +93,11 @@ font-size: 100%; vertical-align: middle; } +// Use Webkit margins for checkboxs and radio buttons. +input[type="checkbox"],input[type="radio"] { + margin-left: 0.5ex; + margin-right: 0.5ex; +} button, input { *overflow: visible; // Inner spacing ie IE6/7 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: use show/hide framework to manage reference track.
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c401bfbbdcc7/ changeset: c401bfbbdcc7 user: jgoecks date: 2012-03-26 16:50:31 summary: Trackster: use show/hide framework to manage reference track. affected #: 1 file diff -r b17faef8f1f36dda41f44206805b35896ce57cdc -r c401bfbbdcc70d50491e87c91fe18d5fb8fa18f7 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -4249,6 +4249,7 @@ this.data_url = reference_url; this.data_url_extra_params = {dbkey: view.dbkey}; this.data_manager = new ReferenceTrackDataManager(DATA_CACHE_SIZE, this, false); + this.hide_contents(); }; extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { build_header_div: function() {}, @@ -4266,7 +4267,7 @@ if (w_scale > this.view.canvas_manager.char_width_px) { if (seq.data === null) { - track.content_div.css("height", "0px"); + this.hide_contents(); return; } var canvas = ctx.canvas; @@ -4277,17 +4278,10 @@ var c_start = Math.floor(c * w_scale); ctx.fillText(seq[c], c_start, 10); } + this.show_contents(); return new Tile(track, tile_index, resolution, canvas, seq); } - track.content_div.css("height", "0px"); - }, - /** - * If there is a tile with sequence data, set content div so that data is visible. - */ - after_show_tile: function(tile) { - if (tile) { - this.content_div.css("height", "12px"); - } + this.hide_contents(); } }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by Bitbucket 26 Mar '12

26 Mar '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e5a58a1d3d90/ changeset: e5a58a1d3d90 user: jgoecks date: 2012-03-26 16:16:39 summary: Trackster: make show/hide content compatible with 8e9d2b492c4c. affected #: 1 file diff -r 4a23e38b7a12d65b50ff274272305f89fb5d0309 -r e5a58a1d3d900105cdedd6ee9249d958834f60c3 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -393,8 +393,8 @@ DATA_ERROR = "There was an error in indexing this dataset. ", DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.", DATA_NONE = "No data for this chrom/contig.", - DATA_PENDING = "Preparing data. This takes seconds for a small dataset but longer for a large dataset.<br/>\ - You can save and close the visualization and preparation will continue.<br/>", + DATA_PENDING = "Preparing data. This is very fast for a small dataset but can take a long time for a large dataset. \ + If visualization is saved and closed, preparation will continue in the background.", DATA_CANNOT_RUN_TOOL = "Tool cannot be rerun: ", DATA_LOADING = "Loading data...", DATA_OK = "Ready for display", @@ -3329,18 +3329,15 @@ * Hide any elements that are part of the tracks contents area. Should * remove as approprite, the track will be redrawn by show_contents. */ - hide_contents : function () { - // Clear contents by removing any elements that are contained in - // the tracks content_div - this.content_div.children().remove(); - // Hide the content div - this.content_div.hide(); - // And any y axis labels (common to several track types) + hide_contents: function () { + // Hide tiles. + this.tiles_div.hide(); + // Hide any y axis labels (common to several track types) this.container_div.find(".yaxislabel, .track-resize").hide() }, - show_contents : function() { + show_contents: function() { // Show the contents div and labels (if present) - this.content_div.show(); + this.tiles_div.show(); this.container_div.find(".yaxislabel, .track-resize").show() // Request a redraw of the content this.request_draw(); @@ -4282,7 +4279,7 @@ } return new Tile(track, tile_index, resolution, canvas, seq); } - this.content_div.css("height", "0px"); + track.content_div.css("height", "0px"); }, /** * If there is a tile with sequence data, set content div so that data is visible. https://bitbucket.org/galaxy/galaxy-central/changeset/3b396a26aaf6/ changeset: 3b396a26aaf6 user: jgoecks date: 2012-03-26 16:17:22 summary: Merge. affected #: 1 file diff -r e5a58a1d3d900105cdedd6ee9249d958834f60c3 -r 3b396a26aaf6d78480750e0a8d038a034153f887 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1183,7 +1183,7 @@ self.job_runners = {} start_job_runners = ["local"] if app.config.start_job_runners is not None: - start_job_runners.extend( app.config.start_job_runners.split(",") ) + start_job_runners.extend( [ x.strip() for x in util.listify( app.config.start_job_runners ) ] ) if app.config.use_tasked_jobs: start_job_runners.append("tasks") for name in start_job_runners: https://bitbucket.org/galaxy/galaxy-central/changeset/b17faef8f1f3/ changeset: b17faef8f1f3 user: jgoecks date: 2012-03-26 16:18:09 summary: Add open ID config to .hgignore affected #: 1 file diff -r 3b396a26aaf6d78480750e0a8d038a034153f887 -r b17faef8f1f36dda41f44206805b35896ce57cdc .hgignore --- a/.hgignore +++ b/.hgignore @@ -36,6 +36,7 @@ tool_data_table_conf.xml tool_sheds_conf.xml integrated_tool_panel.xml +openid_conf.xml static/welcome.html.* static/welcome.html Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Strip whitespace around separators in start_job_runners
by Bitbucket 26 Mar '12

26 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3fb39b478590/ changeset: 3fb39b478590 user: natefoo date: 2012-03-26 16:12:37 summary: Strip whitespace around separators in start_job_runners affected #: 1 file diff -r 4a23e38b7a12d65b50ff274272305f89fb5d0309 -r 3fb39b478590de7f4547766bbd60f3c6f686ab60 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1183,7 +1183,7 @@ self.job_runners = {} start_job_runners = ["local"] if app.config.start_job_runners is not None: - start_job_runners.extend( app.config.start_job_runners.split(",") ) + start_job_runners.extend( [ x.strip() for x in util.listify( app.config.start_job_runners ) ] ) if app.config.use_tasked_jobs: start_job_runners.append("tasks") for name in start_job_runners: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for bug introduced into Tool Shed with last OpenID commit.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/4a23e38b7a12/ changeset: 4a23e38b7a12 user: dan date: 2012-03-24 02:47:14 summary: Fix for bug introduced into Tool Shed with last OpenID commit. affected #: 1 file diff -r 2b27b1e42fc90c4077c9ddcb963612efab28d940 -r 4a23e38b7a12d65b50ff274272305f89fb5d0309 lib/galaxy/webapps/community/app.py --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -3,6 +3,7 @@ import galaxy.quota import galaxy.datatypes.registry import galaxy.webapps.community.model +from galaxy.openid.providers import OpenIDProviders from galaxy.web import security from galaxy.tags.tag_handler import CommunityTagHandler @@ -42,5 +43,6 @@ # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) + self.openid_providers = OpenIDProviders() #TODO: Add OpenID support def shutdown( self ): pass Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Remove print debug.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2b27b1e42fc9/ changeset: 2b27b1e42fc9 user: dan date: 2012-03-24 01:50:32 summary: Remove print debug. affected #: 1 file diff -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 -r 2b27b1e42fc90c4077c9ddcb963612efab28d940 lib/galaxy/openid/providers.py --- a/lib/galaxy/openid/providers.py +++ b/lib/galaxy/openid/providers.py @@ -76,7 +76,6 @@ for store_pref_name, store_pref_value_name in self.store_user_preference.iteritems(): if store_pref_value_name in ( self.sreg_optional + self.sreg_required ): trans.user.preferences[ store_pref_name ] = sreg_attributes.get( store_pref_value_name ) - print 'setting',store_pref_name,'to',trans.user.preferences[ store_pref_name ] else: raise Exception( 'Only sreg is currently supported.' ) trans.sa_session.add( trans.user ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b9e188c4ecba/ changeset: b9e188c4ecba user: dan date: 2012-03-23 18:41:01 summary: Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed. affected #: 17 files diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -13,6 +13,7 @@ from galaxy.tags.tag_handler import GalaxyTagHandler from galaxy.tools.imp_exp import load_history_imp_exp_tools from galaxy.sample_tracking import external_service_types +from galaxy.openid.providers import OpenIDProviders class UniverseApplication( object ): """Encapsulates the state of a Universe application""" @@ -105,6 +106,9 @@ if self.config.enable_openid: from galaxy.web.framework import openid_manager self.openid_manager = openid_manager.OpenIDManager( self.config.openid_consumer_cache_path ) + self.openid_providers = OpenIDProviders.from_file( self.config.openid_config ) + else: + self.openid_providers = OpenIDProviders() # Start the heartbeat process if configured and available if self.config.use_heartbeat: from galaxy.util import heartbeat diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -44,7 +44,9 @@ self.cookie_path = kwargs.get( "cookie_path", "/" ) # web API self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) ) + # Galaxy OpenID settings self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) + self.openid_config = kwargs.get( 'openid_config_file', 'openid_conf.xml' ) self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) ) self.tool_sheds_config = kwargs.get( 'tool_sheds_config_file', 'tool_sheds_conf.xml' ) self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) ) diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/openid/__init__.py --- /dev/null +++ b/lib/galaxy/openid/__init__.py @@ -0,0 +1,3 @@ +""" +OpenID functionality +""" \ No newline at end of file diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/openid/providers.py --- /dev/null +++ b/lib/galaxy/openid/providers.py @@ -0,0 +1,118 @@ +""" +Contains OpenID provider functionality +""" + +import logging, os +from galaxy.util import parse_xml, string_as_bool +from galaxy.util.odict import odict + + +log = logging.getLogger( __name__ ) + +class OpenIDProvider( object ): + '''An OpenID Provider object.''' + @classmethod + def from_file( cls, filename ): + return cls.from_elem( parse_xml( filename ).getroot() ) + @classmethod + def from_elem( cls, xml_root ): + provider_elem = xml_root + provider_id = provider_elem.get( 'id', None ) + provider_name = provider_elem.get( 'name', provider_id ) + op_endpoint_url = provider_elem.find( 'op_endpoint_url' ) + if op_endpoint_url is not None: + op_endpoint_url = op_endpoint_url.text + assert (provider_id and provider_name and op_endpoint_url), Exception( "OpenID Provider improperly configured" ) + sreg_required = [] + sreg_optional = [] + use_for = {} + store_user_preference = {} + use_default_sreg = True + for elem in provider_elem.findall( 'sreg' ): + use_default_sreg = False + for field_elem in elem.findall( 'field' ): + sreg_name = field_elem.get( 'name' ) + assert sreg_name, Exception( 'A name is required for a sreg element' ) + if string_as_bool( field_elem.get( 'required' ) ): + sreg_required.append( sreg_name ) + else: + sreg_optional.append( sreg_name ) + for use_elem in field_elem.findall( 'use_for' ): + use_for[ use_elem.get( 'name' ) ] = sreg_name + for store_user_preference_elem in field_elem.findall( 'store_user_preference' ): + store_user_preference[ store_user_preference_elem.get( 'name' ) ] = sreg_name + if use_default_sreg: + sreg_required = None + sreg_optional = None + use_for = None + return cls( provider_id, provider_name, op_endpoint_url, sreg_required, sreg_optional, use_for, store_user_preference ) + def __init__( self, id, name, op_endpoint_url, sreg_required=None, sreg_optional=None, use_for=None, store_user_preference=None ): + '''When sreg options are not specified, defaults are used.''' + self.id = id + self.name = name + self.op_endpoint_url = op_endpoint_url + if sreg_optional is None: + self.sreg_optional = [ 'nickname', 'email' ] + else: + self.sreg_optional = sreg_optional + if sreg_required: + self.sreg_required = sreg_required + else: + self.sreg_required = [] + if use_for is not None: + self.use_for = use_for + else: + self.use_for = {} + if 'nickname' in ( self.sreg_optional + self.sreg_required ): + self.use_for[ 'username' ] = 'nickname' + if 'email' in ( self.sreg_optional + self.sreg_required ): + self.use_for[ 'email' ] = 'email' + if store_user_preference: + self.store_user_preference = store_user_preference + else: + self.store_user_preference = {} + def post_authentication( self, trans, openid_manager, info ): + sreg_attributes = openid_manager.get_sreg( info ) + for store_pref_name, store_pref_value_name in self.store_user_preference.iteritems(): + if store_pref_value_name in ( self.sreg_optional + self.sreg_required ): + trans.user.preferences[ store_pref_name ] = sreg_attributes.get( store_pref_value_name ) + print 'setting',store_pref_name,'to',trans.user.preferences[ store_pref_name ] + else: + raise Exception( 'Only sreg is currently supported.' ) + trans.sa_session.add( trans.user ) + trans.sa_session.flush() + +class OpenIDProviders( object ): + '''Collection of OpenID Providers''' + @classmethod + def from_file( cls, filename ): + try: + return cls.from_elem( parse_xml( filename ).getroot() ) + except Exception, e: + log.error( 'Failed to load OpenID Providers: %s' % ( e ) ) + return cls() + @classmethod + def from_elem( cls, xml_root ): + oid_elem = xml_root + providers = odict() + for elem in oid_elem.findall( 'provider' ): + try: + provider = OpenIDProvider.from_file( os.path.join( 'openid', elem.get( 'file' ) ) ) + providers[ provider.id ] = provider + log.debug( 'Loaded OpenID provider: %s (%s)' % ( provider.name, provider.id ) ) + except Exception, e: + log.error( 'Failed to add OpenID provider: %s' % ( e ) ) + return cls( providers ) + def __init__( self, providers=None ): + if providers: + self.providers = providers + else: + self.providers = odict() + def __iter__( self ): + for provider in self.providers.itervalues(): + yield provider + def get( self, name, default=None ): + if name in self.providers: + return self.providers[ name ] + else: + return default diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -11,6 +11,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.web.framework.helpers import iff from galaxy.security.validate_user_input import validate_email, validate_publicname, validate_password +from galaxy.openid.providers import OpenIDProvider log = logging.getLogger( __name__ ) @@ -21,12 +22,6 @@ <p/> """ -OPENID_PROVIDERS = { 'Google' : 'https://www.google.com/accounts/o8/id', - 'Yahoo!' : 'http://yahoo.com', - 'AOL/AIM' : 'http://openid.aol.com', - 'Launchpad' : 'http://login.launchpad.net', - } - class UserOpenIDGrid( grids.Grid ): use_panels = False title = "OpenIDs linked to your account" @@ -68,19 +63,26 @@ if not referer: referer = url_for( '/' ) consumer = trans.app.openid_manager.get_consumer( trans ) - process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', referer=referer, auto_associate=auto_associate ) - if not openid_url and openid_provider and openid_provider in OPENID_PROVIDERS: - openid_url = OPENID_PROVIDERS[openid_provider] - if openid_url: + openid_provider_obj = None + if not openid_url and openid_provider and trans.app.openid_providers.get( openid_provider ): + openid_provider_obj = trans.app.openid_providers.get( openid_provider ) + elif openid_url: + openid_provider_obj = OpenIDProvider( openid_url, openid_url, openid_url ) #for manually entered links use the link for id, name and url + elif openid_provider: + message = 'Invalid OpenID provider specified: %s' % ( openid_provider ) + else: + message = 'An OpenID provider was not specified' + process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', referer=referer, auto_associate=auto_associate, openid_provider=openid_provider ) + if openid_provider_obj is not None: request = None try: - request = consumer.begin( openid_url ) + request = consumer.begin( openid_provider_obj.op_endpoint_url ) if request is None: - message = 'No OpenID services are available at %s' % openid_url + message = 'No OpenID services are available at %s' % openid_provider_obj.op_endpoint_url except Exception, e: message = 'Failed to begin OpenID authentication: %s' % str( e ) if request is not None: - trans.app.openid_manager.add_sreg( trans, request, optional=[ 'nickname', 'email' ] ) + sreg_request = trans.app.openid_manager.add_sreg( trans, request, required=openid_provider_obj.sreg_required, optional=openid_provider_obj.sreg_optional ) if request.shouldSendRedirect(): redirect_url = request.redirectURL( trans.request.base, process_url ) @@ -114,6 +116,7 @@ info = consumer.complete( kwd, trans.request.url ) display_identifier = info.getDisplayIdentifier() redirect_url = kwd.get( 'referer', url_for( '/' ) ) + openid_provider = kwd.get( 'openid_provider', '' ) if info.status == trans.app.openid_manager.FAILURE and display_identifier: message = "Login via OpenID failed. The technical reason for this follows, please include this message in your email if you need to %s to resolve this problem: %s" % ( contact, info.message ) return trans.response.send_redirect( url_for( controller='user', @@ -125,6 +128,9 @@ if info.endpoint.canonicalID: display_identifier = info.endpoint.canonicalID user_openid = trans.sa_session.query( trans.app.model.UserOpenID ).filter( trans.app.model.UserOpenID.table.c.openid == display_identifier ).first() + openid_provider_obj = trans.app.openid_providers.get( openid_provider ) + if not openid_provider_obj: + openid_provider_obj = OpenIDProvider( display_identifier, display_identifier, display_identifier ) if not user_openid: user_openid = trans.app.model.UserOpenID( session=trans.galaxy_session, openid=display_identifier ) elif not user_openid.user and user_openid.session.id != trans.galaxy_session.id: @@ -132,6 +138,7 @@ elif user_openid.user and not auto_associate: trans.handle_user_login( user_openid.user, webapp ) trans.log_event( "User logged in via OpenID: %s" % display_identifier ) + openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) trans.response.send_redirect( redirect_url ) return if auto_associate and trans.user: @@ -151,6 +158,7 @@ trans.log_event( "User associated OpenID: %s" % display_identifier ) message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) status = "done" + openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) trans.response.send_redirect( url_for( controller='user', action='openid_manage', use_panels=True, @@ -162,15 +170,18 @@ message = "OpenID authentication was successful, but you need to associate your OpenID with a Galaxy account." sreg_resp = trans.app.openid_manager.get_sreg( info ) try: - username = sreg_resp.get( 'nickname', '' ) + sreg_username_name = openid_provider_obj.use_for.get( 'username' ) + username = sreg_resp.get( sreg_username_name, '' ) except AttributeError: username = '' try: - email = sreg_resp.get( 'email', '' ) + sreg_email_name = openid_provider_obj.use_for.get( 'email' ) + email = sreg_resp.get( sreg_email_name, '' ) except AttributeError: email = '' trans.response.send_redirect( url_for( controller='user', action='openid_associate', + openid_provider=openid_provider, use_panels=True, username=username, email=email, @@ -199,6 +210,8 @@ email = kwd.get( 'email', '' ) username = kwd.get( 'username', '' ) referer = kwd.get( 'referer', trans.request.referer ) + openid_provider = kwd.get( 'openid_provider', '' ) + openid_provider_obj = trans.app.openid_providers.get( openid_provider ) params = util.Params( kwd ) is_admin = cntrller == 'admin' and trans.user_is_admin() openids = trans.galaxy_session.openids @@ -219,8 +232,9 @@ redirect_url = referer if not redirect_url: redirect_url = url_for( '/' ) - trans.response.send_redirect( redirect_url ) - return + if openid_provider_obj: + return trans.response.send_redirect( url_for( controller='user', action='openid_auth', openid_provider=openid_provider, referer=redirect_url ) ) + return trans.response.send_redirect( redirect_url ) if kwd.get( 'create_user_button', False ): password = kwd.get( 'password', '' ) confirm = kwd.get( 'confirm', '' ) @@ -251,7 +265,9 @@ redirect_url = referer if not redirect_url: redirect_url = url_for( '/' ) - trans.response.send_redirect( redirect_url ) + if openid_provider_obj: + return trans.response.send_redirect( url_for( controller='user', action='openid_auth', openid_provider=openid_provider, referer=redirect_url ) ) + return trans.response.send_redirect( redirect_url ) else: message = error status = 'error' @@ -285,7 +301,8 @@ user_type_fd_id_select_field=user_type_fd_id_select_field, user_type_form_definition=user_type_form_definition, widgets=widgets, - openids=openids ) + openids=openids, + openid_provider=openid_provider ) @web.expose @web.require_login( 'manage OpenIDs' ) def openid_disassociate( self, trans, webapp='galaxy', **kwd ): @@ -340,7 +357,7 @@ use_panels=use_panels, id=kwd['id'] ) ) kwd['referer'] = url_for( controller='user', action='openid_manage', use_panels=True ) - kwd['openid_providers'] = OPENID_PROVIDERS + kwd['openid_providers'] = trans.app.openid_providers return self.user_openid_grid( trans, **kwd ) @web.expose def login( self, trans, webapp='galaxy', redirect_url='', refresh_frames=[], **kwd ): @@ -351,6 +368,7 @@ header = '' user = None email = kwd.get( 'email', '' ) + openid_provider = kwd.get( 'openid_provider', '' ) if kwd.get( 'login_button', False ): if webapp == 'galaxy' and not refresh_frames: if trans.app.config.require_login: @@ -385,7 +403,7 @@ refresh_frames=refresh_frames, message=message, status=status, - openid_providers=OPENID_PROVIDERS, + openid_providers=trans.app.openid_providers, active_view="user" ) def __validate_login( self, trans, webapp='galaxy', **kwd ): message = kwd.get( 'message', '' ) diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/web/framework/openid_manager.py --- a/lib/galaxy/web/framework/openid_manager.py +++ b/lib/galaxy/web/framework/openid_manager.py @@ -1,5 +1,5 @@ """ -Mange the OpenID consumer and related data stores. +Manage the OpenID consumer and related data stores. """ import os, pickle, logging diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/aol.xml --- /dev/null +++ b/openid/aol.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="aol" name="AOL/AIM"> + <op_endpoint_url>http://openid.aol.com</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/genomespace.xml --- /dev/null +++ b/openid/genomespace.xml @@ -0,0 +1,16 @@ +<?xml version="1.0"?> +<provider id="genomespace" name="GenomeSpace"> + <op_endpoint_url>https://identity.genomespace.org/identityServer/xrd.jsp</op_endpoint_url> + <sreg> + <field name="nickname" required="True"> + <use_for name="username"/> + <store_user_preference name="genomespace_username"/> + </field> + <field name="email" required="False"> + <use_for name="email"/> + </field> + <field name="gender" required="True"> + <store_user_preference name="genomespace_token"/> + </field> + </sreg> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/google.xml --- /dev/null +++ b/openid/google.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="google" name="Google"> + <op_endpoint_url>https://www.google.com/accounts/o8/id</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/launchpad.xml --- /dev/null +++ b/openid/launchpad.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="launchpad" name="Launchpad"> + <op_endpoint_url>http://login.launchpad.net</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/yahoo.xml --- /dev/null +++ b/openid/yahoo.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="yahoo" name="Yahoo!"> + <op_endpoint_url>http://yahoo.com</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid_conf.xml.sample --- /dev/null +++ b/openid_conf.xml.sample @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<openid> + <provider file="google.xml" /> + <provider file="yahoo.xml" /> + <provider file="aol.xml" /> + <provider file="launchpad.xml" /> + <provider file="genomespace.xml" /> +</openid> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 run.sh --- a/run.sh +++ b/run.sh @@ -15,6 +15,7 @@ tool_conf.xml.sample tool_data_table_conf.xml.sample tool_sheds_conf.xml.sample + openid_conf.xml.sample universe_wsgi.ini.sample tool-data/shared/ucsc/builds.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -59,7 +59,7 @@ </%def> -<%def name="render_login_form( form_action=None )"> +<%def name="render_login_form( form_action=None, openid_provider='' )"><% if form_action is None: @@ -77,6 +77,7 @@ <input type="text" name="email" value="${email}" size="40"/><input type="hidden" name="webapp" value="${webapp}" size="40"/><input type="hidden" name="referer" value="${referer}" size="40"/> + <input type="hidden" name="openid_provider" value="${openid_provider}" /></div><div class="form-row"><label>Password:</label> @@ -94,10 +95,9 @@ </%def><%def name="render_openid_form( referer, auto_associate, openid_providers )"> - <div class="toolForm"><div class="toolFormTitle">OpenID Login</div> - <form name="openid" id="openid" action="${h.url_for( controller='user', action='openid_auth' )}" method="post" > + <form name="openid" id="openid" action="${h.url_for( controller='user', action='openid_auth' )}" method="post" target="_parent" ><div class="form-row"><label>OpenID URL:</label><input type="text" name="openid_url" size="60" style="background-image:url('${h.url_for( '/static/images/openid-16x16.gif' )}' ); background-repeat: no-repeat; padding-right: 20px; background-position: 99% 50%;"/> @@ -107,8 +107,8 @@ </div><div class="form-row"> Or, authenticate with your <select name="openid_provider"> - %for provider in openid_providers.keys(): - <option>${provider}</option> + %for provider in openid_providers: + <option value="${provider.id}">${provider.name}</option> %endfor </select> account. </div> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 templates/user/openid_associate.mako --- a/templates/user/openid_associate.mako +++ b/templates/user/openid_associate.mako @@ -65,11 +65,11 @@ <% form_action = h.url_for( cntrller=cntrller, use_panels=use_panels ) %> - ${render_login_form( form_action=form_action )} + ${render_login_form( form_action=form_action, openid_provider=openid_provider )} <br/> - ${render_registration_form( form_action=form_action )} + ${render_registration_form( form_action=form_action, openid_provider=openid_provider )} </div></div> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -21,7 +21,7 @@ ${render_registration_form()} %endif -<%def name="render_registration_form( form_action=None )"> +<%def name="render_registration_form( form_action=None, openid_provider='' )"><% if form_action is None: @@ -38,6 +38,7 @@ <input type="text" name="email" value="${email}" size="40"/><input type="hidden" name="webapp" value="${webapp}" size="40"/><input type="hidden" name="referer" value="${referer}" size="40"/> + <input type="hidden" name="openid_provider" value="${openid_provider}" /></div><div class="form-row"><label>Password:</label> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -495,6 +495,7 @@ # Enable authentication via OpenID. Allows users to log in to their Galaxy # account by authenticating with an OpenID provider. #enable_openid = False +#openid_config_file = openid_conf.xml # Enable the (experimental! beta!) Web API. Documentation forthcoming. #enable_api = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Convert loc file examples to use tabs instead of spaces.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/463fc935b97c/ changeset: 463fc935b97c user: dannon date: 2012-03-23 13:59:34 summary: Convert loc file examples to use tabs instead of spaces. affected #: 22 files diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/all_fasta.loc.sample --- a/tool-data/all_fasta.loc.sample +++ b/tool-data/all_fasta.loc.sample @@ -4,13 +4,13 @@ #all_fasta.loc. This file has the format (white space characters are #TAB characters): # -#<unique_build_id><dbkey><display_name><file_path> +#<unique_build_id><dbkey><display_name><file_path> # #So, all_fasta.loc could look something like this: # -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa # #Your all_fasta.loc file should contain an entry for each individual #fasta file. So there will be multiple fasta files for each build, diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/blastdb.loc.sample --- a/tool-data/blastdb.loc.sample +++ b/tool-data/blastdb.loc.sample @@ -2,7 +2,7 @@ #list of nucleotide BLAST databases, using three columns tab separated #(longer whitespace are TAB characters): # -#<unique_id><database_caption><base_name_path> +#<unique_id><database_caption><base_name_path> # #The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, @@ -25,9 +25,9 @@ #Your blastdb.loc file should include an entry per line for each "base name" #you have stored. For example: # -#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk -#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk +#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test #...etc... # #See also blastdb_p.loc which is for any protein BLAST database. diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/blastdb_p.loc.sample --- a/tool-data/blastdb_p.loc.sample +++ b/tool-data/blastdb_p.loc.sample @@ -2,25 +2,25 @@ #list of protein BLAST databases, using three columns tab separated #(longer whitespace are TAB characters): # -#<unique_id><database_caption><base_name_path> +#<unique_id><database_caption><base_name_path> # #The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, #and that the first tab that appears in the line is right before the path. # -#So, for example, if your database is NR and the path to your base name +#So, for example, if your database is NR and the path to your base name #is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: # -#nr NCBI NR (non redundant) /data/blastdb/nr +#nr NCBI NR (non redundant) /data/blastdb/nr # #and your /data/blastdb directory would contain all of the files associated #with the database, /data/blastdb/nr.*. # -#Your blastdb_p.loc file should include an entry per line for each "base name" +#Your blastdb_p.loc file should include an entry per line for each "base name" #you have stored. For example: # -#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr -#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr +#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr +#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr #...etc... # #See also blastdb.loc which is for any nucleotide BLAST database. diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bowtie_indices_color.loc.sample --- a/tool-data/bowtie_indices_color.loc.sample +++ b/tool-data/bowtie_indices_color.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The bowtie_indices.loc #file has this format (longer white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_base_path> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/bowtie/hg18/, @@ -25,9 +25,9 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bwa_index.loc.sample --- a/tool-data/bwa_index.loc.sample +++ b/tool-data/bwa_index.loc.sample @@ -25,10 +25,10 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bwa_index_color.loc.sample --- a/tool-data/bwa_index_color.loc.sample +++ b/tool-data/bwa_index_color.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The bwa_index_color.loc #file has this format (longer white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_path> +#<unique_build_id><dbkey><display_name><file_path> # #So, for example, if you had phiX indexed stored in #/depot/data2/galaxy/phiX/color/, @@ -25,10 +25,10 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/faseq.loc.sample --- a/tool-data/faseq.loc.sample +++ b/tool-data/faseq.loc.sample @@ -20,7 +20,7 @@ #Your faseq.loc file should include an entry per line for each set of fasta #sequence files you have stored. For example: # -#hg18 /depot/data2/galaxy/faseq/hg18 -#mm9 /depot/data2/galaxy/faseq/mm9 -#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis +#hg18 /depot/data2/galaxy/faseq/hg18 +#mm9 /depot/data2/galaxy/faseq/mm9 +#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gatk_sorted_picard_index.loc.sample --- a/tool-data/gatk_sorted_picard_index.loc.sample +++ b/tool-data/gatk_sorted_picard_index.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The picard_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in -#/depot/data2/galaxy/srma/hg18/, +#/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.chrlens.loc.sample --- a/tool-data/gd.chrlens.loc.sample +++ b/tool-data/gd.chrlens.loc.sample @@ -6,17 +6,17 @@ # file has the following format (white space characters are TAB # characters): # -#<species><reference_species_file_path> +#<species><reference_species_file_path> # # So, for example, if you used Monodelphis domestica as the reference # species for a collection of Sarcophilus harrisii SNPs, then the # gd.chrlens.loc entry would look like this: # -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt +#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt # # Your gd.chrlens.loc file should include an entry for each pair of # species SNPs and reference species. For example: # -#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt +#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt +#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.primers.loc.sample --- a/tool-data/gd.primers.loc.sample +++ b/tool-data/gd.primers.loc.sample @@ -5,18 +5,18 @@ # primers files are stored. The gd.primers.loc file has the following # format (white space characters are TAB characters): # -#<species><primers_file_path> +#<species><primers_file_path> # # So, for example, if you had a primers file located at # /galaxy/data/location/gd/primers/bighorn_primers.txt for a collection of # Ovis canadensis SNPs, then the gd.primers.loc entry would look like # this: # -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt +#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt # # Your gd.primers.loc file should include an entry for each pair of # species SNPs and primers file. For example: # -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt -#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt +#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt +#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.snps.loc.sample --- a/tool-data/gd.snps.loc.sample +++ b/tool-data/gd.snps.loc.sample @@ -5,17 +5,17 @@ # SNP call files are stored. The gd.snps.loc file has the following # format (white space characters are TAB characters): # -#<species><SNP_call_file_path> +#<species><SNP_call_file_path> # # So, for example, if you had a SNP call file located at # /galaxy/data/location/gd/snps/bighorn_snps.txt for a collection of # Ovis canadensis SNPs, then the gd.snps.loc entry would look like this: # -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt +#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt # # Your gd.snps.loc file should include an entry for each pair of species # SNPs and SNP call file. For example: # -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt -#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt +#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt +#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/lastz_seqs.loc.sample --- a/tool-data/lastz_seqs.loc.sample +++ b/tool-data/lastz_seqs.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The lastz_seqs.loc #file has this format (white space characters are TAB characters): # -#<unique_build_id><display_name><file_path> +#<unique_build_id><display_name><file_path> # #So, for example, if your lastz_seqs.loc began like this: # -#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit -#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit -#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit # #then your /depot/data2/galaxy/twobit/ directory #would need to contain the following 2bit files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/liftOver.loc.sample --- a/tool-data/liftOver.loc.sample +++ b/tool-data/liftOver.loc.sample @@ -8,7 +8,7 @@ #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, #then the liftOver.loc entry would look like this: # -#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain +#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain # #and your /depot/data2/galaxy/anoCar1/liftOver directory would #contain all of your "chain" files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/mosaik_index.loc.sample --- a/tool-data/mosaik_index.loc.sample +++ b/tool-data/mosaik_index.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The mosaik_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/mosaik/hg18/ #then the mosaik_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa # #and your /depot/data2/galaxy/mosaik/hg18/ directory #would contain the following files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/ngs_sim_fasta.loc.sample --- a/tool-data/ngs_sim_fasta.loc.sample +++ b/tool-data/ngs_sim_fasta.loc.sample @@ -4,17 +4,17 @@ #in this directory) that points to the locations of those files. The ngs_sim.loc #file has this format (white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_base_path> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18chrM.fa in #/data/path/hg18/seq/, #then the ngs_sim.loc entry would look like this: # -#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa +#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa # #Your ngs_sim.loc file should include an entry per line for each FASTA file you #have stored. # -#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa -#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa -#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa +#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa +#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa +#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/perm_base_index.loc.sample --- a/tool-data/perm_base_index.loc.sample +++ b/tool-data/perm_base_index.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The perm_base_index.loc #file has this format (longer white space characters are TAB characters): # -#<build_seed_readlength><display_name><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_base_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_base_F3_50.index: @@ -21,7 +21,7 @@ #Your perm_base_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index -#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/perm_color_index.loc.sample --- a/tool-data/perm_color_index.loc.sample +++ b/tool-data/perm_color_index.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The perm_color_index.loc #file has this format (white space characters are TAB characters): # -#<build_seed_readlength><display_name><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_color_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_color_F3_50.index: @@ -21,8 +21,8 @@ #Your perm_color_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index -#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index # diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/picard_index.loc.sample --- a/tool-data/picard_index.loc.sample +++ b/tool-data/picard_index.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The picard_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/quality_scores.loc.sample --- a/tool-data/quality_scores.loc.sample +++ b/tool-data/quality_scores.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/panTro2/quality_scores, then the quality_scores.loc entry #would look like this: # -#panTro2 /depot/data2/galaxy/panTro2/quality_scores +#panTro2 /depot/data2/galaxy/panTro2/quality_scores # #and your /depot/data2/galaxy/panTro2/quality_scores directory would #contain all of your quality score files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/regions.loc.sample --- a/tool-data/regions.loc.sample +++ b/tool-data/regions.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed, then the #regions.loc entry would look like this: # -#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed +#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed # #and your /depot/data2/galaxy/regions/ directory would #contain all of your regions files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/srma_index.loc.sample --- a/tool-data/srma_index.loc.sample +++ b/tool-data/srma_index.loc.sample @@ -8,13 +8,13 @@ #the directories in which those files are stored. The srma_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/twobit.loc.sample --- a/tool-data/twobit.loc.sample +++ b/tool-data/twobit.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/droPer1/, then the twobit.loc entry #would look like this: # -#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit # #and your /depot/data2/galaxy/droPer1/ directory would #contain all of your twobit files (e.g.): @@ -19,8 +19,8 @@ #Your twobit.loc file should include an entry per line for each twobit #file you have stored. For example: # -#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit -#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit -#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit -#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit +#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit +#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit #...etc... Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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