[galaxy-commits] commit/galaxy-central: carlfeberhard: Visualizations framework: allow users to associate custom visualizations with models, datatypes, etc. via an xml configuration file (visualizations_conf.xml)

17 May 2013

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/ffc6ff4fe6df/
Changeset:   ffc6ff4fe6df
User:        carlfeberhard
Date:        2013-05-17 20:45:07
Summary:     Visualizations framework: allow users to associate custom visualizations with models, datatypes, etc. via an xml configuration file (visualizations_conf.xml)
Affected #:  19 files

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d .hgignore

--- a/.hgignore
+++ b/.hgignore
@@ -60,7 +60,7 @@
 job_conf.xml
 data_manager_conf.xml
 shed_data_manager_conf.xml
-
+visualizations_conf.xml
 static/welcome.html.*
 static/welcome.html
 

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d lib/galaxy/app.py
--- a/lib/galaxy/app.py
+++ b/lib/galaxy/app.py
@@ -15,6 +15,7 @@
 from galaxy.tags.tag_handler import GalaxyTagHandler
 from galaxy.visualization.genomes import Genomes
 from galaxy.visualization.data_providers.registry import DataProviderRegistry
+from galaxy.visualization.registry import VisualizationsRegistry
 from galaxy.tools.imp_exp import load_history_imp_exp_tools
 from galaxy.tools.genome_index import load_genome_index_tools
 from galaxy.sample_tracking import external_service_types
@@ -120,6 +121,9 @@
         load_history_imp_exp_tools( self.toolbox )
         # Load genome indexer tool.
         load_genome_index_tools( self.toolbox )
+        # visualizations registry: associates resources with visualizations, controls how to render
+        self.visualizations_registry = ( VisualizationsRegistry( self.config.root, self.config.visualizations_conf_path )
+                                         if self.config.visualizations_conf_path else None )
         # Load security policy.
         self.security_agent = self.model.security_agent
         self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions )

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -275,6 +275,8 @@
         self.fluent_log = string_as_bool( kwargs.get( 'fluent_log', False ) )
         self.fluent_host = kwargs.get( 'fluent_host', 'localhost' )
         self.fluent_port = int( kwargs.get( 'fluent_port', 24224 ) )
+        # visualizations registry config path
+        self.visualizations_conf_path = kwargs.get( 'visualizations_conf_path', None )
 
     @property
     def sentry_dsn_public( self ):

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d lib/galaxy/datatypes/registry.py
--- a/lib/galaxy/datatypes/registry.py
+++ b/lib/galaxy/datatypes/registry.py
@@ -379,6 +379,36 @@
                 if not included:
                     self.sniff_order.append(datatype)
         append_to_sniff_order()
+        
+    def get_datatype_class_by_name( self, name ):
+        """
+        Return the datatype class where the datatype's `type` attribute
+        (as defined in the datatype_conf.xml file) contains `name`.
+        """
+        #TODO: too roundabout - would be better to generate this once as a map and store in this object
+        found_class = None
+        for ext, datatype_obj in self.datatypes_by_extension.items():
+            datatype_obj_class = datatype_obj.__class__
+            datatype_obj_class_str = str( datatype_obj_class )
+            #print datatype_obj_class_str
+            if name in datatype_obj_class_str:
+                return datatype_obj_class
+        return None
+        # these seem to be connected to the dynamic classes being generated in this file, lines 157-158
+        #   they appear when a one of the three are used in inheritance with subclass="True"
+        #TODO: a possible solution is to def a fn in datatypes __init__ for creating the dynamic classes
+
+        #remap = {
+        #    'galaxy.datatypes.registry.Tabular'   : galaxy.datatypes.tabular.Tabular,
+        #    'galaxy.datatypes.registry.Text'      : galaxy.datatypes.data.Text,
+        #    'galaxy.datatypes.registry.Binary'    : galaxy.datatypes.binary.Binary
+        #}
+        #datatype_str = str( datatype )
+        #if datatype_str in remap:
+        #    datatype = remap[ datatype_str ]
+        #
+        #return datatype
+
     def get_available_tracks(self):
         return self.available_tracks
     def get_mimetype_by_extension(self, ext, default = 'application/octet-stream' ):

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d lib/galaxy/visualization/data_providers/registry.py
--- a/lib/galaxy/visualization/data_providers/registry.py
+++ b/lib/galaxy/visualization/data_providers/registry.py
@@ -30,7 +30,9 @@
             "bai": genome.BamDataProvider,
             "bam": genome.SamDataProvider,
             "bigwig": genome.BigWigDataProvider,
-            "bigbed": genome.BigBedDataProvider
+            "bigbed": genome.BigBedDataProvider,
+
+            "column": ColumnDataProvider
         }
 
     def get_data_provider( self, trans, name=None, source='data', raw=False, original_dataset=None ):
@@ -105,4 +107,4 @@
                         except NoConverterException:
                             pass
 
-        return data_provider
\ No newline at end of file
+        return data_provider

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d lib/galaxy/visualization/registry.py
--- /dev/null
+++ b/lib/galaxy/visualization/registry.py
@@ -0,0 +1,808 @@
+"""
+Lower level of visualization framework which does three main things:
+    - associate visualizations with objects
+    - create urls to visualizations based on some target object(s)
+    - unpack a query string into the desired objects needed for rendering
+"""
+import os
+import shutil
+
+from galaxy import util
+import galaxy.model
+from galaxy.web import url_for
+
+import logging
+log = logging.getLogger( __name__ )
+
+__TODO__ = """
+    BUGS:
+        anon users clicking a viz link gets 'must be' msg in galaxy_main (w/ masthead)
+            should not show visualizations (no icon)?
+        newick files aren't being sniffed prop? - datatype is txt
+
+    have parsers create objects instead of dicts
+    allow data_sources with no model_class but have tests (isAdmin, etc.)
+        maybe that's an instance of User model_class?
+    some confused vocabulary in docs, var names
+    tests:
+        anding, grouping, not
+    data_sources:
+        lists of
+    add description element to visualization.
+"""
+
+class VisualizationsRegistry( object ):
+    """
+    Main responsibilities are:
+        - testing if an object has a visualization that can be applied to it
+        - generating a link to controllers.visualization.render with
+            the appropriate params
+        - validating and parsing params into resources (based on a context)
+            used in the visualization template
+    """
+    # these should be handled somewhat differently - and be passed onto their resp. methods in ctrl.visualization
+    #TODO: change/remove if/when they can be updated to use this system
+    BUILT_IN_VISUALIZATIONS = [
+        'trackster',
+        'circster',
+        'sweepster',
+        'phyloviz'
+    ]
+    # where to search for visualiztion templates (relative to templates/webapps/galaxy)
+    # this can be overridden individually in the config entries
+    TEMPLATE_ROOT = 'visualization'
+
+    def __str__( self ):
+        listings_keys_str = ','.join( self.listings.keys() ) if self.listings else ''
+        return 'VisualizationsRegistry(%s)' %( listings_keys_str )
+
+    def __init__( self, galaxy_root, configuration_filepath ):
+        # load the registry from the given xml file using the given parser
+        configuration_filepath = os.path.join( galaxy_root, configuration_filepath )
+        configuration_filepath = self.check_conf_filepath( configuration_filepath )
+        self.configuration_filepath = configuration_filepath
+        self.load()
+
+        # what to use to parse query strings into resources/vars for the template
+        self.resource_parser = ResourceParser()
+
+    def check_conf_filepath( self, configuration_filepath ):
+        """
+        If given file at filepath exists, return that filepath. If not,
+        see if filepath + '.sample' exists and, if so, copy that into filepath.
+
+        If neither original or sample exist, throw an IOError (currently,
+        this is a requireed file).
+        """
+        if os.path.exists( configuration_filepath ):
+            return configuration_filepath
+        else:
+            sample_file = configuration_filepath + '.sample'
+            if os.path.exists( sample_file ):
+                shutil.copy2( sample_file, configuration_filepath )
+                return configuration_filepath
+        raise IOError( 'visualization configuration file (%s) not found' %( configuration_filepath ) )
+
+    def load( self ):
+        """
+        Builds the registry by parsing the xml in `self.configuration_filepath`
+        and stores the results in `self.listings`.
+
+        Provided as separate method from `__init__` in order to re-load a
+        new configuration without restarting the instance.
+        """
+        self.listings = VisualizationsConfigParser.parse( self.configuration_filepath )
+
+    # -- building links to visualizations from objects --
+    def get_visualizations( self, trans, target_object ):
+        """
+        Get the names of visualizations usable on the `target_object` and
+        the urls to call in order to render the visualizations.
+        """
+        #TODO:?? a list of objects? YAGNI?
+        # a little weird to pass trans because this registry is part of the trans.app
+        applicable_visualizations = []
+        for vis_name, listing_data in self.listings.items():
+
+            data_sources = listing_data[ 'data_sources' ]
+            for data_source in data_sources:
+                # currently a model class is required
+                model_class = data_source[ 'model_class' ]
+                if not isinstance( target_object, model_class ):
+                    continue
+
+                # tests are optional - default is the above class test
+                tests = data_source[ 'tests' ]
+                if tests and not self.is_object_applicable( trans, target_object, tests ):
+                    continue
+
+                param_data = data_source[ 'to_params' ]
+                url = self.get_visualization_url( trans, target_object, vis_name, param_data )
+                link_text = listing_data.get( 'link_text', None )
+                if not link_text:
+                    # default to visualization name, titlecase, and replace underscores
+                    link_text = vis_name.title().replace( '_', ' ' )
+                render_location = listing_data.get( 'render_location' )
+                # remap some of these vars for direct use in ui.js, PopupMenu (e.g. text->html)
+                applicable_visualizations.append({
+                    'href'  : url,
+                    'html'  : link_text,
+                    'target': render_location
+                })
+
+        return applicable_visualizations
+
+    def is_object_applicable( self, trans, target_object, data_source_tests ):
+        """
+        Run a visualization's data_source tests to find out if
+        it be applied to the target_object.
+        """
+        for test in data_source_tests:
+            test_type   = test[ 'type' ]
+            result_type = test[ 'result_type' ]
+            test_result = test[ 'result' ]
+            test_fn     = test[ 'fn' ]
+            #log.debug( '%s %s: %s, %s, %s, %s', str( target_object ), 'is_object_applicable',
+            #           test_type, result_type, test_result, test_fn )
+
+            if test_type == 'isinstance':
+                # parse test_result based on result_type (curr: only datatype has to do this)
+                if result_type == 'datatype':
+                    # convert datatypes to their actual classes (for use with isinstance)
+                    test_result = trans.app.datatypes_registry.get_datatype_class_by_name( test_result )
+                    if not test_result:
+                        # warn if can't find class, but continue
+                        log.warn( 'visualizations_registry cannot find class (%s) for applicability test', test_result )
+                        continue
+
+            if test_fn( target_object, test_result ):
+                #log.debug( 'test passed' )
+                return True
+
+        return False
+
+    def get_visualization_url( self, trans, target_object, visualization_name, param_data ):
+        """
+        Generates a url for the visualization with `visualization_name`
+        for use with the given `target_object` with a query string built
+        from the configuration data in `param_data`.
+        """
+        #precondition: the target_object should be usable by the visualization (accrd. to data_sources)
+        # convert params using vis.data_source.to_params
+        params = self.get_url_params( trans, target_object, param_data )
+
+        # we want existing visualizations to work as normal but still be part of the registry (without mod'ing)
+        #   so generate their urls differently
+        url = None
+        if visualization_name in self.BUILT_IN_VISUALIZATIONS:
+            url = url_for( controller='visualization', action=visualization_name, **params )
+        else:
+            url = url_for( controller='visualization', action='render',
+                           visualization_name=visualization_name, **params )
+
+        #TODO:?? not sure if embedded would fit/used here? or added in client...
+        return url
+
+    def get_url_params( self, trans, target_object, param_data ):
+        """
+        Convert the applicable objects and assoc. data into a param dict
+        for a url query string to add to the url that loads the visualization.
+        """
+        params = {}
+        for to_param_name, to_param_data in param_data.items():
+            #TODO??: look into params as well? what is required, etc.
+            target_attr = to_param_data.get( 'param_attr', None )
+            assign = to_param_data.get( 'assign', None )
+            # one or the other is needed
+            # assign takes precedence (goes last, overwrites)?
+            #NOTE this is only one level
+            if target_attr and hasattr( target_object, target_attr ):
+                params[ to_param_name ] = getattr( target_object, target_attr )
+            if assign:
+                params[ to_param_name ] = assign
+
+        #NOTE!: don't expose raw ids: encode id, _id
+        if params:
+            params = trans.security.encode_dict_ids( params )
+        return params
+
+    # -- getting resources for visualization templates from link query strings --
+    def get_resource_params_and_modifiers( self, visualization_name ):
+        """
+        Get params and modifiers for the given visualization as a 2-tuple.
+
+        Both `params` and `param_modifiers` default to an empty dictionary.
+        """
+        visualization = self.listings.get( visualization_name )
+        expected_params = visualization.get( 'params', {} )
+        param_modifiers = visualization.get( 'param_modifiers', {} )
+        return ( expected_params, param_modifiers )
+
+    def query_dict_to_resources( self, trans, controller, visualization_name, query_dict ):
+        """
+        Use a resource parser, controller, and a visualization's param configuration
+        to convert a query string into the resources and variables a visualization
+        template needs to start up.
+        """
+        param_confs, param_modifiers = self.get_resource_params_and_modifiers( visualization_name )
+        resources = self.resource_parser.parse_parameter_dictionary(
+            trans, controller, param_confs, query_dict, param_modifiers )
+        return resources
+
+
+# ------------------------------------------------------------------- parsing the config file
+class ParsingException( ValueError ):
+    """
+    An exception class for errors that occur during parsing of the visualizations
+    framework configuration XML file.
+    """
+    pass
+
+
+class VisualizationsConfigParser( object ):
+    """
+    Class that parses a visualizations configuration XML file.
+
+    Each visualization will get the following info:
+        - how to load a visualization:
+            -- how to find the proper template
+            -- how to convert query string into DB models
+        - when/how to generate a link to the visualization
+            -- what provides the data
+            -- what information needs to be added to the query string
+    """
+    VALID_RENDER_LOCATIONS = [ 'galaxy_main', '_top', '_blank' ]
+
+    @classmethod
+    def parse( cls, xml_filepath, debug=True ):
+        """
+        Static class interface
+        """
+        return cls( debug ).parse_file( xml_filepath )
+
+    def __init__( self, debug=False ):
+        self.debug = debug
+
+        # what parsers should be used for sub-components
+        self.data_source_parser = DataSourceParser()
+        self.param_parser = ParamParser()
+        self.param_modifier_parser = ParamModifierParser()
+
+    def parse_file( self, xml_filepath ):
+        """
+        Parse the given XML file for visualizations data.
+
+        If an error occurs while parsing a visualizations entry it is skipped.
+        """
+        returned = {}
+        try:
+            xml_tree = galaxy.util.parse_xml( xml_filepath )
+            for visualization_conf in xml_tree.getroot().findall( 'visualization' ):
+                visualization = None
+                visualization_name = visualization_conf.get( 'name' )
+
+                try:
+                    visualization = self.parse_visualization( visualization_conf )
+                # skip vis' with parsing errors - don't shutdown the startup
+                except ParsingException, parse_exc:
+                    log.error( 'Skipped visualization configuration "%s" due to parsing errors: %s',
+                        visualization_name, str( parse_exc ), exc_info=self.debug )
+
+                if visualization:
+                    returned[ visualization_name ] = visualization
+
+        except Exception, exc:
+            log.error( 'Error parsing visualization configuration file %s: %s',
+                xml_filepath, str( exc ), exc_info=( not self.debug ) )
+            #TODO: change when this is required
+            if self.debug:
+                raise
+
+        return returned
+
+    def parse_visualization( self, xml_tree ):
+        """
+        Parse the template, name, and any data_sources and params from the
+        given `xml_tree` for a visualization.
+        """
+        returned = {}
+
+        # data_sources are the kinds of objects/data associated with the visualization
+        #   e.g. views on HDAs can use this to find out what visualizations are applicable to them
+        data_sources = []
+        data_sources_confs = xml_tree.find( 'data_sources' )
+        for data_source_conf in data_sources_confs.findall( 'data_source' ):
+            data_source = self.data_source_parser.parse( data_source_conf )
+            if data_source:
+                data_sources.append( data_source )
+        # data_sources are not required
+        if not data_sources:
+            raise ParsingException( 'No valid data_sources for visualization' )
+        returned[ 'data_sources' ] = data_sources
+
+        # parameters spell out how to convert query string params into resources and data
+        #   that will be parsed, fetched, etc. and passed to the template
+        # list or dict? ordered or not?
+        params = {}
+        param_confs = xml_tree.find( 'params' )
+        for param_conf in param_confs.findall( 'param' ):
+            param = self.param_parser.parse( param_conf )
+            if param:
+                params[ param_conf.text ]= param
+        # params are not required
+        if params:
+            returned[ 'params' ] = params
+
+        # param modifiers provide extra information for other params (e.g. hda_ldda='hda' -> dataset_id is an hda id)
+        # store these modifiers in a 2-level dictionary { target_param: { param_modifier_key: { param_mod_data }
+        # ugh - wish we didn't need these
+        param_modifiers = {}
+        for param_modifier_conf in param_confs.findall( 'param_modifier' ):
+            param_modifier = self.param_modifier_parser.parse( param_modifier_conf )
+            # param modifiers map accrd. to the params they modify (for faster lookup)
+            target_param = param_modifier_conf.get( 'modifies' )
+            param_modifier_key = param_modifier_conf.text
+            if param_modifier and target_param in params:
+                # multiple params can modify a single, other param,
+                #   so store in a sub-dict, initializing if this is the first
+                if target_param not in param_modifiers:
+                    param_modifiers[ target_param ] = {}
+                param_modifiers[ target_param ][ param_modifier_key ] = param_modifier
+
+        # not required
+        if param_modifiers:
+            returned[ 'param_modifiers' ] = param_modifiers
+
+        # the template to use in rendering the visualization (required)
+        template = xml_tree.find( 'template' )
+        if template == None or not template.text:
+            raise ParsingException( 'template filename required' )
+        returned[ 'template' ] = template.text
+
+        # link_text: the string to use for the text of any links/anchors to this visualization
+        link_text = xml_tree.find( 'link_text' )
+        if link_text != None and link_text.text:
+            returned[ 'link_text' ] = link_text
+
+        # render_location: where in the browser to open the rendered visualization
+        # defaults to: galaxy_main
+        render_location = xml_tree.find( 'render_location' )
+        if( ( render_location != None and render_location.text )
+        and ( render_location.text in self.VALID_RENDER_LOCATIONS ) ):
+            returned[ 'render_location' ] = render_location.text
+        else:
+            returned[ 'render_location' ] = 'galaxy_main'
+        # consider unifying the above into it's own element and parsing method
+
+        return returned
+
+
+# ------------------------------------------------------------------- parsing a query string into resources
+class DataSourceParser( object ):
+    """
+    Component class of VisualizationsConfigParser that parses data_source elements
+    within visualization elements.
+
+    data_sources are (in the extreme) any object that can be used to produce
+    data for the visualization to consume (e.g. HDAs, LDDAs, Jobs, Users, etc.).
+    There can be more than one data_source associated with a visualization.
+    """
+    # these are the allowed classes to associate visualizations with (as strings)
+    #   any model_class element not in this list will throw a parsing ParsingExcepion
+    ALLOWED_MODEL_CLASSES = [
+        'HistoryDatasetAssociation',
+        'LibraryDatasetDatasetAssociation'
+    ]
+    ATTRIBUTE_SPLIT_CHAR = '.'
+    # these are the allowed object attributes to use in data source tests
+    #   any attribute element not in this list will throw a parsing ParsingExcepion
+    ALLOWED_DATA_SOURCE_ATTRIBUTES = [
+        'datatype'
+    ]
+
+    def parse( self, xml_tree ):
+        """
+        Return a visualization data_source dictionary parsed from the given
+        XML element.
+        """
+        returned = {}
+        # model_class (required, only one) - look up and convert model_class to actual galaxy model class
+        model_class = self.parse_model_class( xml_tree.find( 'model_class' ) )
+        if not model_class:
+            raise ParsingException( 'data_source needs a model class' )
+        returned[ 'model_class' ] = model_class
+
+        # tests (optional, 0 or more) - data for boolean test: 'is the visualization usable by this object?'
+        tests = self.parse_tests( xml_tree.findall( 'test' ) )
+        # when no tests are given, default to isinstance( object, model_class )
+        if tests:
+            returned[ 'tests' ] = tests
+
+        # to_params (optional, 0 or more) - tells the registry to set certain params based on the model_clas, tests
+        to_params = self.parse_to_params( xml_tree.findall( 'to_param' ) )
+        if to_params:
+            returned[ 'to_params' ] = to_params
+
+        return returned
+
+    def parse_model_class( self, xml_tree ):
+        """
+        Convert xml model_class element to a galaxy model class
+        (or None if model class is not found).
+
+        This element is required and only the first element is used.
+        The model_class string must be in ALLOWED_MODEL_CLASSES.
+        """
+        if xml_tree is None or not xml_tree.text:
+            raise ParsingException( 'data_source entry requires a model_class' )
+
+        if xml_tree.text not in self.ALLOWED_MODEL_CLASSES:
+            log.debug( 'available data_source model_classes: %s' %( str( self.ALLOWED_MODEL_CLASSES ) ) )
+            raise ParsingException( 'Invalid data_source model_class: %s' %( xml_tree.text ) )
+
+        # look up the model from the model module returning an empty data_source if not found
+        model_class = getattr( galaxy.model, xml_tree.text, None )
+        return model_class
+
+    def _build_getattr_lambda( self, attr_name_list ):
+        """
+        Recursively builds a compound lambda function of getattr's
+        from the attribute names given in `attr_name_list`.
+        """
+        if len( attr_name_list ) == 0:
+            # identity - if list is empty, return object itself
+            return lambda o: o
+
+        next_attr_name = attr_name_list[-1]
+        if len( attr_name_list ) == 1:
+            # recursive base case
+            return lambda o: getattr( o, next_attr_name )
+
+        # recursive case
+        return lambda o: getattr( self._build_getattr_lambda( attr_name_list[:-1] ), next_attr_name )
+
+    def parse_tests( self, xml_tree_list ):
+        """
+        Returns a list of test dictionaries that the registry can use
+        against a given object to determine if the visualization can be
+        used with the object.
+        """
+        # tests should NOT include expensive operations: reading file data, running jobs, etc.
+        # do as much here as possible to reduce the overhead of seeing if a visualization is applicable
+        # currently tests are or'd only (could be and'd or made into compound boolean tests)
+        tests = []
+        if not xml_tree_list:
+            return tests
+
+        for test_elem in xml_tree_list:
+            test_type = test_elem.get( 'type' )
+            test_result = test_elem.text
+            if not test_type or not test_result:
+                log.warn( 'Skipping test. Needs both type attribute and text node to be parsed: '
+                        + '%s, %s' %( test_type, test_elem.text ) )
+                continue
+
+            # test_attr can be a dot separated chain of object attributes (e.g. dataset.datatype) - convert to list
+            #TODO: too dangerous - constrain these to some allowed list
+            test_attr = test_elem.get( 'test_attr' )
+            test_attr = test_attr.split( self.ATTRIBUTE_SPLIT_CHAR ) if isinstance( test_attr, str ) else []
+            # build a lambda function that gets the desired attribute to test
+            getter = self._build_getattr_lambda( test_attr )
+
+            # result type should tell the registry how to convert the result before the test
+            test_result_type = test_elem.get( 'result_type' ) or 'string'
+
+            # test functions should be sent an object to test, and the parsed result expected from the test
+            #TODO: currently, isinstance and string equivalance are the only test types supported
+            if test_type == 'isinstance':
+                #TODO: wish we could take this further but it would mean passing in the datatypes_registry
+                test_fn = lambda o, result: isinstance( getter( o ), result )
+
+            # default to simple (string) equilavance (coercing the test_attr to a string)
+            else:
+                test_fn = lambda o, result: str( getter( o ) ) == result
+
+            tests.append({
+                'type'          : test_type,
+                'result'        : test_result,
+                'result_type'   : test_result_type,
+                'fn'            : test_fn
+            })
+
+        return tests
+
+    def parse_to_params( self, xml_tree_list ):
+        """
+        Given a list of `to_param` elements, returns a dictionary that allows
+        the registry to convert the data_source into one or more appropriate
+        params for the visualization.
+        """
+        to_param_dict = {}
+        if not xml_tree_list:
+            return to_param_dict
+
+        for element in xml_tree_list:
+            # param_name required
+            param_name = element.text
+            if not param_name:
+                raise ParsingException( 'to_param requires text (the param name)' )
+
+            param = {}
+            # assign is a shortcut param_attr that assigns a value to a param (as text)
+            assign = element.get( 'assign' )
+            if assign != None:
+                param[ 'assign' ] = assign
+
+            # param_attr is the attribute of the object (that the visualization will be applied to)
+            #   that should be converted into a query param (e.g. param_attr="id" -> dataset_id)
+            #TODO:?? use the build attr getter here?
+            # simple (1 lvl) attrs for now
+            param_attr = element.get( 'param_attr' )
+            if param_attr != None:
+                param[ 'param_attr' ] = param_attr
+            # element must have either param_attr or assign? what about no params (the object itself)
+            if not param_attr and not assign:
+                raise ParsingException( 'to_param requires either assign or param_attr attributes: %s', param_name )
+
+            #TODO: consider making the to_param name an attribute (param="hda_ldda") and the text what would
+            #           be used for the conversion - this would allow CDATA values to be passed
+            #<to_param param="json" type="assign"><![CDATA[{ "one": 1, "two": 2 }]]></to_param>
+
+            if param:
+                to_param_dict[ param_name ] = param
+
+        return to_param_dict
+
+
+class ParamParser( object ):
+    """
+    Component class of VisualizationsConfigParser that parses param elements
+    within visualization elements.
+
+    params are parameters that will be parsed (based on their `type`, etc.)
+    and sent to the visualization template by controllers.visualization.render.
+    """
+    DEFAULT_PARAM_TYPE = 'str'
+
+    def parse( self, xml_tree ):
+        """
+        Parse a visualization parameter from the given `xml_tree`.
+        """
+        returned = {}
+
+        # don't store key, just check it
+        param_key = xml_tree.text
+        if not param_key:
+            raise ParsingException( 'Param entry requires text' )
+
+        returned[ 'type' ] = self.parse_param_type( xml_tree )
+
+        # is the parameter required in the template and,
+        #   if not, what is the default value?
+        required = xml_tree.get( 'required' ) == "true"
+        returned[ 'required' ] = required
+        if not required:
+            # default defaults to None
+            default = None
+            if 'default' in xml_tree.attrib:
+                default = xml_tree.get( 'default' )
+                # convert default based on param_type here
+            returned[ 'default' ] = default
+
+        # does the param have to be within a list of certain values
+        # NOTE: the interpretation of this list is deferred till parsing and based on param type
+        #   e.g. it could be 'val in constrain_to', or 'constrain_to is min, max for number', etc.
+        #TODO: currently unused
+        constrain_to = xml_tree.get( 'constrain_to' )
+        if constrain_to:
+            returned[ 'constrain_to' ] = constrain_to.split( ',' )
+
+        # is the param a comma-separated-value list?
+        returned[ 'csv' ] = xml_tree.get( 'csv' ) == "true"
+
+        # remap keys in the params/query string to the var names used in the template
+        var_name_in_template = xml_tree.get( 'var_name_in_template' )
+        if var_name_in_template:
+            returned[ 'var_name_in_template' ] = var_name_in_template
+
+        return returned
+
+    def parse_param_type( self, xml_tree ):
+        """
+        Parse a param type from the given `xml_tree`.
+        """
+        # default to string as param_type
+        param_type = xml_tree.get( 'type' ) or self.DEFAULT_PARAM_TYPE
+        #TODO: set parsers and validaters, convert here
+        return param_type
+
+
+class ParamModifierParser( ParamParser ):
+    """
+    Component class of VisualizationsConfigParser that parses param_modifier
+    elements within visualization elements.
+
+    param_modifiers are params from a dictionary (such as a query string)
+    that are not standalone but modify the parsing/conversion of a separate
+    (normal) param (e.g. 'hda_ldda' can equal 'hda' or 'ldda' and control
+    whether a visualizations 'dataset_id' param is for an HDA or LDDA).
+    """
+    def parse( self, element ):
+        # modifies is required
+        modifies = element.get( 'modifies' )
+        if not modifies:
+            raise ParsingException( 'param_modifier entry requires a target param key (attribute "modifies")' )
+        returned = super( ParamModifierParser, self).parse( element )
+        return returned
+
+
+class ResourceParser( object ):
+    """
+    Given a parameter dictionary (often a converted query string) and a
+    configuration dictionary (curr. only VisualizationsRegistry uses this),
+    convert the entries in the parameter dictionary into resources (Galaxy
+    models, primitive types, lists of either, etc.) and return
+    in a new dictionary.
+
+    The keys used to store the new values can optionally be re-mapped to
+    new keys (e.g. dataset_id="NNN" -> hda=<HistoryDatasetAsscoation>).
+    """
+    #TODO: kinda torn as to whether this belongs here or in controllers.visualization
+    #   taking the (questionable) design path of passing a controller in
+    #       (which is the responsible party for getting model, etc. resources )
+    # consider making this a base controller? use get_object for the model resources
+    #   don't like passing in the app, tho
+    def parse_parameter_dictionary( self, trans, controller, param_config_dict, query_params, param_modifiers=None ):
+        """
+        Parse all expected params from the query dictionary `query_params`.
+
+        If param is required and not present, raises a `KeyError`.
+        """
+        # parse the modifiers first since they modify the params coming next
+        #TODO: this is all really for hda_ldda - which we could replace with model polymorphism
+        params_that_modify_other_params = self.parse_parameter_modifiers(
+            trans, controller, param_modifiers, query_params )
+
+        resources = {}
+        for param_name, param_config in param_config_dict.items():
+            # optionally rename the variable returned, defaulting to the original name
+            var_name_in_template = param_config.get( 'var_name_in_template', param_name )
+
+            # if the param is present, get it's value, any param modifiers for that param, and parse it into a resource
+            # use try catch here and not caller to fall back on the default value or re-raise if required
+            resource = None
+            query_val = query_params.get( param_name, None )
+            if query_val is not None:
+                try:
+                    target_param_modifiers = params_that_modify_other_params.get( param_name, None )
+                    resource = self.parse_parameter( trans, controller, param_config,
+                        query_val, param_modifiers=target_param_modifiers )
+
+                except Exception, exception:
+                    log.warn( 'Exception parsing visualization param from query: '
+                            + '%s, %s, (%s) %s' %( param_name, query_val, str( type( exception ) ), str( exception ) ))
+                    resource = None
+
+            # here - we've either had no value in the query_params or there was a failure to parse
+            #   so: error if required, otherwise get a default (which itself defaults to None)
+            if resource == None:
+                if param_config[ 'required' ]:
+                    raise KeyError( 'required param %s not found in URL' %( param_name ) )
+                resource = self.parse_parameter_default( trans, param_config )
+
+            resources[ var_name_in_template ] = resource
+
+        return resources
+
+    #TODO: I would LOVE to rip modifiers out completely
+    def parse_parameter_modifiers( self, trans, controller, param_modifiers, query_params ):
+        """
+        Parse and return parameters that are meant to modify other parameters,
+        be grouped with them, or are needed to successfully parse other parameters.
+        """
+        # only one level of modification - down that road lies madness
+        # parse the modifiers out of query_params first since they modify the other params coming next
+        parsed_modifiers = {}
+        if not param_modifiers:
+            return parsed_modifiers
+        #precondition: expects a two level dictionary
+        # { target_param_name -> { param_modifier_name -> { param_modifier_data }}}
+        for target_param_name, modifier_dict in param_modifiers.items():
+            parsed_modifiers[ target_param_name ] = target_modifiers = {}
+
+            for modifier_name, modifier_config in modifier_dict.items():
+                query_val = query_params.get( modifier_name, None )
+                if query_val is not None:
+                    modifier = self.parse_parameter( trans, controller, modifier_config, query_val )
+                    target_modifiers[ modifier_name ] = modifier
+                else:
+                    #TODO: required attr?
+                    target_modifiers[ modifier_name ] = self.parse_parameter_default( trans, modifier_config )
+
+        return parsed_modifiers
+
+    def parse_parameter_default( self, trans, param_config ):
+        """
+        Parse any default values for the given param, defaulting the default
+        to `None`.
+        """
+        # currently, *default* default is None, so this is quaranteed to be part of the dictionary
+        default = param_config[ 'default' ]
+        # if default is None, do not attempt to parse it
+        if default == None:
+            return default
+        # otherwise, parse (currently param_config['default'] is a string just like query param and needs to be parsed)
+        #   this saves us the trouble of parsing the default when the config file is read
+        #   (and adding this code to the xml parser)
+        return self.parse_parameter( trans, param_config, default )
+
+    def parse_parameter( self, trans, controller, expected_param_data, query_param,
+                         recurse=True, param_modifiers=None ):
+        """
+        Use data in `expected_param_data` to parse `query_param` from a string into
+        a resource usable directly by a template.
+
+        'Primitive' types (string, int, etc.) are parsed here and more complex
+        resources (such as ORM models) are parsed via the `controller` passed
+        in.
+        """
+        param_type = expected_param_data.get( 'type' )
+        constrain_to = expected_param_data.get( 'constrain_to' )
+        csv = expected_param_data.get( 'csv' )
+
+        parsed_param = None
+
+        # handle recursion for csv values
+        if csv and recurse:
+            parsed_param = []
+            query_param_list = galaxy.util.listify( query_param )
+            for query_param in query_param_list:
+                parsed_param.append( self._parse_param( trans, expected_param_data, query_param, recurse=False ) )
+            return parsed_param
+
+        primitive_parsers = {
+            'str'   : lambda param: galaxy.util.sanitize_html.sanitize_html( param, 'utf-8' ),
+            'bool'  : lambda param: galaxy.util.string_as_bool( param ),
+            'int'   : lambda param: int( param ),
+            'float' : lambda param: float( param ),
+            #'date'  : lambda param: ,
+            'json'  : ( lambda param: galaxy.util.json.from_json_string(
+                            galaxy.util.sanitize_html.sanitize_html( param ) ) ),
+        }
+        parser = primitive_parsers.get( param_type, None )
+        if parser:
+            #TODO: what about param modifiers on primitives?
+            parsed_param = parser( query_param )
+
+        #TODO: constrain_to
+        # this gets complicated - for strings - relatively simple but still requires splitting and using in
+        # for more complicated cases (ints, json) this gets weird quick
+        #TODO:?? remove?
+
+        # db models
+        #TODO: subclass here?
+        elif param_type == 'visualization':
+            encoded_visualization_id = query_param
+            #TODO:?? some fallback if there's no get_X in controller that's passed?
+            parsed_param = controller.get_visualization( trans, encoded_visualization_id,
+                check_ownership=False, check_accessible=True )
+
+        elif param_type == 'dataset':
+            encoded_dataset_id = query_param
+            # really an hda...
+            parsed_param = controller.get_dataset( trans, encoded_dataset_id,
+                check_ownership=False, check_accessible=True )
+
+        elif param_type == 'hda_or_ldda':
+            encoded_dataset_id = query_param
+            # needs info from another param...
+            hda_ldda = param_modifiers.get( 'hda_ldda' )
+            parsed_param = controller.get_hda_or_ldda( trans, hda_ldda, encoded_dataset_id )
+
+        #TODO: ideally this would check v. a list of valid dbkeys
+        elif param_type == 'dbkey':
+            dbkey = query_param
+            parsed_param = galaxy.util.sanitize_html.sanitize_html( dbkey, 'utf-8' )
+
+        #print ( '%s, %s -> %s, %s' %( param_type, query_param, str( type( parsed_param ) ), parsed_param ) )
+        return parsed_param

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -14,7 +14,7 @@
 from sqlalchemy import func, and_, select
 from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError, HTTPNotImplemented, HTTPRequestRangeNotSatisfiable
 
-from galaxy import util, web
+from galaxy import util, web, model
 from gettext import gettext
 from galaxy.datatypes.interval import ChromatinInteractions
 from galaxy.exceptions import ItemAccessibilityException, ItemDeletionException, ItemOwnershipException, MessageException
@@ -28,7 +28,6 @@
 from galaxy.model.orm import eagerload, eagerload_all
 from galaxy.datatypes.data import Text
 
-
 from galaxy.datatypes.display_applications import util as da_util
 from galaxy.datatypes.metadata import FileParameter
 
@@ -486,6 +485,25 @@
                     error( "Please wait until this dataset finishes uploading before attempting to view it." )
         return hda
 
+    def get_hda_list( self, trans, hda_ids, check_ownership=True, check_accessible=False, check_state=True ):
+        """
+        Returns one or more datasets in a list.
+
+        If a dataset is not found or is inaccessible to trans.user,
+        add None in its place in the list.
+        """
+        # precondtion: dataset_ids is a list of encoded id strings
+        hdas = []
+        for id in hda_ids:
+            hda = None
+            try:
+                hda = self.get_dataset( trans, id,
+                    check_ownership=check_ownership, check_accesible=check_accesible, check_state=check_state )
+            except Exception, exception:
+                pass
+            hdas.append( hda )
+        return hdas
+
     def get_data( self, dataset, preview=True ):
         """
         Gets a dataset's data.
@@ -552,9 +570,13 @@
         if meta_files:
             hda_dict[ 'meta_files' ] = meta_files
 
-        #hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda )
-        #hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda )
-        hda_dict[ 'visualizations' ] = hda.get_visualizations()
+        # currently, the viz reg is optional - handle on/off
+        if trans.app.visualizations_registry:
+            hda_dict[ 'visualizations' ] = trans.app.visualizations_registry.get_visualizations( trans, hda )
+        else:
+            hda_dict[ 'visualizations' ] = hda.get_visualizations()
+        #TODO: it may also be wiser to remove from here and add as API call that loads the visualizations
+        #           when the visualizations button is clicked (instead of preloading/pre-checking)
 
         # ---- return here if deleted
         if hda.deleted and not purged:
@@ -662,18 +684,187 @@
         return self.get_object( trans, id, 'LibraryDataset', check_ownership=False, check_accessible=check_accessible )
 
 
-class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin,
-                              UsesLibraryMixinItems ):
-    """ Mixin for controllers that use Visualization objects. """
+class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems ):
+    """
+    Mixin for controllers that use Visualization objects.
+    """
 
+    DEFAULT_ORDER_BY = [ model.Visualization.title ]
     viz_types = [ "trackster" ]
 
-    def create_visualization( self, trans, type, title="Untitled Genome Vis", slug=None, dbkey=None, annotation=None, config={}, save=True ):
-        """ Create visualiation and first revision. """
+    def get_visualization( self, trans, id, check_ownership=True, check_accessible=False ):
+        """
+        Get a Visualization from the database by id, verifying ownership.
+        """
+        # Load workflow from database
+        try:
+            visualization = trans.sa_session.query( trans.model.Visualization ).get( trans.security.decode_id( id ) )
+        except TypeError:
+            visualization = None
+        if not visualization:
+            error( "Visualization not found" )
+        else:
+            return self.security_check( trans, visualization, check_ownership, check_accessible )
+
+    def get_visualizations_by_user( self, trans, user, order_by=None, query_only=False ):
+        """
+        Return query or query results of visualizations filtered by a user.
+
+        Set `order_by` to a column or list of columns to change the order
+        returned. Defaults to `DEFAULT_ORDER_BY`.
+        Set `query_only` to return just the query for further filtering or
+        processing.
+        """
+        if not order_by:
+            order_by = self.DEFAULT_ORDER_BY
+        if not isinstance( order_by, list ):
+            order_by = [ order_by ]
+        query = trans.sa_session.query( model.Visualization )
+        query = query.filter( model.Visualization.user == user )
+        if order_by:
+            query = query.order_by( *order_by )
+        if query_only:
+            return query
+        return query.all()
+
+    def get_visualizations_shared_with_user( self, trans, user, order_by=None, query_only=False ):
+        """
+        Return query or query results for visualizations shared with the given user.
+
+        Set `order_by` to a column or list of columns to change the order
+        returned. Defaults to `DEFAULT_ORDER_BY`.
+        Set `query_only` to return just the query for further filtering or
+        processing.
+        """
+        if not order_by:
+            order_by = self.DEFAULT_ORDER_BY
+        if not isinstance( order_by, list ):
+            order_by = [ order_by ]
+        query = trans.sa_session.query( model.Visualization ).join( model.VisualizationUserShareAssociation )
+        query = query.filter( model.VisualizationUserShareAssociation.user_id == user.id )
+        # remove duplicates when a user shares with themselves?
+        query = query.filter( model.Visualization.user_id != user.id )
+        if order_by:
+            query = query.order_by( *order_by )
+        if query_only:
+            return query
+        return query.all()
+
+    def get_published_visualizations( self, trans, exclude_user=None, order_by=None, query_only=False ):
+        """
+        Return query or query results for published visualizations optionally excluding
+        the user in `exclude_user`.
+
+        Set `order_by` to a column or list of columns to change the order
+        returned. Defaults to `DEFAULT_ORDER_BY`.
+        Set `query_only` to return just the query for further filtering or
+        processing.
+        """
+        if not order_by:
+            order_by = self.DEFAULT_ORDER_BY
+        if not isinstance( order_by, list ):
+            order_by = [ order_by ]
+        query = trans.sa_session.query( model.Visualization )
+        query = query.filter( model.Visualization.published == True )
+        if exclude_user:
+            query = query.filter( model.Visualization.user != exclude_user )
+        if order_by:
+            query = query.order_by( *order_by )
+        if query_only:
+            return query
+        return query.all()
+
+    #TODO: move into model (get_api_value)
+    def get_visualization_summary_dict( self, visualization ):
+        """
+        Return a set of summary attributes for a visualization in dictionary form.
+        NOTE: that encoding ids isn't done here should happen at the caller level.
+        """
+        #TODO: deleted
+        #TODO: importable
+        return {
+            'id'        : visualization.id,
+            'title'     : visualization.title,
+            'type'      : visualization.type,
+            'dbkey'     : visualization.dbkey,
+        }
+
+    def get_visualization_dict( self, visualization ):
+        """
+        Return a set of detailed attributes for a visualization in dictionary form.
+        The visualization's latest_revision is returned in its own sub-dictionary.
+        NOTE: that encoding ids isn't done here should happen at the caller level.
+        """
+        return {
+            'model_class': 'Visualization',
+            'id'        : visualization.id,
+            'title'     : visualization.title,
+            'type'      : visualization.type,
+            'user_id'   : visualization.user.id,
+            'dbkey'     : visualization.dbkey,
+            'slug'      : visualization.slug,
+            # dictify only the latest revision (allow older to be fetched elsewhere)
+            'latest_revision' : self.get_visualization_revision_dict( visualization.latest_revision ),
+            'revisions' : [ r.id for r in visualization.revisions ],
+        }
+
+    def get_visualization_revision_dict( self, revision ):
+        """
+        Return a set of detailed attributes for a visualization in dictionary form.
+        NOTE: that encoding ids isn't done here should happen at the caller level.
+        """
+        return {
+            'model_class': 'VisualizationRevision',
+            'id'        : revision.id,
+            'visualization_id' : revision.visualization.id,
+            'title'     : revision.title,
+            'dbkey'     : revision.dbkey,
+            'config'    : revision.config,
+        }
+
+    def import_visualization( self, trans, id, user=None ):
+        """
+        Copy the visualization with the given id and associate the copy
+        with the given user (defaults to trans.user).
+
+        Raises `ItemAccessibilityException` if `user` is not passed and
+        the current user is anonymous, and if the visualization is not `importable`.
+        Raises `ItemDeletionException` if the visualization has been deleted.
+        """
+        # default to trans.user, error if anon
+        if not user:
+            if not trans.user:
+                raise ItemAccessibilityException( "You must be logged in to import Galaxy visualizations" )
+            user = trans.user
+
+        # check accessibility
+        visualization = self.get_visualization( trans, id, check_ownership=False )
+        if not visualization.importable:
+            raise ItemAccessibilityException( "The owner of this visualization has disabled imports via this link." )
+        if visualization.deleted:
+            raise ItemDeletionException( "You can't import this visualization because it has been deleted." )
+
+        # copy vis and alter title
+        #TODO: need to handle custom db keys.
+        imported_visualization = visualization.copy( user=user, title="imported: " + visualization.title )
+        trans.sa_session.add( imported_visualization )
+        trans.sa_session.flush()
+        return imported_visualization
+
+    def create_visualization( self, trans, type, title="Untitled Genome Vis", slug=None,
+                              dbkey=None, annotation=None, config={}, save=True ):
+        """
+        Create visualiation and first revision.
+        """
         visualization = self._create_visualization( trans, title, type, dbkey, slug, annotation, save )
+        #TODO: handle this error structure better either in _create or here
+        if isinstance( visualization, dict ):
+            err_dict = visualization
+            raise ValueError( err_dict[ 'title_err' ] or err_dict[ 'slug_err' ] )
 
         # Create and save first visualization revision
-        revision = trans.model.VisualizationRevision( visualization=visualization, title=title, config=config, dbkey=dbkey )
+        revision = trans.model.VisualizationRevision( visualization=visualization, title=title,
+                                                      config=config, dbkey=dbkey )
         visualization.latest_revision = revision
 
         if save:
@@ -683,6 +874,21 @@
 
         return visualization
 
+    def add_visualization_revision( self, trans, visualization, config, title, dbkey ):
+        """
+        Adds a new `VisualizationRevision` to the given `visualization` with
+        the given parameters and set its parent visualization's `latest_revision`
+        to the new revision.
+        """
+        #precondition: only add new revision on owned vis's
+        #TODO:?? should we default title, dbkey, config? to which: visualization or latest_revision?
+        revision = trans.model.VisualizationRevision( visualization, title, dbkey, config )
+        visualization.latest_revision = revision
+        #TODO:?? does this automatically add revision to visualzation.revisions?
+        trans.sa_session.add( revision )
+        trans.sa_session.flush()
+        return revision
+
     def save_visualization( self, trans, config, type, id=None, title=None, dbkey=None, slug=None, annotation=None ):
         session = trans.sa_session
 
@@ -697,8 +903,10 @@
         # Create new VisualizationRevision that will be attached to the viz
         vis_rev = trans.model.VisualizationRevision()
         vis_rev.visualization = vis
-        vis_rev.title = vis.title
-        vis_rev.dbkey = dbkey
+        # do NOT alter the dbkey
+        vis_rev.dbkey = vis.dbkey
+        # do alter the title and config
+        vis_rev.title = title
 
         # -- Validate config. --
 
@@ -760,18 +968,6 @@
         encoded_id = trans.security.encode_id( vis.id )
         return { "vis_id": encoded_id, "url": url_for( controller='visualization', action=vis.type, id=encoded_id ) }
 
-    def get_visualization( self, trans, id, check_ownership=True, check_accessible=False ):
-        """ Get a Visualization from the database by id, verifying ownership. """
-        # Load workflow from database
-        try:
-            visualization = trans.sa_session.query( trans.model.Visualization ).get( trans.security.decode_id( id ) )
-        except TypeError:
-            visualization = None
-        if not visualization:
-            error( "Visualization not found" )
-        else:
-            return self.security_check( trans, visualization, check_ownership, check_accessible )
-
     def get_visualization_config( self, trans, visualization ):
         """ Returns a visualization's configuration. Only works for trackster visualizations right now. """
         config = None
@@ -911,7 +1107,6 @@
         if title_err or slug_err:
             return { 'title_err': title_err, 'slug_err': slug_err }
 
-
         # Create visualization
         visualization = trans.model.Visualization( user=user, title=title, dbkey=dbkey, type=type )
         if slug:
@@ -920,6 +1115,8 @@
             self.create_item_slug( trans.sa_session, visualization )
         if annotation:
             annotation = sanitize_html( annotation, 'utf-8', 'text/html' )
+            #TODO: if this is to stay in the mixin, UsesAnnotations should be added to the superclasses
+            #   right now this is depending on the classes that include this mixin to have UsesAnnotations
             self.add_item_annotation( trans.sa_session, trans.user, visualization, annotation )
 
         if save:

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -51,17 +51,20 @@
     webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None )
     webapp.add_route( '/:controller/:action', action='index' )
     webapp.add_route( '/:action', controller='root', action='index' )
+    
     # allow for subdirectories in extra_files_path
     webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None)
     webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None)
-    webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', controller='dataset', action='display_application', dataset_id=None, user_id=None, app_name = None, link_name = None, app_action = None, action_param = None )
+    webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param',
+        controller='dataset', action='display_application', dataset_id=None, user_id=None,
+        app_name = None, link_name = None, app_action = None, action_param = None )
     webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None )
     webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' )
     webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' )
     webapp.add_route( '/u/:username/w/:slug', controller='workflow', action='display_by_username_and_slug' )
     webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' )
     webapp.add_route( '/search', controller='search', action='index' )
-    
+
     # Add the web API
     webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app )
     # The /folders section is experimental at this point:
@@ -144,6 +147,10 @@
     #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) )
     webapp.mapper.resource( 'search', 'search', path_prefix='/api' )    
 
+    # visualizations registry generic template renderer
+    webapp.add_route( '/visualization/show/:visualization_name',
+        controller='visualization', action='render', visualization_name=None )
+
     # "POST /api/workflows/import"  =>  ``workflows.import_workflow()``.
     # Defines a named route "import_workflow".
     webapp.mapper.connect("import_workflow", "/api/workflows/upload", controller="workflows", action="import_new_workflow", conditions=dict(method=["POST"]))

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d lib/galaxy/webapps/galaxy/controllers/visualization.py
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -1,6 +1,10 @@
 from __future__ import absolute_import
 
+import os
+
 from sqlalchemy import desc, or_, and_
+from paste.httpexceptions import HTTPNotFound
+
 from galaxy import model, web
 from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
 from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin
@@ -16,6 +20,9 @@
 
 from .library import LibraryListGrid
 
+import logging
+log = logging.getLogger( __name__ )
+
 #
 # -- Grids --
 #
@@ -689,6 +696,54 @@
                                     default_dbkey=kwargs.get("default_dbkey", None) )
         
     @web.expose
+    @web.require_login( "use Galaxy visualizations", use_panels=True )
+    def render( self, trans, visualization_name, embedded=None, **kwargs ):
+        """
+        Render the appropriate visualization template, parsing the `kwargs`
+        into appropriate variables and resources (such as ORM models)
+        based on this visualizations `param` data in visualizations_conf.xml.
+
+        URL: /visualization/show/{visualization_name}
+        """
+        # validate name vs. registry
+        registry = trans.app.visualizations_registry
+        if not registry:
+            raise HTTPNotFound( 'No visualization registry (possibly disabled in universe_wsgi.ini)')
+        if visualization_name not in registry.listings:
+            raise HTTPNotFound( 'Unknown or invalid visualization: ' + visualization_name )
+            # or redirect to list?
+        registry_listing = registry.listings[ visualization_name ]
+
+        returned = None
+        try:
+            # convert query string to resources for template based on registry config
+            #NOTE: passing in controller to keep resource lookup within the controller's responsibilities
+            #   (and not the ResourceParser)
+            resources = registry.query_dict_to_resources( trans, self, visualization_name, kwargs )
+
+            # look up template and render
+            template_root = registry_listing.get( 'template_root', registry.TEMPLATE_ROOT )
+            template = registry_listing[ 'template' ]
+            template_path = os.path.join( template_root, template )
+            #NOTE: passing *unparsed* kwargs as query_args
+            #NOTE: shared_vars is a dictionary for shared data in the template
+            #   this feels hacky to me but it's what mako recommends:
+            #   http://docs.makotemplates.org/en/latest/runtime.html
+            #TODO: embedded
+            returned = trans.fill_template( template_path, visualization_name=visualization_name,
+                embedded=embedded, query_args=kwargs, shared_vars={}, **resources )
+
+        except Exception, exception:
+            log.exception( 'error rendering visualization (%s): %s', visualization_name, str( exception ) )
+            if trans.debug: raise
+            returned = trans.show_error_message(
+                "There was an error rendering the visualization. " +
+                "Contact your Galaxy administrator if the problem persists." +
+                "<br/>Details: " + str( exception ), use_panels=False )
+
+        return returned
+
+    @web.expose
     @web.require_login()
     def trackster(self, trans, id=None, **kwargs):
         """
@@ -792,6 +847,8 @@
         get the visualization with the given id; otherwise, create a new visualization using
         a given dataset and regions.
         """
+        print 'sweepster:', id, hda_ldda, dataset_id, regions
+        regions = regions or '{}'
         # Need to create history if necessary in order to create tool form.
         trans.get_history( create=True )
 
@@ -803,6 +860,7 @@
         else:
             # Loading new visualization.
             dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id )
+            print 'dataset:', dataset
             job = get_dataset_job( dataset )
             viz_config = {
                 'dataset_id': dataset_id,

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d static/scripts/mvc/dataset/hda-edit.js
--- a/static/scripts/mvc/dataset/hda-edit.js
+++ b/static/scripts/mvc/dataset/hda-edit.js
@@ -239,8 +239,25 @@
      *  @returns {jQuery} rendered DOM
      */
     _render_visualizationsButton : function(){
+        var visualizations = this.model.get( 'visualizations' );
+        if( ( !this.model.hasData() )
+        ||  ( _.isEmpty( visualizations ) ) ){
+            this.visualizationsButton = null;
+            return null;
+        }
+
+        //TODO: this is a bridge to allow the framework to be switched off
+        // remove this fn and use the other when fully integrated
+        if( _.isObject( visualizations[0] ) ){
+            return this._render_visualizationsFrameworkButton( visualizations );
+        }
+
+        if( !this.urls.visualization ){
+            this.visualizationsButton = null;
+            return null;
+        }
+
         var dbkey = this.model.get( 'dbkey' ),
-            visualizations = this.model.get( 'visualizations' ),
             visualization_url = this.urls.visualization,
             popup_menu_dict = {},
             params = {
@@ -250,17 +267,10 @@
         // Add dbkey to params if it exists.
         if( dbkey ){ params.dbkey = dbkey; }
 
-        if( !( this.model.hasData() )
-        ||  !( visualizations && visualizations.length )
-        ||  !( visualization_url ) ){
-            this.visualizationsButton = null;
-            return null;
-        }
-        
         // render the icon from template
         this.visualizationsButton = new IconButtonView({ model : new IconButton({
             title       : _l( 'Visualize' ),
-            href        : visualization_url,
+            href        : this.urls.visualization,
             icon_class  : 'chart_curve'
         })});
         var $icon = this.visualizationsButton.render().$el;
@@ -299,6 +309,40 @@
         }
         return $icon;
     },
+
+    /** Render an icon-button or popupmenu of links based on the applicable visualizations
+     *  @returns {jQuery} rendered DOM
+     */
+    _render_visualizationsFrameworkButton : function( visualizations ){
+        if( !( this.model.hasData() )
+        ||  !( visualizations && !_.isEmpty( visualizations ) ) ){
+            this.visualizationsButton = null;
+            return null;
+        }
+
+        // render the icon from template
+        this.visualizationsButton = new IconButtonView({ model : new IconButton({
+            title       : _l( 'Visualize' ),
+            icon_class  : 'chart_curve'
+        })});
+        var $icon = this.visualizationsButton.render().$el;
+        $icon.addClass( 'visualize-icon' ); // needed?
+
+        // No need for popup menu because there's a single visualization.
+        if( _.keys( visualizations ).length === 1 ) {
+            $icon.attr( 'title', _.keys( visualizations )[0] );
+            $icon.attr( 'href', _.values( visualizations )[0] );
+
+        // >1: Populate menu dict with visualization fns, make the popupmenu
+        } else {
+            var popup_menu_options = [];
+            _.each( visualizations, function( linkData ) {
+                popup_menu_options.push( linkData );
+            });
+            var popup = new PopupMenu( $icon, popup_menu_options );
+        }
+        return $icon;
+    },
     
     // ......................................................................... secondary actions
     /** Render secondary actions: currently tagging and annotation (if user is allowed).

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d static/scripts/packed/mvc/dataset/hda-edit.js
--- a/static/scripts/packed/mvc/dataset/hda-edit.js
+++ b/static/scripts/packed/mvc/dataset/hda-edit.js
@@ -1,1 +1,1 @@
-var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}};
\ No newline at end of file
+var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}};
\ No newline at end of file

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d static/scripts/packed/utils/config.js
--- a/static/scripts/packed/utils/config.js
+++ b/static/scripts/packed/utils/config.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/trackster/util"],function(b,e){var c=Backbone.Model.extend({initialize:function(f){var g=this.get("key");this.set("id",g);var h=b.find(c.known_settings_defaults,function(i){return i.key===g});if(h){this.set(b.extend({},h,f))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",e.get_random_color())}this.on("change:value",this.cast_value,this)},cast_value:function(){var f=this.get("type"),g=this.get("value");if(f==="float"){g=parseFloat(g)}else{if(f==="int"){g=parseInt(g,10)}}this.set("value")}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{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},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",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}]});var d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var f={};this.each(function(g){f[g.get("key")]=g.get("value")});return f},get_value:function(f){var g=this.get(f);if(g){return g.get("value")}return undefined}},{from_config_dict:function(g){var f=b.map(b.keys(g),function(h){return{key:h,value:g[h]}});return new d(f)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var i=this.model;var f=this.$el;var h;function g(n,j){for(var r=0;r<n.length;r++){h=n[r];if(h.hidden){continue}var l="param_"+r;var v=i.values[h.key];var x=$("<div class='form-row' />").appendTo(j);x.append($("<label />").attr("for",l).text(h.label+":"));if(type==="bool"){x.append($('<input type="checkbox" />').attr("id",l).attr("name",l).attr("checked",v))}else{if(type==="text"){x.append($('<input type="text"/>').attr("id",l).val(v).click(function(){$(this).select()}))}else{if(type==="select"){var t=$("<select />").attr("id",l);for(var p=0;p<h.options.length;p++){$("<option/>").text(h.options[p].label).attr("value",h.options[p].value).appendTo(t)}t.val(v);x.append(t)}else{if(type==="color"){var w=$("<div/>").appendTo(x),s=$("<input />").attr("id",l).attr("name",l).val(v).css("float","left").appendTo(w).click(function(z){$(".bs-tooltip").removeClass("in");var y=$(this).siblings(".bs-tooltip").addClass("in");y.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(y).height()/2)+($(this).height()/2)}).show();y.click(function(A){A.stopPropagation()});$(document).bind("click.color-picker",function(){y.hide();$(document).unbind("click.color-picker")});z.stopPropagation()}),q=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(w).attr("title","Set new random color").tooltip(),u=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(w).hide(),m=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(u),k=$("<div class='tooltip-arrow'></div>").appendTo(u),o=$.farbtastic(m,{width:100,height:100,callback:s,color:v});w.append($("<div/>").css("clear","both"));(function(y){q.click(function(){y.setColor(e.get_random_color())})})(o)}else{x.append($("<input />").attr("id",l).attr("name",l).val(v))}}}}if(h.help){x.append($("<div class='help'/>").text(h.help))}}}g(this.params,f);return this},render_in_modal:function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){this.update_from_form();hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(i){if((i.keyCode||i.which)===27){h()}else{if((i.keyCode||i.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);if(this.$el.children().length===0){this.render()}show_modal("Configure",drawable.config.build_form(),{Cancel:h,OK:f})},update_from_form:function(){var f=this;this.collection.each(function(h,g){if(!h.get("hidden")){var j="param_"+g;var i=f.$el.find("#"+j).val();if(type==="bool"){i=container.find("#"+j).is(":checked")}h.set("value",i)}})}});return{ConfigSettingCollection:d,ConfigSettingCollectionView:a}});
\ No newline at end of file
+define(["libs/underscore","viz/trackster/util"],function(b,e){var c=Backbone.Model.extend({initialize:function(f){var g=this.get("key");this.set("id",g);var h=b.find(c.known_settings_defaults,function(i){return i.key===g});if(h){this.set(b.extend({},h,f))}if(this.get("type")==="color"&&!this.get("value")){this.set("value",e.get_random_color())}this.on("change:value",this.cast_value,this)},cast_value:function(){var f=this.get("type"),g=this.get("value");if(f==="float"){g=parseFloat(g)}else{if(f==="int"){g=parseInt(g,10)}}this.set("value")}},{known_settings_defaults:[{key:"name",label:"Name",type:"text",default_value:""},{key:"color",label:"Color",type:"color",default_value:null},{key:"min_value",label:"Min Value",type:"float",default_value:null},{key:"max_value",label:"Max Value",type:"float",default_value:null},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"block_color",label:"Block color",type:"color",default_value:null},{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},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:null},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}]});var d=Backbone.Collection.extend({model:c,to_key_value_dict:function(){var f={};this.each(function(g){f[g.get("key")]=g.get("value")});return f},get_value:function(f){var g=this.get(f);if(g){return g.get("value")}return undefined}},{from_config_dict:function(g){var f=b.map(b.keys(g),function(h){return{key:h,value:g[h]}});return new d(f)}});var a=Backbone.View.extend({className:"config-settings-view",render:function(){var i=this.model;var f=this.$el;var h;function g(n,j){for(var r=0;r<n.length;r++){h=n[r];if(h.hidden){continue}var l="param_"+r;var v=i.values[h.key];var x=$("<div class='form-row' />").appendTo(j);x.append($("<label />").attr("for",l).text(h.label+":"));if(type==="bool"){x.append($('<input type="checkbox" />').attr("id",l).attr("name",l).attr("checked",v))}else{if(type==="text"){x.append($('<input type="text"/>').attr("id",l).val(v).click(function(){$(this).select()}))}else{if(type==="select"){var t=$("<select />").attr("id",l);for(var p=0;p<h.options.length;p++){$("<option/>").text(h.options[p].label).attr("value",h.options[p].value).appendTo(t)}t.val(v);x.append(t)}else{if(type==="color"){var w=$("<div/>").appendTo(x),s=$("<input />").attr("id",l).attr("name",l).val(v).css("float","left").appendTo(w).click(function(z){$(".bs-tooltip").removeClass("in");var y=$(this).siblings(".bs-tooltip").addClass("in");y.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(y).height()/2)+($(this).height()/2)}).show();y.click(function(A){A.stopPropagation()});$(document).bind("click.color-picker",function(){y.hide();$(document).unbind("click.color-picker")});z.stopPropagation()}),q=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(w).attr("title","Set new random color").tooltip(),u=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(w).hide(),m=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(u),k=$("<div class='tooltip-arrow'></div>").appendTo(u),o=$.farbtastic(m,{width:100,height:100,callback:s,color:v});w.append($("<div/>").css("clear","both"));(function(y){q.click(function(){y.setColor(e.get_random_color())})})(o)}else{x.append($("<input />").attr("id",l).attr("name",l).val(v))}}}}if(h.help){x.append($("<div class='help'/>").text(h.help))}}}g(this.params,f);return this},render_in_modal:function(){var h=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},f=function(){this.update_from_form();hide_modal();$(window).unbind("keypress.check_enter_esc")},g=function(i){if((i.keyCode||i.which)===27){h()}else{if((i.keyCode||i.which)===13){f()}}};$(window).bind("keypress.check_enter_esc",g);if(this.$el.children().length===0){this.render()}show_modal("Configure",drawable.config.build_form(),{Cancel:h,OK:f})},update_from_form:function(){var f=this;this.collection.each(function(h,g){if(!h.get("hidden")){var j="param_"+g;var i=f.$el.find("#"+j).val();if(type==="bool"){i=container.find("#"+j).is(":checked")}h.set("value",i)}})}});return{ConfigSettingCollection:d,ConfigSettingCollectionView:a}});
\ No newline at end of file

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d static/scripts/packed/viz/trackster/painters.js
--- a/static/scripts/packed/viz/trackster/painters.js
+++ b/static/scripts/packed/viz/trackster/painters.js
@@ -1,1 +1,1 @@
-define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height,delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),j;if(this.prefs.show_sample_data){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));ctx.fillStyle="#999999";ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}if(!this.prefs.show_sample_data){continue}draw_y_start=this.prefs.summary_height+this.divider_height;for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.4}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}}});return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}});
\ No newline at end of file
+define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);if(this.prefs.min_value===undefined){this.prefs.min_value=_.min(_.map(this.data,function(d){return d[1]}))||0}if(this.prefs.max_value===undefined){this.prefs.max_value=_.max(_.map(this.data,function(d){return d[1]}))||0}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var painter_color=this.prefs.block_color||this.prefs.color,pref_color=parseInt(painter_color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=painter_color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=painter_color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},_parse_cigar:function(cigar_str){var cigar_ops="MIDNSHP=X";var blocks=[[0,0]],cur_block=blocks[0],base_pos=0,parsed_cigar=_.map(cigar_str.match(/[0-9]+[MIDNSHP=X]/g),function(op){var op_len=parseInt(op.slice(0,-1),10),op_char=op.slice(-1);if(op_char==="N"){if(cur_block[1]!==0){cur_block=[base_pos+op_len,base_pos+op_len];blocks.push(cur_block)}}else{if("ISHP".indexOf(op_char)===-1){cur_block[1]+=op_len;base_pos+=op_len}}return[cigar_ops.indexOf(op_char),op_len]});return{blocks:blocks,cigar:parsed_cigar}},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":seq_offset+=cig_len;break;case"M":case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var RefBasedReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){ReadPainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn)};extend(RefBasedReadPainter.prototype,ReadPainter.prototype,FeaturePainter,{draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack"),drawing_blocks=[];var draw_last=[];var t=this._parse_cigar(cigar);cigar=t.cigar;drawing_blocks=t.blocks;for(var i=0;i<drawing_blocks.length;i++){var block=drawing_blocks[i];if(is_overlap([feature_start+block[0],feature_start+block[1]],tile_region)){var s_start=Math.floor(Math.max(-0.5*w_scale,(feature_start+block[0]-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(feature_start+block[1]-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":case"S":case"P":break;case"M":base_offset+=cig_len;break;case"=":case"X":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var cur_seq="";if(cig_op==="X"){cur_seq=read_seq.slice(seq_offset,seq_offset+cig_len)}else{if(this.ref_seq){cur_seq=this.ref_seq.slice(Math.max(0,seq_start-tile_low),Math.min(seq_start-tile_low+cig_len,tile_high-tile_low))}}var start_pos=Math.max(seq_start,tile_low);for(var c=0;c<cur_seq.length;c++){if(cur_seq&&!this.prefs.show_differences||cig_op==="X"){var c_start=Math.floor(Math.max(0,(start_pos+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(cur_seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(cur_seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start-gap,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}if(cig_op==="X"){seq_offset+=cig_len}base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="black";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};var VariantPainter=function(data,view_start,view_end,prefs,mode,base_color_fn){Painter.call(this,data,view_start,view_end,prefs,mode);this.base_color_fn=base_color_fn;this.divider_height=1};extend(VariantPainter.prototype,Painter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}return height},get_required_height:function(num_samples){var height=this.prefs.summary_height;if(this.prefs.show_sample_data){height+=this.divider_height+num_samples*this.get_row_height()}return height},draw:function(ctx,width,height,w_scale){var locus_data,pos,id,ref,alt,qual,filter,sample_gts,allele_counts,variant,draw_x_start,char_x_start,draw_y_start,genotype,base_px=Math.max(1,Math.floor(w_scale)),row_height=(this.mode==="Squish"?SQUISH_TRACK_HEIGHT:PACK_TRACK_HEIGHT),feature_height=(w_scale<0.1?row_height:(this.mode==="Squish"?SQUISH_FEATURE_HEIGHT:PACK_FEATURE_HEIGHT)),j;if(this.prefs.show_sample_data){ctx.fillStyle="#F3F3F3";ctx.globalAlpha=1;ctx.fillRect(0,this.prefs.summary_height-this.divider_height,width,this.divider_height)}ctx.textAlign="center";for(var i=0;i<this.data.length;i++){locus_data=this.data[i];pos=locus_data[1];alt=locus_data[4].split(",");sample_gts=locus_data[7].split(",");allele_counts=locus_data.slice(8);draw_x_start=Math.floor(Math.max(-0.5*w_scale,(pos-this.view_start-0.5)*w_scale));char_x_start=Math.floor(Math.max(0,(pos-this.view_start)*w_scale));ctx.fillStyle="#999999";ctx.fillRect(draw_x_start,0,base_px,this.prefs.summary_height);draw_y_start=this.prefs.summary_height;for(j=0;j<alt.length;j++){ctx.fillStyle=this.base_color_fn(alt[j]);allele_frac=allele_counts/sample_gts.length;draw_height=Math.ceil(this.prefs.summary_height*allele_frac);ctx.fillRect(draw_x_start,draw_y_start-draw_height,base_px,draw_height);draw_y_start-=draw_height}if(!this.prefs.show_sample_data){continue}draw_y_start=this.prefs.summary_height+this.divider_height;for(j=0;j<sample_gts.length;j++,draw_y_start+=row_height){genotype=(sample_gts[j]?sample_gts[j].split(/\/|\|/):["0","0"]);variant=null;if(genotype[0]===genotype[1]){if(genotype[0]==="."){}else{if(genotype[0]!=="0"){variant=alt[parseInt(genotype[0],10)-1];ctx.globalAlpha=1}}}else{variant=(genotype[0]!=="0"?genotype[0]:genotype[1]);variant=alt[parseInt(variant,10)-1];ctx.globalAlpha=0.4}if(variant){ctx.fillStyle=this.base_color_fn(variant);if(this.mode==="Squish"||w_scale<ctx.canvas.manager.char_width_px){ctx.fillRect(draw_x_start,draw_y_start+1,base_px,feature_height)}else{ctx.fillText(variant,char_x_start,draw_y_start+row_height)}}}}}});return{Scaler:Scaler,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,RefBasedReadPainter:RefBasedReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter,VariantPainter:VariantPainter}});
\ No newline at end of file

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d static/scripts/packed/viz/trackster/tracks.js
--- a/static/scripts/packed/viz/trackster/tracks.js
+++ b/static/scripts/packed/viz/trackster/tracks.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,X,i){var q=ab.extend;var U=function(ac){return("isResolved" in ac)};var n={};var k=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=$(this),at=$(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=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(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(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,R=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",Q=10,H=20;function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<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)}};r.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){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(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).tooltip().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(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,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},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(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 i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<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=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(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 i.NumberFilter({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 af=[];for(var ad=0;ad<this.drawables.length;ad++){af.push(this.drawables[ad].name)}var ae=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.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(af,ae,ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(af,ae,ac)}}});var Y=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.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.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ac.prefs,onchange:function(){track.request_redraw(true)}})},render: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=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<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").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=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).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 W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]||this.config.values.n_color}});q(Y.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.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();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&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.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){z.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(ac,aj,ak){var ai=this,ag=(ak?[ak]: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()});this.requested_redraw=true}},_redraw:function(){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.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;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 am=13;this.overview_box.css({left:ac,width:Math.max(am,ai)}).show();if(ai<am){this.overview_box.css("left",ac-(am-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}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(){$(".bs-tooltip").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 s=function(ae,aj,af){this.track=ae;this.id=aj.id;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 e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(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=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new x.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:this.id,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new X.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.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 F=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};q(F.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(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(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()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag,10)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(false,true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(false,true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.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"?V(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(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new X.Dataset(ae.dataset);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,genome:new x.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<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()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.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)}},r.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()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset.id&&r.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},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw(true)},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(){r.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 W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof S){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(T);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.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(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);this.left_offset=0;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)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.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){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.request_draw(true);this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ae,ad,ac){if(ae){this.tile_cache.clear()}this.view.request_redraw(ad,ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*R)),am,ai,aj=[],ao=[];while((ac*R*ag)<ah){am=this._get_tile_bounds(ac,ag);ai=this.draw_helper(ad,am,ag,this.tiles_div,ap);aj.push(ai);$.when(ai).then(function(aq){ao.push(aq)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();if(ao[0]){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(af,aj,ad,ah){var ac=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ah=ah||function(){ac.request_draw(true)},ae=this.container_div.find(".yaxislabel."+ag);if(ae.length!==0){ae.text(aj)}else{ae=$("<div/>").text(aj).make_text_editable({num_cols:12,on_finish:function(ak){$(".bs-tooltip").remove();var ak=parseFloat(ak);ac.prefs[ad]=(!isNaN(ak)?ak:null);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(ae,af,aj,ac){var ag=ab.find(ae,function(ak){return ak.has_icons});if(ag){ab.each(ae,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}var ad=this,ah=ae[0];if(ah instanceof j){var ai=(this.prefs.histogram_max?this.prefs.histogram_max:ah.max_val);this._add_yaxis_label("max",ai,"histogram_max")}},draw_helper:function(ac,af,ar,ag,ah,ap){var an=this,ax=this._gen_tile_cache_key(ah,af),aj=function(ay){return(ay&&"track" in ay)};if(!ap){ap={}}var aw=(ac?undefined:an.tile_cache.get_elt(ax));if(aw){if(aj(aw)){an.show_tile(aw,ag,ah)}return aw}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(U(at)){al=false}var ai;if(view.reference_track){ai=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(U(ai)){al=false}else{ai=view.reference_track.data_manager.subset_entry(ai,af)}}if(al){q(at,ap.more_tile_data);var ak=an.mode;if(ak==="Auto"&&an.get_mode){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),au=af.get("start"),ad=af.get("end"),ao=Math.ceil((ad-au)*ah)+an.left_offset,am=an.get_canvas_height(at,ak,ah,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,af,ah,ai);if(aw!==undefined){an.tile_cache.set_elt(ax,aw);an.show_tile(aw,ag,ah)}return aw}var av=$.Deferred();an.tile_cache.set_elt(ax,av);$.when(at,ai).then(function(){aw=an.draw_helper(true,af,ar,ag,ah,ap);av.resolve(aw)});return av},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_summary_tree_tile:function(ac,ae,ag,af,ah){var ad=new L.SummaryTreePainter(ac,ag.get("start"),ag.get("end"),this.prefs);ad.draw(ae,ae.canvas.width,ae.canvas.height,ah);return new j(this,ag,af,ae.canvas,ac.data,ac.max)},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_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 new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.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_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda")},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.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();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,ah,av,ai,ak,at){var aq=this,aC=this._gen_tile_cache_key(ak,ah),am=function(aD){return(aD&&"track" in aD)};if(!at){at={}}var aB=(ad?undefined:aq.tile_cache.get_elt(aC));if(aB){if(am(aB)){aq.show_tile(aB,ai,ak)}return aB}var aj=[],aq,ao=true,aw,al;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(ah,aq.mode,av,aq.data_url_extra_params);if(U(aw)){ao=false}aj.push(aw);al=null;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ah,aq.mode,av,view.reference_track.data_url_extra_params);if(U(al)){ao=false}}aj.push(al)}if(ao){q(aw,at.more_tile_data);var ag=aq.view.canvas_manager.new_canvas(),ay=ah.get("start"),ae=ah.get("end"),az=0,ar=Math.ceil((ae-ay)*ak)+this.left_offset,ap=0,af=[],ax;var ac=0;for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=aj[az];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,ak,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);az=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=aj[az];al=aj[az+1];aB=aq.draw_tile(aw,au,af[ax],av,ah,ak,al)}this.tile_cache.set_elt(aC,aB);this.show_tile(aB,ai,ak);return aB}var aA=$.Deferred();aq=this;aq.tile_cache.set_elt(aC,aA);$.when.apply($,aj).then(function(){aB=aq.draw_helper(true,ah,av,ai,ak,at);aA.resolve(aB)});return aA},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();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(true)},before_draw:function(){M.prototype.before_draw.call(this);var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}this.prefs.min_value=af;this.prefs.max_value=ac;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw(true)},postdraw_actions:function(ai,ac,al,ah){M.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1;for(var ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(var ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(true,af.region,af.resolution,af.html_elt.parent(),al,{height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",this.drawables[0].prefs.min_value,"min_value",ak);this._add_yaxis_label("max",this.drawables[0].prefs.max_value,"max_value",ak)}});var B=function(ac){M.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.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();return M.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.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.request_redraw(true)}});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};q(h.prototype,r.prototype,M.prototype,{predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=af.total_frequency})},before_draw:function(){},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max",V(this.prefs.max_value,3),"max_value");this._add_yaxis_label("min",V(this.prefs.min_value,3),"min_value")}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,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;this.request_redraw(true)}});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};q(t.prototype,r.prototype,M.prototype,{draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{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_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:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.set_painter_from_config();ad.request_draw(true)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");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()};q(c.prototype,r.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(ap,ae,aq,ao){M.prototype.postdraw_actions.call(this,ap,ao);var ag=this,ah;if(ag.mode==="Coverage"){var ak=-1;for(ah=0;ah<ap.length;ah++){var an=ap[ah].max_val;if(an>ak){ak=an}}for(ah=0;ah<ap.length;ah++){var am=ap[ah];if(am.max_val!==ak){am.html_elt.remove();ag.draw_helper(true,am.index,am.resolution,am.html_elt.parent(),aq,{more_tile_data:{max:ak}})}}}if(ag.filters_manager){var af=ag.filters_manager.filters;for(var aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,al,ad;for(ah=0;ah<ap.length;ah++){if(ap[ah].data.length){al=ap[ah].data[0];for(var aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(al)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(ap[0] instanceof O){var ac=true;for(ah=0;ah<ap.length;ah++){if(!ap[ah].all_slotted){ac=false;break}}if(!ac){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 (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},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>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){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(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){return this._draw_summary_tree_tile(am,aq,af,ar,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}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||ac.extra_info==="no_detail"){return false}return true}});var Z=function(ad,ac,ae){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{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.request_draw(true)}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};q(Z.prototype,r.prototype,M.prototype,{draw_tile:function(ac,af,ai,ag,ah,aj){if(ac.dataset_type==="summary_tree"){return this._draw_summary_tree_tile(ac,af,ah,ag,aj)}else{var ae=this.view,ad=new (this.painter)(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return ae.get_base_color(ak)});ad.draw(af,af.canvas.width,af.canvas.height,aj);return new b(this,ah,ag,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="summary_tree"){return this.summary_draw_height}else{var af=new (this.painter)(null,null,null,this.prefs,ag);var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}return af.get_required_height(ad)}},predraw_init:function(){if(!this.dataset.get_metadata("sample_names")){return this.dataset.fetch()}},postdraw_actions:function(ae,af,ah,ad){M.prototype.postdraw_actions.call(this,ae,af,ah,ad);if(!(ae[0] instanceof j)&&this.prefs.show_labels){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ag=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ag).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var S=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({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.request_draw(true)}});this.prefs=this.config.values;this.painter=(ae.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(S.prototype,r.prototype,M.prototype,c.prototype);var d={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:c,LineTrack:h,ReadTrack:S,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:S,VariantTrack:Z,CompositeTrack:f,object_from_template:p}});
\ No newline at end of file
+define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,w,k,t,L,X,i){var p=ab.extend;var m={};var j=function(ac,ad){m[ac.attr("id")]=ad};var l=function(ac,ae,ag,af){ag=".group";var ad={};m[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=m[$(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=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=m[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(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)}m[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);m[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));m[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)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,n="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",R=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/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 F({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()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").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(){},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).tooltip().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(){},get_drawables:function(){}});var y=function(ad,ac,ae){q.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};p(y.prototype,q.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=o(ae[ac],this.view,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},get_drawables:function(){return this.drawables},get_tracks:function(af){var ac=this.drawables.slice(0),ad=[],ae;while(ac.length!==0){ae=ac.shift();if(ae instanceof af){ad.push(ae)}else{if(ae.drawables){ac=ac.concat(ae.drawables)}}}return ad}});var Q=function(ad,ac,af){p(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);j(this.container_div,this);j(this.content_div,this);l(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};p(Q.prototype,q.prototype,y.prototype,{action_icons_def:[q.prototype.action_icons_def[0],q.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").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 f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(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 i.NumberFilter({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 ad=new f(this.view,this.view,{name:this.name,drawables:this.drawables});var ac=this.container.replace_drawable(this,ad,true);ad.request_draw()},add_drawable:function(ac){y.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){y.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=p(y.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(af,ae,ac){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(af,ae,ac)}}});var Y=Backbone.View.extend({initialize:function(ac){p(ac,{obj_type:"View"});y.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.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"},],saved_values:ac.prefs,onchange:function(){track.request_redraw(true)}})},render: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;j(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(){w.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(o(ah,ac,ac))})})});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=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(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").tooltip({placement:"bottom"}).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();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(c),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});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").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(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 W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.values[ac.toLowerCase()+"_color"]||this.config.values.n_color}});p(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=v;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+v+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+v+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-v});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+v});return}var ai=$.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();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&&aj){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/,/g,"");ag=ag.replace(/:|\-/g," ");var ad=ag.split(/\s+/),af=ad[0],ae=(ad[1]?parseInt(ad[1],10):null),ac=(ad[2]?parseInt(ad[2],10):null);if(!ac){ae=ae-15;ac=ae+15}this.change_chrom(af,ae,ac)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){y.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){y.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(ac,aj,ak){var ai=this,ag=(ak?[ak]: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()});this.requested_redraw=true}},_redraw:function(){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.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;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 am=13;this.overview_box.css({left:ac,width:Math.max(am,ai)}).show();if(ai<am){this.overview_box.css("left",ac-(am-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}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(){$(".bs-tooltip").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.id=aj.id;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 e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new O(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=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};p(r.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:ac.id},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new w.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.dataset.id,action:"rerun",tool_id:this.id,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new Q(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new X.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new k.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(x+ag.message)}else{af(ag)}}})}});var O=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};p(O.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){O.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};p(e.prototype,O.prototype,{update_value:function(){O.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.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 F=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(F.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(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(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()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(k.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag,10)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ac,ag,ae,ad,af){b.call(this,ac,ag,ae,ad,af)};M.prototype.predisplay_actions=function(){};var P=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(false,true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(false,true)}).dblclick(function(ar){ar.stopPropagation()})}};p(P.prototype,b.prototype);P.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"?V(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(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){p(ae,{drag_handle_class:"draghandle"});q.call(this,ad,ac,ae);this.dataset=new X.Dataset(ae.dataset);this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<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(g.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()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new w.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},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},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw(true)},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 W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.tiles_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset.id){return}var ac=$.Deferred(),af={hda_ldda:ad.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(n);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(u);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,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 ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;l(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new r(this,af.tool,af.tool_state):null);this.tile_cache=new w.Cache(R);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};p(N.prototype,q.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").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,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw(true);this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ae,ad,ac){if(ae){this.tile_cache.clear()}this.view.request_redraw(ad,ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(ad,an){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,ak=ah-al,ae=this.view.container.width(),ap=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;ap=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),am,ai,aj=[],ao=[];while((ac*S*ag)<ah){am=this._get_tile_bounds(ac,ag);ai=this.draw_helper(ad,am,ag,this.tiles_div,ap);aj.push(ai);$.when(ai).then(function(aq){ao.push(aq)});ac+=1}if(!an){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();if(ao[0]){af.postdraw_actions(ao,ae,ap,an)}})},_add_yaxis_label:function(af,ah){var ad=this,ag=(af==="max"?"top":"bottom"),ai=(af==="max"?"max":"min"),ac=(af==="max"?"max_value":"min_value"),ah=ah||function(){ad.request_draw(true)},ae=this.container_div.find(".yaxislabel."+ag);if(ae.length!==0){ae.text(ad.prefs[ac])}else{ae=$("<div/>").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".bs-tooltip").remove();var aj=V(parseFloat(aj),3);ad.prefs[ac]=(!isNaN(aj)?aj:null);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return !(aj instanceof M)});if(ae.length>0&&ae.length<af.length){this.max_height_px=0;var ad=this;ab.each(ae,function(aj){aj.html_elt.remove();ad.draw_helper(true,aj.region,aj.resolution,ad.tiles_div,ai,{mode:"Coverage"})});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove()}var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",D)}})}},_get_drawables:function(){return[this]},draw_helper:function(ad,am,ag,ao,ap,ae){if(!ae){ae={}}var af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(aq){return(aq&&"track" in aq)},aj=ae.mode||af.mode;var ak=(ad?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ao,ap)}return ak}var al=function(){var aq=(ab.find(A,function(at){return at===aj})?"Coverage":aj);var ar=ab.map(ah,function(at){return at.data_manager.get_data(am,aq,ag,af.data_url_extra_params)});if(view.reference_track){ar.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return ar};var ac=$.Deferred();af.tile_cache.set_elt(an,ac);$.when.apply($,al()).then(function(){var aq=al(),aw=aq,aC;if(view.reference_track){aC=view.reference_track.data_manager.subset_entry(aq.pop(),am)}var ax=[],au=[];ab.each(ah,function(aH,aE){var aG=aH.mode,aF=aw[aE];if(aG==="Auto"){aG=aH.get_mode(aF);aH.update_auto_mode(aG)}ax.push(aG);au.push(aH.get_canvas_height(aF,aG,ap,ar))});var av=af.view.canvas_manager.new_canvas(),ay=am.get("start"),aD=am.get("end"),at=0,ar=Math.ceil((aD-ay)*ap)+af.left_offset,aA=ab.max(au),az;av.width=ar;av.height=(ae.height?ae.height:aA);var aB=av.getContext("2d");aB.translate(af.left_offset,0);if(ah.length>1){aB.globalAlpha=0.5;aB.globalCompositeOperation="source-over"}ab.each(ah,function(aF,aE){az=aF.draw_tile(aw[aE],aB,ax[aE],ag,am,ap,aC)});if(az!==undefined){af.tile_cache.set_elt(an,az);af.show_tile(az,ao,ap)}ac.resolve(az)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.LinePainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new M(this,ah,ag,af,ac.data)},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new w.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.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_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new k.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda")},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};p(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_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 f=function(ad,ac,ag){this.display_modes=A;N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=o(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof c||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};p(f.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.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();this.action_icons.param_space_viz_icon.hide()},can_draw:q.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var af=new Q(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();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(true)},before_draw:function(){N.prototype.before_draw.call(this);var ad=ab.min(ab.map(this.drawables,function(ae){return ae.prefs.min_value})),ac=ab.max(ab.map(this.drawables,function(ae){return ae.prefs.max_value}));this.prefs.min_value=ad;this.prefs.max_value=ac;ab.each(this.drawables,function(ae){ae.prefs.min_value=ad;ae.prefs.max_value=ac})},update_all_min_max:function(){var ac=this;ab.each(this.drawables,function(ad){ad.prefs.min_value=ac.prefs.min_value;ad.prefs.max_value=ac.prefs.max_value});this.request_draw(true)},postdraw_actions:function(ai,ac,al,ah){N.prototype.postdraw_actions.call(this,ai,ac,al,ah);var ag=-1;for(var ae=0;ae<ai.length;ae++){var aj=ai[ae].html_elt.find("canvas").height();if(aj>ag){ag=aj}}for(var ae=0;ae<ai.length;ae++){var af=ai[ae];if(af.html_elt.find("canvas").height()!==ag){this.draw_helper(true,af.region,af.resolution,af.html_elt.parent(),al,{height:ag});af.html_elt.remove()}}var ad=this,ak=function(){ad.update_all_min_max()};this._add_yaxis_label("min",ak);this._add_yaxis_label("max",ak)}});var B=function(ac){N.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.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};p(B.prototype,q.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:q.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(af,al,ag,ad,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ac=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,ad,ac,ae)}});var h=function(ae,ad,af){var ac=this;this.display_modes=A;this.mode="Histogram";N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:k.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.request_redraw(true)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(h.prototype,q.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ac,ad,ag,ae,af,ah){return this._draw_line_track_tile(ac,ad,ag,ae,af,ah)},can_subset:function(ac){return(ac.data[1][0]-ac.data[0][0]===1)},postdraw_actions:function(ad,ae,af,ac){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var s=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);this.request_redraw(true)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};p(s.prototype,q.prototype,N.prototype,{draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,af,ae,ah);var ag=k.get_random_color(),ac=k.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{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_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",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:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.set_painter_from_config();ad.request_draw(true)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");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(c.prototype,q.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(am,ae,an,al){N.prototype.postdraw_actions.call(this,am,ae,an,al);var ag=this,ah;if(ag.filters_manager){var af=ag.filters_manager.filters;for(var aj=0;aj<af.length;aj++){af[aj].update_ui_elt()}var ai=false,ak,ad;for(ah=0;ah<am.length;ah++){if(am[ah].data.length){ak=am[ah].data[0];for(var aj=0;aj<af.length;aj++){ad=af[aj];if(ad.applies_to(ak)&&ad.min!==ad.max){ai=true;break}}}}if(ag.filters_available!==ai){ag.filters_available=ai;if(!ag.filters_available){ag.filters_manager.hide()}ag.update_icons()}}if(am[0] instanceof P){var ac=true;for(ah=0;ah<am.length;ah++){if(!am[ah].all_slotted){ac=false;break}}if(!ac){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"}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 (t.FeatureSlotter)(ag,af,z,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){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(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,ar,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae,function(aD){return ap.view.get_base_color(aD)});var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new P(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="bigwig"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var Z=function(ad,ac,ae){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{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.request_draw(true)}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};p(Z.prototype,q.prototype,N.prototype,{draw_tile:function(ac,af,ai,ag,ah,aj){if(ac.dataset_type==="bigwig"){return this._draw_line_track_tile(ac,af,"Histogram",ag,ah,aj)}else{var ae=this.view,ad=new (this.painter)(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return ae.get_base_color(ak)});ad.draw(af,af.canvas.width,af.canvas.height,aj);return new b(this,ah,ag,af.canvas,ac.data)}},get_canvas_height:function(ac,ag,ah,ae){if(ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=new (this.painter)(null,null,null,this.prefs,ag);var ad=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ad===0&&ac.data.length!==0){ad=ac.data[0][7].match(/,/g);if(ad===null){ad=1}else{ad=ad.length+1}}return af.get_required_height(ad)}},predraw_init:function(){var ac=[g.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ac.push(this.dataset.fetch())}return ac},postdraw_actions:function(ae,af,ah,ad){N.prototype.postdraw_actions.call(this,ae,af,ah,ad);if(!(ae[0] instanceof M)&&this.prefs.show_labels){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ag=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ag).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=k.get_random_color(),ac=k.get_random_color([af,"#ffffff"]);this.config=new F({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:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw(true)}});this.prefs=this.config.values;this.painter=(ae.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};p(T.prototype,q.prototype,N.prototype,c.prototype);var d={CompositeTrack:f,DrawableGroup:Q,DiagonalHeatmapTrack:s,FeatureTrack:c,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var o=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:Q,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:s,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:o}});
\ No newline at end of file

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d static/scripts/packed/viz/visualization.js
--- a/static/scripts/packed/viz/visualization.js
+++ b/static/scripts/packed/viz/visualization.js
@@ -1,1 +1,1 @@
-define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,o){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){show_modal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=function(u){return("isResolved" in u)};var f=function(u){this.default_font=u!==undefined?u:"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")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_paths.attributes.image_path+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=x.indexOf(v);if(u!==-1){if(w[v].stale){x.splice(u,1);delete w[v]}else{this.move_key_to_end(v,u)}}return w[v]},set_elt:function(v,x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=this.attributes.num_elements;if(!y[v]){if(z.length>=w){var u=z.shift();delete y[u]}z.push(v)}y[v]=x;return x},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){G.region=C;w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(B,A,w,y){var C=this.get_elt(B);if(C&&(j(C)||this.get("data_mode_compatible")(C,A))){return C}var D=this.get("key_ary"),v=this.get("obj_cache"),E,u,z;for(var x=0;x<D.length;x++){E=D[x];u=new g({from_str:E});if(u.contains(B)){z=true;C=v[E];if(j(C)||(this.get("data_mode_compatible")(C,A)&&this.get("can_subset")(C))){this.move_key_to_end(E,x);if(!j(C)){var G=this.subset_entry(C,B);this.set(B,G);C=G}return C}}}if(!z&&B.length()<this.attributes.min_region_size){var F=new g({from_str:this.most_recently_added()});if(!F||(B.get("start")>F.get("start"))){B.set("end",B.get("start")+this.attributes.min_region_size)}else{B.set("start",B.get("end")-this.attributes.min_region_size)}B.set("genome",this.attributes.genome);B.trim()}return this.load_data(B,A,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}else{if(u.dataset_type==="summary_tree"){w.level=Math.min(u.level-1,2)}}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},subset_entry:function(w,x){var u={bigwig:function(y,z){return s.filter(y,function(A){return A[0]>=z.get("start")&&A[0]<=z.get("end")})},refseq:function(z,A){var B=A.get("start")-w.region.get("start"),y=w.data.length-(w.region.get("end")-A.get("end"));return w.data.slice(B,y)}};var v=w.data;if(!w.region.same(x)&&w.dataset_type in u){v=u[w.dataset_type](w.data,x)}return{region:x,data:v,dataset_type:w.dataset_type}},get_elt:function(u){return q.prototype.get_elt.call(this,u.toString())},set_elt:function(v,u){return q.prototype.set_elt.call(this,v.toString(),u)}});var p=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){return(w.length()<=100000?d.prototype.load_data.call(this,w,x,u,v):{data:null,region:w})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})},get_chrom_len:function(u){return s.find(this.get_chroms_info(),function(v){return v.chrom===u}).len}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,genome:null},same:function(u){return this.attributes.chrom===u.get("chrom")&&this.attributes.start===u.get("start")&&this.attributes.end===u.get("end")},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>x){if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}else{u=(y>=w?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return u},trim:function(u){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var v=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>v){this.attributes.end=v-1}}return this},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=i.Dataset.extend({initialize:function(u){this.set("id",u.dataset_id);this.set("config",o.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this,init_data:v}))}});var n=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_paths.get("visualization_url"),save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:s.extend({},n.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,GenomeReferenceDataManager:p,TrackBrowserRouter:h,TrackConfig:b,Visualization:n,select_datasets:a}});
\ No newline at end of file
+define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,o){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){show_modal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=function(u){return("isResolved" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_paths.attributes.image_path+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=x.indexOf(v);if(u!==-1){if(w[v].stale){x.splice(u,1);delete w[v]}else{this.move_key_to_end(v,u)}}return w[v]},set_elt:function(v,x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=this.attributes.num_elements;if(!y[v]){if(z.length>=w){var u=z.shift();delete y[u]}z.push(v)}y[v]=x;return x},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){G.region=C;w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(B,A,w,y){var C=this.get_elt(B);if(C&&(j(C)||this.get("data_mode_compatible")(C,A))){return C}var D=this.get("key_ary"),v=this.get("obj_cache"),E,u,z;for(var x=0;x<D.length;x++){E=D[x];u=new g({from_str:E});if(u.contains(B)){z=true;C=v[E];if(j(C)||(this.get("data_mode_compatible")(C,A)&&this.get("can_subset")(C))){this.move_key_to_end(E,x);if(!j(C)){var G=this.subset_entry(C,B);this.set(B,G);C=G}return C}}}if(!z&&B.length()<this.attributes.min_region_size){var F=new g({from_str:this.most_recently_added()});if(!F||(B.get("start")>F.get("start"))){B.set("end",B.get("start")+this.attributes.min_region_size)}else{B.set("start",B.get("end")-this.attributes.min_region_size)}B.set("genome",this.attributes.genome);B.trim()}return this.load_data(B,A,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},subset_entry:function(w,x){var u={bigwig:function(y,z){return s.filter(y,function(A){return A[0]>=z.get("start")&&A[0]<=z.get("end")})},refseq:function(z,A){var B=A.get("start")-w.region.get("start"),y=w.data.length-(w.region.get("end")-A.get("end"));return w.data.slice(B,y)}};var v=w.data;if(!w.region.same(x)&&w.dataset_type in u){v=u[w.dataset_type](w.data,x)}return{region:x,data:v,dataset_type:w.dataset_type}},get_elt:function(u){return q.prototype.get_elt.call(this,u.toString())},set_elt:function(v,u){return q.prototype.set_elt.call(this,v.toString(),u)}});var p=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){return(w.length()<=100000?d.prototype.load_data.call(this,w,x,u,v):{data:null,region:w})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})},get_chrom_len:function(u){return s.find(this.get_chroms_info(),function(v){return v.chrom===u}).len}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,genome:null},same:function(u){return this.attributes.chrom===u.get("chrom")&&this.attributes.start===u.get("start")&&this.attributes.end===u.get("end")},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>x){if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}else{u=(y>=w?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return u},trim:function(u){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var v=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>v){this.attributes.end=v-1}}return this},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=i.Dataset.extend({initialize:function(u){this.set("id",u.dataset_id);this.set("config",o.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this,init_data:v}))}});var n=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_paths.get("visualization_url"),save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:s.extend({},n.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,GenomeReferenceDataManager:p,TrackBrowserRouter:h,TrackConfig:b,Visualization:n,select_datasets:a}});
\ No newline at end of file

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d templates/webapps/galaxy/visualization/scatterplot.mako
--- a/templates/webapps/galaxy/visualization/scatterplot.mako
+++ b/templates/webapps/galaxy/visualization/scatterplot.mako
@@ -222,9 +222,9 @@
 <script type="text/javascript">
 $(function(){
 
-    var hda             = ${h.to_json_string( hda )},
-        historyID       = '${historyID}',
-        querySettings   = ${h.to_json_string( kwargs )},
+    var hda             = ${h.to_json_string( hda.get_api_value() )},
+        historyID       = '${trans.security.encode_id( hda.history.id )}',
+        querySettings   = ${h.to_json_string( query_args )},
         chartConfig     = _.extend( querySettings, {
             containerSelector : '#chart',
             //TODO: move to ScatterplotControlForm.initialize
@@ -250,8 +250,8 @@
 <%def name="body()"><!--dataset info--><div id="chart-header" class="header">
-        <h2 class="title">Scatterplot of '${hda['name']}'</h2>
-        <p class="subtitle">${hda['misc_info']}</p>
+        <h2 class="title">Scatterplot of '${hda.name}'</h2>
+        <p class="subtitle">${hda.info}</p></div><div id="scatterplot" class="scatterplot-control-form"></div></%def>

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d templates/webapps/galaxy/visualization/v_fwork_test.mako
--- /dev/null
+++ b/templates/webapps/galaxy/visualization/v_fwork_test.mako
@@ -0,0 +1,132 @@
+<%inherit file="/base.mako"/>
+<%def name="title()">
+${visualization_name}
+</%def>
+
+
+<%def name="stylesheets()">
+${parent.stylesheets()}
+${h.css(
+    "base",
+)}
+
+<style type="text/css">
+/*TODO: use/move into base.less*/
+* { margin: 0px; padding: 0px; }
+</style>
+    
+</%def>
+
+<%def name="process_hda( hda )">
+<%
+    hda_dict = hda.get_api_value()
+    hda_dict[ 'id' ] = trans.security.encode_id( hda_dict[ 'id' ] )
+    hda_dict[ 'history_id' ] = trans.security.encode_id( hda_dict[ 'history_id' ] )
+    del hda_dict[ 'peek' ]
+    return hda_dict
+%>
+</%def>
+
+<%def name="javascripts()">
+${parent.javascripts()}
+<script type="text/javascript">
+$(function(){
+
+//var data = {
+//        title   : 'shared with user visualization',
+//        type    : 'test',
+//        slug    : 'shared',
+//        annotation : 'a visualization shared with a specific user',
+//        config  : {
+//            x : 10,
+//            y : 10
+//        }
+//    };
+
+//var creationPromise = jQuery.ajax( '/api/visualizations', {
+//        type        : 'POST',
+//        contentType : 'application/json',
+//        data        : JSON.stringify( data )
+//    });
+//creationPromise.success(function(){
+//    console.debug( 'success' );
+//});
+//creationPromise.error(function(){
+//    console.debug( 'error' );
+//});
+
+
+});
+</script>
+</%def>
+
+<%def name="print_var( name, var )">
+%if var is not None:
+    <% t = str( type( var ) )[1:-1] %>
+    <p>${name}: ${t}, ${var}</p>
+%else:
+    <p>No ${name}</p>
+%endif
+</%def>
+
+<%def name="body()">
+    <%
+        import pprint
+        print self
+        print self.context
+        pprint.pprint( self.context.kwargs, indent=4 )
+    %>
+    <%
+        vars_to_print = [
+            ( 'default', default ),
+            ( 'string', string ),
+            ( 'boolean', boolean ),
+            ( 'integer', integer ),
+            ( 'float', float ),
+            ( 'json', json ),
+        ]
+    %>
+    %for name, var in vars_to_print:
+        ${print_var( name, var )}
+    %endfor
+
+    %if visualization:
+        <h1>${visualization.title}</h1>
+        <p>id: ${trans.security.encode_id( visualization.id )}</p>
+        <p>dbkey: ${visualization.dbkey}</p>
+        <p>config:
+            <pre>${h.to_json_string( visualization.latest_revision.config, sort_keys=True, indent=( 4 * ' ' ) )}</pre>
+        </p>
+    %endif
+
+    %if dataset:
+        <h1>${dataset.name}</h1>
+        <p>id: ${trans.security.encode_id( dataset.id )}</p>
+        <p>history id: ${trans.security.encode_id( dataset.history.id )}</p>
+        <pre>
+            ${h.to_json_string( process_hda( dataset ), sort_keys=True, indent=( 4 * ' ' ) )}
+        </pre>
+    %endif
+
+    %if dataset_instance:
+        <h1>${dataset_instance.name}</h1>
+        <p>id: ${trans.security.encode_id( dataset_instance.id )}</p>
+        %if hda_ldda == 'hda':
+        <p>history id: ${trans.security.encode_id( dataset_instance.history.id )}</p>
+        <pre>
+            ${h.to_json_string( process_hda( dataset_instance ), sort_keys=True, indent=( 4 * ' ' ) )}
+        </pre>
+        %else:
+        <p>(LibraryDatasetDatasetAssociation)</p>
+        %endif
+    %endif
+
+    %if query_args:
+    <ul>
+        %for key, val in query_args.items():
+        <li>${key} : ${val}</li>
+        %endfor
+    </ul>
+    %endif
+    
+</%def>

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -171,6 +171,10 @@
 # Galaxy.
 #datatypes_config_file = datatypes_conf.xml
 
+# Visualizations config file, defines what visualizations apply to particular data and how to pass them
+# the necessary parameters
+#visualizations_conf_path = visualizations_conf.xml
+
 # Each job is given a unique empty directory as its current working directory.
 # This option defines in what parent directory those directories will be
 # created.

diff -r 718f2f51ed019319a0406b5dd7d679be8f0c35ae -r ffc6ff4fe6dfef48d6440c1cdb910661010f559d visualizations_conf.xml.sample
--- /dev/null
+++ b/visualizations_conf.xml.sample
@@ -0,0 +1,292 @@
+<?xml version="1.0"?>
+<!--
+  This is the xml file to edit to add new visualizations to the framework.
+  NOTE!: this is a work in progress!
+
+  Note: also that visualizations that fail to parse in visualizations/registry will
+    produce an error in the server log, but otherwise will be skipped and not available.
+    If you can't find your visualization in the UI, check the server logs for errors
+    during start up.
+-->
+
+<!-- .......................................................................... DTD -->
+<!-- runnable on NIX with xmllint -->
+<!DOCTYPE visualizations [
+  <!-- 0 or more visualizations -->
+  <!ELEMENT visualizations (visualization*)>
+  <!-- each visualization must have a template (all other elements are optional) -->
+  <!ELEMENT visualization (data_sources*,params*,template_root*,template,link_text*,render_location*)>
+  <!-- visualization name (e.g. 'trackster', 'scatterplot', etc.) is required -->
+  <!ATTLIST visualization
+      name        CDATA #REQUIRED
+  >
+
+  <!ELEMENT data_sources (data_source*)>
+  <!-- data sources are elements that describe what objects (HDAs, LDDAs, Job, User, etc.)
+          are applicable to a visualization. Often these are used to fetch applicable links
+          to the visualizations that use them.
+  -->
+    <!ELEMENT data_source (model_class,(test|to_param)*)>
+      <!ELEMENT model_class (#PCDATA)>
+      <!-- model_class is currently the class name of the object you want to make a visualization
+            applicable to (e.g. HistoryDatasetAssociation). Currently only classes in galaxy.model
+            can be used.
+            REQUIRED and currently limited to: 'HistoryDatasetAssociation', 'LibraryDatasetDatasetAssociation'
+      -->
+      <!ELEMENT test (#PCDATA)>
+      <!-- tests help define what conditions the visualization can be applied to the model_class/target.
+            Currently, all tests are OR'd and there is no logical grouping. Tests are run in order.
+          (text): the text of this element is what the given target will be compared to (REQUIRED)
+          type: what type of test to run (e.g. when the target is an HDA the test will often be of type 'isinstance'
+                  and test whether the HDA's datatype isinstace of a class)
+                  DEFAULT: string comparison.
+          test_attr: what attribute of the target object should be used in the test. For instance, 'datatype'
+                  will attempt to get the HDA.datatype from a target HDA. If the given object doesn't have
+                  that attribute the test will fail (with no error). test_attr can be dot separated attributes,
+                  looking up each in turn. For example, if the target was a history, one could access the
+                  history.user.email by setting test_attr to 'user.email' (why you would want that, I don't know)
+                  DEFAULT: to comparing the object itself (and not any of it's attributes)
+          result_type: if the result (the text of the element mentioned above) needs to be parsed into
+                  something other than a string, result_type will tell the registry how to do this. E.g.
+                  if result_type is 'datatype' the registry will assume the text is a datatype class name
+                  and parse it into the proper class before the test (often 'isinstance') is run.
+                  DEFAULT: no parsing (result should be a string)
+      -->
+      <!ATTLIST test
+          type        CDATA #IMPLIED
+          test_attr   CDATA #IMPLIED
+          result_type CDATA #IMPLIED
+      >
+
+      <!ELEMENT to_param (#PCDATA)>
+      <!-- to_param tells the registry how to parse the data_source into a query string param.
+            For example, HDA data_sources can set param_to text to 'dataset_id' and param_attr to 'id' and the
+              the target HDA (if it passes the tests) will be passed as "dataset_id=HDA.id"
+          (text): the query string param key this source will be parsed into (e.g. dataset_id)
+                  REQUIRED
+          param_attr: the attribute of the data_source object to use as the value in the query string param.
+                  E.g. param_attr='id' for an HDA data_source would use the (encoded) id.
+                  NOTE: a to_param MUST have either a param_attr or assign
+          assign: you can use this to directly assign a value to a query string's param. E.g. if the
+                  data_source is a LDDA we can set 'hda_or_ldda=ldda' using assign='ldda'.
+                  NOTE: a to_param MUST have either a param_attr or assign
+      -->
+      <!ATTLIST to_param
+          param_attr  CDATA #IMPLIED
+          assign      CDATA #IMPLIED
+      >
+
+  <!ELEMENT params ((param|param_modifier)*)>
+  <!-- params describe what data will be sent to a visualization template and
+        how to convert them from a query string in a URL into variables usable in a template.
+        For example,
+       param_modifiers are a special class of parameters that modify other params
+        (e.g. hda_ldda can be 'hda' or 'ldda' and modifies/informs dataset_id to fetch an HDA or LDDA)
+  -->
+    <!ELEMENT param (#PCDATA)>
+      <!-- param tells the registry how to parse the query string param back into a resource/data_source.
+            For example, if a query string has "dataset_id=NNN" and the type is 'dataset', the registry
+            will attempt to fetch the hda with id of NNN from the database and pass it to the template.
+          (text): the query string param key this source will be parsed from (e.g. dataset_id)
+                  REQUIRED
+          type: the type of the resource.
+                  Can be: str (DEFAULT), bool, int, float, json, visualization, dbkey, dataset, or hda_ldda.
+          default: if a param is not passed on the query string (and is not required) OR the given param
+                  fails to parse, this value is used instead.
+                  DEFAULT: None
+          required: set this to true if the param is required for the template. Rendering will with an error
+                  if the param hasn't been sent.
+                  DEFAULT: false
+          csv: set this to true if the param is a comma separated list. The registry will attempt to
+                  parse each value as the given type and send the result as a list to the template.
+                  DEFAULT: false
+          constrain_to: (currently unused) constain a param to a set of values, error if not valid.
+                  DEFAULT: don't constrain
+          var_name_in_template: a new name for the resource/variable to use in the template. E.g. an initial
+                  query string param key might be 'dataset_id' in the URL, the registry parses it into an HDA,
+                  and if var_name_in_template is set to 'hda', the template will be able to access the HDA
+                  with the variable name 'hda' (as in hda.title).
+                  DEFAULT: keep the original query string name
+      -->
+    <!ATTLIST param
+        type        CDATA #IMPLIED
+        default     CDATA #IMPLIED
+        required    CDATA #IMPLIED
+        csv         CDATA #IMPLIED
+        constrain_to          CDATA #IMPLIED
+        var_name_in_template  CDATA #IMPLIED
+    >
+    <!-- param_modifiers are the same as param but have a REQUIRED 'modifies' attribute.
+          'modifies' must point to the param name (the text part of param element) that it will modify.
+          E.g. <param_modifier modifies="dataset_id">hda_ldda</param_modifier>
+    -->
+    <!ELEMENT param_modifier (#PCDATA)>
+    <!ATTLIST param_modifier
+        modifies    CDATA #REQUIRED
+        type        CDATA #IMPLIED
+        default     CDATA #IMPLIED
+        required    CDATA #IMPLIED
+        csv         CDATA #IMPLIED
+        constrain_to          CDATA #IMPLIED
+        var_name_in_template  CDATA #IMPLIED
+    >
+
+  <!-- template_root: the directory to search for the template relative to templates/webapps/galaxy
+        (optional) DEFAULT: visualizations
+  -->
+  <!ELEMENT template_root (#PCDATA)>
+  <!-- template: the template used to render the visualization. REQUIRED -->
+  <!ELEMENT template (#PCDATA)>
+  <!-- link_text: the text component of an html anchor displayed when the registry builds the link information -->
+  <!ELEMENT link_text (#PCDATA)>
+  <!-- render_location: used as the target attribute of the link to the visualization.
+        Can be 'galaxy_main', '_top', '_blank'. DEFAULT: 'galaxy_main'
+  -->
+  <!-- TODO: rename -> render_target -->
+  <!ELEMENT render_location (#PCDATA)>
+]>
+
+<!-- .......................................................................... configuration xml -->
+<visualizations>
+  <visualization name="trackster">
+    <!--not tested yet -->
+    <data_sources>
+      <data_source>
+        <model_class>HistoryDatasetAssociation</model_class>
+        <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+        <to_param param_attr="id">dataset_id</to_param>
+        <to_param assign="hda">hda_ldda</to_param>
+        <to_param param_attr="dbkey">dbkey</to_param>
+      </data_source>
+      <data_source>
+        <model_class>LibraryDatasetDatasetAssociation</model_class>
+        <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+        <to_param param_attr="id">dataset_id</to_param>
+        <to_param assign="ldda">hda_ldda</to_param>
+      </data_source>
+    </data_sources>
+    <params>
+      <param type="visualization">id</param>
+      <param type="dataset">dataset_id</param>
+      <param type="genome_region">genome_region</param>
+      <param type="dbkey">dbkey</param>
+    </params>
+    <template_root>tracks</template_root>
+    <template>browser.mako</template>
+    <render_location>_top</render_location>
+  </visualization>
+
+  <visualization name="circster">
+    <data_sources>
+      <data_source>
+        <model_class>HistoryDatasetAssociation</model_class>
+        <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+        <to_param param_attr="id">dataset_id</to_param>
+        <to_param assign="hda">hda_ldda</to_param>
+      </data_source>
+      <data_source>
+        <model_class>LibraryDatasetDatasetAssociation</model_class>
+        <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+        <to_param param_attr="id">dataset_id</to_param>
+        <to_param assign="ldda">hda_ldda</to_param>
+      </data_source>
+    </data_sources>
+    <params>
+      <param type="visualization">id</param>
+      <param type="hda_or_ldda">dataset_id</param>
+      <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier>
+      <param type="dbkey">dbkey</param>
+    </params>
+    <template>circster.mako</template>
+    <render_location>_top</render_location>
+  </visualization>
+
+  <!--
+  <visualization name="sweepster">
+    <data_sources>
+      <data_source>
+        <model_class>HistoryDatasetAssociation</model_class>
+        <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+        <to_param param_attr="id">dataset_id</to_param>
+        <to_param assign="hda">hda_ldda</to_param>
+      </data_source>
+      <data_source>
+        <model_class>LibraryDatasetDatasetAssociation</model_class>
+        <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+        <to_param param_attr="id">dataset_id</to_param>
+        <to_param assign="ldda">hda_ldda</to_param>
+      </data_source>
+    </data_sources>
+    <params>
+      <param type="visualization" var_name_in_template="viz">visualization</param>
+      <param type="hda_or_ldda" var_name_in_template="dataset">dataset_id</param>
+      <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier>
+    </params>
+    <template>sweepster.mako</template>
+    <render_location>_top</render_location>
+  </visualization>
+  -->
+
+  <visualization name="phyloviz">
+    <data_sources>
+      <data_source>
+        <model_class>HistoryDatasetAssociation</model_class>
+        <test type="isinstance" test_attr="datatype" result_type="datatype">data.Newick</test>
+        <test type="isinstance" test_attr="datatype" result_type="datatype">data.Nexus</test>
+        <to_param param_attr="id">dataset_id</to_param>
+      </data_source>
+    </data_sources>
+    <params>
+      <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+      <param type="integer" default="0">tree_index</param>
+    </params>
+    <template>phyloviz.mako</template>
+    <render_location>_top</render_location>
+  </visualization>
+
+  <visualization name="scatterplot">
+    <data_sources>
+      <data_source>
+        <model_class>HistoryDatasetAssociation</model_class>
+        <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
+        <to_param param_attr="id">dataset_id</to_param>
+      </data_source>
+    </data_sources>
+    <params>
+      <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <template>scatterplot.mako</template>
+  </visualization>
+
+  <!--
+  <visualization name="test">
+    <data_sources>
+      <data_source>
+        <model_class>HistoryDatasetAssociation</model_class>
+        <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+        <to_param param_attr="id">dataset_id</to_param>
+        <to_param assign="bler">string</to_param>
+        <to_param assign="False">boolean</to_param>
+        <to_param assign="-5">integer</to_param>
+        <to_param assign="3.14">float</to_param>
+        <to_param assign="{}">json</to_param>
+      </data_source>
+    </data_sources>
+    <params>
+      <param>default</param>
+      <param type="str">string</param>
+      <param type="bool">boolean</param>
+      <param type="int">integer</param>
+      <param type="float">float</param>
+      <param type="json">json</param>
+      <param type="str" required="true">string</param>
+      <param type="visualization" var_name_in_template="visualization">visualization_id</param>
+      <param type="dataset" var_name_in_template="dataset">dataset_id</param>
+      <param type="hda_or_ldda">dataset_instance</param>
+      <param_modifier type="str" modifies="dataset_instance">hda_ldda</param_modifier>
+    </params>
+    <template>v_fwork_test.mako</template>
+  </visualization>
+  -->
+
+</visualizations>

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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[galaxy-commits] commit/galaxy-central: carlfeberhard: Visualizations framework: allow users to associate custom visualizations with models, datatypes, etc. via an xml configuration file (visualizations_conf.xml)

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