galaxy-commits May 2011

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commit/galaxy-central: kanwei: update JSON2.js
by Bitbucket 06 May '11

06 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4d2d6eb829fb/ changeset: r5506:4d2d6eb829fb user: kanwei date: 2011-05-06 19:44:21 summary: update JSON2.js affected #: 2 files (55 bytes) --- a/static/scripts/json2.js Fri May 06 12:09:58 2011 -0400 +++ b/static/scripts/json2.js Fri May 06 13:44:21 2011 -0400 @@ -1,6 +1,6 @@ /* http://www.JSON.org/json2.js - 2010-03-20 + 2011-02-23 Public Domain. @@ -146,7 +146,7 @@ redistribute. */ -/*jslint evil: true, strict: false */ +/*jslint evil: true, strict: false, regexp: false */ /*members "", "\b", "\t", "\n", "\f", "\r", "\"", JSON, "\\", apply, call, charCodeAt, getUTCDate, getUTCFullYear, getUTCHours, @@ -159,11 +159,13 @@ // Create a JSON object only if one does not already exist. We create the // methods in a closure to avoid creating global variables. -if (!this.JSON) { - this.JSON = {}; +var JSON; +if (!JSON) { + JSON = {}; } (function () { + "use strict"; function f(n) { // Format integers to have at least two digits. @@ -175,19 +177,19 @@ Date.prototype.toJSON = function (key) { return isFinite(this.valueOf()) ? - this.getUTCFullYear() + '-' + - f(this.getUTCMonth() + 1) + '-' + - f(this.getUTCDate()) + 'T' + - f(this.getUTCHours()) + ':' + - f(this.getUTCMinutes()) + ':' + - f(this.getUTCSeconds()) + 'Z' : null; + this.getUTCFullYear() + '-' + + f(this.getUTCMonth() + 1) + '-' + + f(this.getUTCDate()) + 'T' + + f(this.getUTCHours()) + ':' + + f(this.getUTCMinutes()) + ':' + + f(this.getUTCSeconds()) + 'Z' : null; }; - String.prototype.toJSON = - Number.prototype.toJSON = - Boolean.prototype.toJSON = function (key) { - return this.valueOf(); - }; + String.prototype.toJSON = + Number.prototype.toJSON = + Boolean.prototype.toJSON = function (key) { + return this.valueOf(); + }; } var cx = /[\u0000\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g, @@ -214,13 +216,11 @@ // sequences. escapable.lastIndex = 0; - return escapable.test(string) ? - '"' + string.replace(escapable, function (a) { - var c = meta[a]; - return typeof c === 'string' ? c : - '\\u' + ('0000' + a.charCodeAt(0).toString(16)).slice(-4); - }) + '"' : - '"' + string + '"'; + return escapable.test(string) ? '"' + string.replace(escapable, function (a) { + var c = meta[a]; + return typeof c === 'string' ? c : + '\\u' + ('0000' + a.charCodeAt(0).toString(16)).slice(-4); + }) + '"' : '"' + string + '"'; } @@ -303,11 +303,9 @@ // Join all of the elements together, separated with commas, and wrap them in // brackets. - v = partial.length === 0 ? '[]' : - gap ? '[\n' + gap + - partial.join(',\n' + gap) + '\n' + - mind + ']' : - '[' + partial.join(',') + ']'; + v = partial.length === 0 ? '[]' : gap ? + '[\n' + gap + partial.join(',\n' + gap) + '\n' + mind + ']' : + '[' + partial.join(',') + ']'; gap = mind; return v; } @@ -317,8 +315,8 @@ if (rep && typeof rep === 'object') { length = rep.length; for (i = 0; i < length; i += 1) { - k = rep[i]; - if (typeof k === 'string') { + if (typeof rep[i] === 'string') { + k = rep[i]; v = str(k, value); if (v) { partial.push(quote(k) + (gap ? ': ' : ':') + v); @@ -330,7 +328,7 @@ // Otherwise, iterate through all of the keys in the object. for (k in value) { - if (Object.hasOwnProperty.call(value, k)) { + if (Object.prototype.hasOwnProperty.call(value, k)) { v = str(k, value); if (v) { partial.push(quote(k) + (gap ? ': ' : ':') + v); @@ -342,9 +340,9 @@ // Join all of the member texts together, separated with commas, // and wrap them in braces. - v = partial.length === 0 ? '{}' : - gap ? '{\n' + gap + partial.join(',\n' + gap) + '\n' + - mind + '}' : '{' + partial.join(',') + '}'; + v = partial.length === 0 ? '{}' : gap ? + '{\n' + gap + partial.join(',\n' + gap) + '\n' + mind + '}' : + '{' + partial.join(',') + '}'; gap = mind; return v; } @@ -385,7 +383,7 @@ rep = replacer; if (replacer && typeof replacer !== 'function' && (typeof replacer !== 'object' || - typeof replacer.length !== 'number')) { + typeof replacer.length !== 'number')) { throw new Error('JSON.stringify'); } @@ -415,7 +413,7 @@ var k, v, value = holder[key]; if (value && typeof value === 'object') { for (k in value) { - if (Object.hasOwnProperty.call(value, k)) { + if (Object.prototype.hasOwnProperty.call(value, k)) { v = walk(value, k); if (v !== undefined) { value[k] = v; @@ -455,10 +453,10 @@ // we look to see that the remaining characters are only whitespace or ']' or // ',' or ':' or '{' or '}'. If that is so, then the text is safe for eval. - if (/^[\],:{}\s]*$/. -test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g, '@'). -replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g, ']'). -replace(/(?:^|:|,)(?:\s*\[)+/g, ''))) { + if (/^[\],:{}\s]*$/ + .test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g, '@') + .replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g, ']') + .replace(/(?:^|:|,)(?:\s*\[)+/g, ''))) { // In the third stage we use the eval function to compile the text into a // JavaScript structure. The '{' operator is subject to a syntactic ambiguity --- a/static/scripts/packed/json2.js Fri May 06 12:09:58 2011 -0400 +++ b/static/scripts/packed/json2.js Fri May 06 13:44:21 2011 -0400 @@ -1,1 +1,1 @@ -if(!this.JSON){this.JSON={}}(function(){function f(n){return n<10?"0"+n:n}if(typeof Date.prototype.toJSON!=="function"){Date.prototype.toJSON=function(key){return isFinite(this.valueOf())?this.getUTCFullYear()+"-"+f(this.getUTCMonth()+1)+"-"+f(this.getUTCDate())+"T"+f(this.getUTCHours())+":"+f(this.getUTCMinutes())+":"+f(this.getUTCSeconds())+"Z":null};String.prototype.toJSON=Number.prototype.toJSON=Boolean.prototype.toJSON=function(key){return this.valueOf()}}var cx=/[\u0000\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,escapable=/[\\\"\x00-\x1f\x7f-\x9f\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,gap,indent,meta={"\b":"\\b","\t":"\\t","\n":"\\n","\f":"\\f","\r":"\\r",'"':'\\"',"\\":"\\\\"},rep;function quote(string){escapable.lastIndex=0;return escapable.test(string)?'"'+string.replace(escapable,function(a){var c=meta[a];return typeof c==="string"?c:"\\u"+("0000"+a.charCodeAt(0).toString(16)).slice(-4)})+'"':'"'+string+'"'}function str(key,holder){var i,k,v,length,mind=gap,partial,value=holder[key];if(value&&typeof value==="object"&&typeof value.toJSON==="function"){value=value.toJSON(key)}if(typeof rep==="function"){value=rep.call(holder,key,value)}switch(typeof value){case"string":return quote(value);case"number":return isFinite(value)?String(value):"null";case"boolean":case"null":return String(value);case"object":if(!value){return"null"}gap+=indent;partial=[];if(Object.prototype.toString.apply(value)==="[object Array]"){length=value.length;for(i=0;i<length;i+=1){partial[i]=str(i,value)||"null"}v=partial.length===0?"[]":gap?"[\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"]":"["+partial.join(",")+"]";gap=mind;return v}if(rep&&typeof rep==="object"){length=rep.length;for(i=0;i<length;i+=1){k=rep[i];if(typeof k==="string"){v=str(k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}else{for(k in value){if(Object.hasOwnProperty.call(value,k)){v=str(k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}v=partial.length===0?"{}":gap?"{\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"}":"{"+partial.join(",")+"}";gap=mind;return v}}if(typeof JSON.stringify!=="function"){JSON.stringify=function(value,replacer,space){var i;gap="";indent="";if(typeof space==="number"){for(i=0;i<space;i+=1){indent+=" "}}else{if(typeof space==="string"){indent=space}}rep=replacer;if(replacer&&typeof replacer!=="function"&&(typeof replacer!=="object"||typeof replacer.length!=="number")){throw new Error("JSON.stringify")}return str("",{"":value})}}if(typeof JSON.parse!=="function"){JSON.parse=function(text,reviver){var j;function walk(holder,key){var k,v,value=holder[key];if(value&&typeof value==="object"){for(k in value){if(Object.hasOwnProperty.call(value,k)){v=walk(value,k);if(v!==undefined){value[k]=v}else{delete value[k]}}}}return reviver.call(holder,key,value)}text=String(text);cx.lastIndex=0;if(cx.test(text)){text=text.replace(cx,function(a){return"\\u"+("0000"+a.charCodeAt(0).toString(16)).slice(-4)})}if(/^[\],:{}\s]*$/.test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))){j=eval("("+text+")");return typeof reviver==="function"?walk({"":j},""):j}throw new SyntaxError("JSON.parse")}}}()); \ No newline at end of file +var JSON;if(!JSON){JSON={}}(function(){function f(n){return n<10?"0"+n:n}if(typeof Date.prototype.toJSON!=="function"){Date.prototype.toJSON=function(key){return isFinite(this.valueOf())?this.getUTCFullYear()+"-"+f(this.getUTCMonth()+1)+"-"+f(this.getUTCDate())+"T"+f(this.getUTCHours())+":"+f(this.getUTCMinutes())+":"+f(this.getUTCSeconds())+"Z":null};String.prototype.toJSON=Number.prototype.toJSON=Boolean.prototype.toJSON=function(key){return this.valueOf()}}var cx=/[\u0000\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,escapable=/[\\\"\x00-\x1f\x7f-\x9f\u00ad\u0600-\u0604\u070f\u17b4\u17b5\u200c-\u200f\u2028-\u202f\u2060-\u206f\ufeff\ufff0-\uffff]/g,gap,indent,meta={"\b":"\\b","\t":"\\t","\n":"\\n","\f":"\\f","\r":"\\r",'"':'\\"',"\\":"\\\\"},rep;function quote(string){escapable.lastIndex=0;return escapable.test(string)?'"'+string.replace(escapable,function(a){var c=meta[a];return typeof c==="string"?c:"\\u"+("0000"+a.charCodeAt(0).toString(16)).slice(-4)})+'"':'"'+string+'"'}function str(key,holder){var i,k,v,length,mind=gap,partial,value=holder[key];if(value&&typeof value==="object"&&typeof value.toJSON==="function"){value=value.toJSON(key)}if(typeof rep==="function"){value=rep.call(holder,key,value)}switch(typeof value){case"string":return quote(value);case"number":return isFinite(value)?String(value):"null";case"boolean":case"null":return String(value);case"object":if(!value){return"null"}gap+=indent;partial=[];if(Object.prototype.toString.apply(value)==="[object Array]"){length=value.length;for(i=0;i<length;i+=1){partial[i]=str(i,value)||"null"}v=partial.length===0?"[]":gap?"[\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"]":"["+partial.join(",")+"]";gap=mind;return v}if(rep&&typeof rep==="object"){length=rep.length;for(i=0;i<length;i+=1){if(typeof rep[i]==="string"){k=rep[i];v=str(k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}else{for(k in value){if(Object.prototype.hasOwnProperty.call(value,k)){v=str(k,value);if(v){partial.push(quote(k)+(gap?": ":":")+v)}}}}v=partial.length===0?"{}":gap?"{\n"+gap+partial.join(",\n"+gap)+"\n"+mind+"}":"{"+partial.join(",")+"}";gap=mind;return v}}if(typeof JSON.stringify!=="function"){JSON.stringify=function(value,replacer,space){var i;gap="";indent="";if(typeof space==="number"){for(i=0;i<space;i+=1){indent+=" "}}else{if(typeof space==="string"){indent=space}}rep=replacer;if(replacer&&typeof replacer!=="function"&&(typeof replacer!=="object"||typeof replacer.length!=="number")){throw new Error("JSON.stringify")}return str("",{"":value})}}if(typeof JSON.parse!=="function"){JSON.parse=function(text,reviver){var j;function walk(holder,key){var k,v,value=holder[key];if(value&&typeof value==="object"){for(k in value){if(Object.prototype.hasOwnProperty.call(value,k)){v=walk(value,k);if(v!==undefined){value[k]=v}else{delete value[k]}}}}return reviver.call(holder,key,value)}text=String(text);cx.lastIndex=0;if(cx.test(text)){text=text.replace(cx,function(a){return"\\u"+("0000"+a.charCodeAt(0).toString(16)).slice(-4)})}if(/^[\],:{}\s]*$/.test(text.replace(/\\(?:["\\\/bfnrt]|u[0-9a-fA-F]{4})/g,"@").replace(/"[^"\\\n\r]*"|true|false|null|-?\d+(?:\.\d*)?(?:[eE][+\-]?\d+)?/g,"]").replace(/(?:^|:|,)(?:\s*\[)+/g,""))){j=eval("("+text+")");return typeof reviver==="function"?walk({"":j},""):j}throw new SyntaxError("JSON.parse")}}}()); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Fix a typo in the sample tool_conf.xml, thanks Marina Gourtovaia.
by Bitbucket 06 May '11

06 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9f6a7491fae8/ changeset: r5505:9f6a7491fae8 user: natefoo date: 2011-05-06 18:09:58 summary: Fix a typo in the sample tool_conf.xml, thanks Marina Gourtovaia. affected #: 1 file (1 byte) --- a/tool_conf.xml.sample Fri May 06 11:49:02 2011 -0400 +++ b/tool_conf.xml.sample Fri May 06 12:09:58 2011 -0400 @@ -319,7 +319,7 @@ <section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /><tool file="indels/indel_sam2interval.xml" /> - <tool file="indels/indel_table.xml" />" + <tool file="indels/indel_table.xml" /><tool file="indels/indel_analysis.xml" /></section><section name="NGS: RNA Analysis" id="ngs-rna-tools"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Standardize naming of reserved/predefined values in the param_dict. Old values are maintaned as well.
by Bitbucket 06 May '11

06 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2f2a223f1dde/ changeset: r5504:2f2a223f1dde user: natefoo date: 2011-05-06 17:49:02 summary: Standardize naming of reserved/predefined values in the param_dict. Old values are maintaned as well. affected #: 2 files (156 bytes) --- a/lib/galaxy/jobs/__init__.py Fri May 06 10:28:54 2011 -0400 +++ b/lib/galaxy/jobs/__init__.py Fri May 06 11:49:02 2011 -0400 @@ -352,8 +352,8 @@ else: userId = 'Anonymous' userEmail = 'Anonymous' - incoming['userId'] = userId - incoming['userEmail'] = userEmail + incoming['__user_id__'] = incoming['userId'] = userId + incoming['__user_email__'] = incoming['userEmail'] = userEmail # Build params, done before hook so hook can use param_dict = self.tool.build_param_dict( incoming, inp_data, out_data, self.get_output_fnames(), self.working_directory ) # Certain tools require tasks to be completed prior to job execution --- a/lib/galaxy/tools/__init__.py Fri May 06 10:28:54 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Fri May 06 11:49:02 2011 -0400 @@ -1514,11 +1514,11 @@ param_dict['__new_file_path__'] = os.path.abspath(self.app.config.new_file_path) # The following points to location (xxx.loc) files which are pointers # to locally cached data - param_dict['GALAXY_DATA_INDEX_DIR'] = self.app.config.tool_data_path + param_dict['__tool_data_path__'] = param_dict['GALAXY_DATA_INDEX_DIR'] = self.app.config.tool_data_path # For the upload tool, we need to know the root directory and the # datatypes conf path, so we can load the datatypes registry - param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root ) - param_dict['GALAXY_DATATYPES_CONF_FILE'] = os.path.abspath( self.app.config.datatypes_config ) + param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root ) + param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = os.path.abspath( self.app.config.datatypes_config ) # Return the dictionary of parameters return param_dict Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guru: Commented out 'Wavelet analysis' section from tool_conf.xml.sample - will be reverted once functional tests are written for these tools.
by Bitbucket 06 May '11

06 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/551e6526954a/ changeset: r5503:551e6526954a user: guru date: 2011-05-06 16:28:54 summary: Commented out 'Wavelet analysis' section from tool_conf.xml.sample - will be reverted once functional tests are written for these tools. affected #: 1 file (87 bytes) --- a/tool_conf.xml.sample Thu May 05 19:05:39 2011 -0400 +++ b/tool_conf.xml.sample Fri May 06 10:28:54 2011 -0400 @@ -146,12 +146,15 @@ <label text="GFF" id="gff" /><tool file="stats/count_gff_features.xml" /></section> + <section name="Graph/Display Data" id="plots"><tool file="plotting/histogram2.xml" /><tool file="plotting/scatterplot.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: use GTF metadata to create dynamic filters.
by Bitbucket 05 May '11

05 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4ba34b095a79/ changeset: r5502:4ba34b095a79 user: jgoecks date: 2011-05-06 01:05:39 summary: Trackster: use GTF metadata to create dynamic filters. affected #: 1 file (448 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Thu May 05 16:51:56 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Thu May 05 19:05:39 2011 -0400 @@ -394,6 +394,14 @@ filters = [ { 'name': 'Score', 'type': 'int', 'index': filter_col } ] filter_col += 1 if isinstance( self.original_dataset.datatype, Gtf ): + # Create filters based on dataset metadata. + for name, a_type in self.original_dataset.metadata.attribute_types.items(): + if a_type in [ 'int', 'float' ]: + filters.append( { 'name': name, 'type': a_type, 'index': filter_col } ) + filter_col += 1 + + ''' + # Old code: use first line in dataset to find attributes. for i, line in enumerate( open(self.original_dataset.file_name) ): if not line.startswith('#'): # Look at first line for attributes and types. @@ -411,10 +419,11 @@ filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } ) filter_col += 1 break + ''' elif isinstance( self.original_dataset.datatype, Bed ): # Can filter by score column only. filters = [ { 'name': 'Score', 'type': 'int', 'index': filter_col } ] - + return filters class TabixDataProvider( FilterableMixin, TracksDataProvider ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Enable GFF filter attributes tool to accept arbitrary conditions.
by Bitbucket 05 May '11

05 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/aab333e661a2/ changeset: r5501:aab333e661a2 user: jgoecks date: 2011-05-05 22:51:56 summary: Enable GFF filter attributes tool to accept arbitrary conditions. affected #: 5 files (1.3 KB) --- a/lib/galaxy/datatypes/interval.py Wed May 04 16:45:10 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Thu May 05 16:51:56 2011 -0400 @@ -889,7 +889,7 @@ MetadataElement( name="column_types", default=['str','str','str','int','int','float','str','int','list'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) MetadataElement( name="attributes", default=0, desc="Number of attributes", readonly=True, visible=False, no_value=0 ) - MetadataElement( name="attribute_types", default={}, desc="Attribute types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[] ) + MetadataElement( name="attribute_types", default={}, desc="Attribute types", param=metadata.DictParameter, readonly=True, visible=False, no_value=[] ) def sniff( self, filename ): """ --- a/lib/galaxy/datatypes/metadata.py Wed May 04 16:45:10 2011 -0400 +++ b/lib/galaxy/datatypes/metadata.py Thu May 05 16:51:56 2011 -0400 @@ -358,6 +358,11 @@ def to_string( self, value ): return ",".join( map( str, value ) ) + +class DictParameter( MetadataParameter ): + + def to_string( self, value ): + return simplejson.dumps( value ) class PythonObjectParameter( MetadataParameter ): --- a/tools/filters/gff/gff_filter_by_attribute.py Wed May 04 16:45:10 2011 -0400 +++ b/tools/filters/gff/gff_filter_by_attribute.py Thu May 05 16:51:56 2011 -0400 @@ -5,7 +5,9 @@ # abstracted and leveraged in each filtering tool. from __future__ import division -import sys, re, os.path +import sys +from galaxy import eggs +from galaxy.util.json import to_json_string, from_json_string # Older py compatibility try: @@ -15,6 +17,10 @@ assert sys.version_info[:2] >= ( 2, 4 ) +# +# Helper functions. +# + def get_operands( filter_condition ): # Note that the order of all_operators is important items_to_strip = ['+', '-', '**', '*', '//', '/', '%', '<<', '>>', '&', '|', '^', '~', '<=', '<', '>=', '>', '==', '!=', '<>', ' and ', ' or ', ' not ', ' is ', ' is not ', ' in ', ' not in '] @@ -28,12 +34,31 @@ sys.stderr.write( msg ) sys.exit() +def check_for_executable( text, description='' ): + # Attempt to determine if the condition includes executable stuff and, if so, exit. + secured = dir() + operands = get_operands( text ) + for operand in operands: + try: + check = int( operand ) + except: + if operand in secured: + stop_err( "Illegal value '%s' in %s '%s'" % ( operand, description, text ) ) + +# +# Process inputs. +# + in_fname = sys.argv[1] out_fname = sys.argv[2] -attribute_type = sys.argv[3] -attribute_name = sys.argv[4] -cond_text = sys.argv[5] +cond_text = sys.argv[3] +attribute_types = from_json_string( sys.argv[4] ) +# Convert types from str to type objects. +for name, a_type in attribute_types.items(): + check_for_executable(a_type) + attribute_types[ name ] = eval( a_type ) + # Unescape if input has been escaped mapped_str = { '__lt__': '<', @@ -47,26 +72,22 @@ } for key, value in mapped_str.items(): cond_text = cond_text.replace( key, value ) + +# Attempt to determine if the condition includes executable stuff and, if so, exit. +check_for_executable( cond_text, 'condition') + +# Prepare the column variable names and wrappers for column data types. Only +# prepare columns up to largest column in condition. +attrs, type_casts = [], [] +for name, attr_type in attribute_types.items(): + attrs.append( name ) + type_cast = "get_value('%(name)s', attribute_types['%(name)s'], attribute_values)" % ( {'name': name} ) + type_casts.append( type_cast ) -# Condition text is 'attribute meets condition.' -cond_text = attribute_name + cond_text +attr_str = ', '.join( attrs ) # 'c1, c2, c3, c4' +type_cast_str = ', '.join( type_casts ) # 'str(c1), int(c2), int(c3), str(c4)' +wrap = "%s = %s" % ( attr_str, type_cast_str ) -# Attempt to determine if the condition includes executable stuff and, if so, exit -secured = dir() -operands = get_operands(cond_text) -for operand in operands: - try: - check = int( operand ) - except: - if operand in secured: - stop_err( "Illegal value '%s' in condition '%s'" % ( operand, cond_text ) ) - -# Set up assignment. -assignment = "%s = attributes.get('%s', None)" % ( attribute_name, attribute_name ) - -# Set up type casting based on attribute type. -type_cast = "%s = %s(%s)" % ( attribute_name, attribute_type, attribute_name) - # Stats skipped_lines = 0 first_invalid_line = 0 @@ -74,6 +95,13 @@ lines_kept = 0 total_lines = 0 out = open( out_fname, 'wt' ) + +# Helper function to safely get and type cast a value in a dict. +def get_value(name, a_type, values_dict): + if name in values_dict: + return (a_type)(values_dict[ name ]) + else: + return None # Read and filter input file, skipping invalid lines code = ''' @@ -87,34 +115,30 @@ invalid_line = line continue try: - # GTF format: chrom source, name, chromStart, chromEnd, score, strand, frame, attributes. - # Attributes format: name1 "value1" ; name2 "value2" ; ... + # Place attribute values into variables with attribute + # name; type casting is done as well. elems = line.split( '\t' ) - attributes_list = elems[8].split(";") - attributes = {} - for name_value_pair in attributes_list: + attribute_values = {} + for name_value_pair in elems[8].split(";"): pair = name_value_pair.strip().split(" ") if pair == '': continue name = pair[0].strip() if name == '': continue - # Need to strip double quote from values - value = pair[1].strip(" \\"") - attributes[name] = value + # Need to strip double quote from value and typecast. + attribute_values[name] = pair[1].strip(" \\"") %s if %s: - %s - if %s: - lines_kept += 1 - print >> out, line + lines_kept += 1 + print >> out, line except Exception, e: + print e skipped_lines += 1 if not invalid_line: first_invalid_line = i + 1 invalid_line = line -''' % ( assignment, attribute_name, type_cast, cond_text ) - +''' % ( wrap, cond_text ) valid_filter = True try: --- a/tools/filters/gff/gff_filter_by_attribute.xml Wed May 04 16:45:10 2011 -0400 +++ b/tools/filters/gff/gff_filter_by_attribute.xml Thu May 05 16:51:56 2011 -0400 @@ -1,23 +1,11 @@ <tool id="gff_filter_by_attribute" name="Filter GFF data by attribute" version="0.1"><description>using simple expressions</description><command interpreter="python"> - gff_filter_by_attribute.py $input $out_file1 "$attribute_type" "$attribute_name" "$cond" + gff_filter_by_attribute.py $input $out_file1 "$cond" '${input.metadata.attribute_types}' </command><inputs><param format="gff" name="input" type="data" label="Filter" help="Dataset missing? See TIP below."/> - <param name="attribute_name" type="select" label="Attribute name" help=""> - <options from_dataset="input"> - <column name="name" index="8"/> - <column name="value" index="8"/> - <filter type="attribute_value_splitter" pair_separator=";" column="8"/> - </options> - </param> - <param name="attribute_type" type="select" label="Attribute type"> - <option value="float">Float</option> - <option value="int">Integer</option> - <option value="str">String</option> - </param> - <param name="cond" size="40" type="text" value=">0" label="With following condition" help="Double equal signs, ==, must be used as shown above. To filter for an arbitrary string, use the Select tool."> + <param name="cond" size="40" type="text" value="gene_id=='uc002loc.1'" label="With following condition" help="Double equal signs, ==, must be used as shown above. To filter for an arbitrary string, use the Select tool."><validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/></param></inputs> @@ -27,11 +15,14 @@ <tests><test><param name="input" value="gff_filter_attr_in1.gff"/> - <param name="attribute_name" value="conf_lo"/> - <param name="attribute_type" value="float"/> - <param name="cond" value=">0"/> + <param name="cond" value="conf_lo>0"/><output name="out_file1" file="gff_filter_by_attribute_out1.gff"/></test> + <test> + <param name="input" value="gff_filter_attr_in1.gff"/> + <param name="cond" value="conf_lo==0 or conf_hi>125"/> + <output name="out_file1" file="gff_filter_by_attribute_out2.gff"/> + </test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Add metadata for GTF attribute values.
by Bitbucket 04 May '11

04 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0921bff6e81a/ changeset: r5500:0921bff6e81a user: jgoecks date: 2011-05-04 22:45:10 summary: Add metadata for GTF attribute values. affected #: 1 file (2.0 KB) --- a/lib/galaxy/datatypes/interval.py Wed May 04 10:20:54 2011 -0400 +++ b/lib/galaxy/datatypes/interval.py Wed May 04 16:45:10 2011 -0400 @@ -5,17 +5,17 @@ import pkg_resources pkg_resources.require( "bx-python" ) -import logging, os, sys, time, tempfile, shutil +import logging, os, sys, tempfile import data from galaxy import util from galaxy.datatypes.sniff import * from galaxy.web import url_for -from cgi import escape import urllib from bx.intervals.io import * from galaxy.datatypes import metadata from galaxy.datatypes.metadata import MetadataElement from galaxy.datatypes.tabular import Tabular +from galaxy.datatypes.util.gff_util import parse_gff_attributes import math log = logging.getLogger(__name__) @@ -888,6 +888,8 @@ MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False ) MetadataElement( name="column_types", default=['str','str','str','int','int','float','str','int','list'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) + MetadataElement( name="attributes", default=0, desc="Number of attributes", readonly=True, visible=False, no_value=0 ) + MetadataElement( name="attribute_types", default={}, desc="Attribute types", param=metadata.ColumnTypesParameter, readonly=True, visible=False, no_value=[] ) def sniff( self, filename ): """ @@ -960,6 +962,42 @@ return True except: return False + + def set_meta( self, dataset, overwrite = True, **kwd ): + # Use first N lines to set metadata for dataset attributes. Attributes + # not found in the first N lines will not have metadata. + num_lines = 200 + attribute_types = {} + for i, line in enumerate( file ( dataset.file_name ) ): + if line and not line.startswith( '#' ): + elems = line.split( '\t' ) + if len( elems ) == 9: + try: + # Loop through attributes to set types. + for name, value in parse_gff_attributes( elems[8] ).items(): + # Default type is string. + value_type = "str" + try: + # Try int. + int( value ) + value_type = "int" + except: + try: + # Try float. + float( value ) + value_type = "float" + except: + pass + attribute_types[ name ] = value_type + except: + pass + if i + 1 == num_lines: + break + + # Set attribute metadata and then set additional metadata. + dataset.metadata.attribute_types = attribute_types + dataset.metadata.attributes = len( attribute_types ) + Gff.set_meta( self, dataset, overwrite = overwrite, skip = i ) class Wiggle( Tabular, _RemoteCallMixin ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Trackster: enable a tool to be run on complete dataset or a visible region.
by Bitbucket 04 May '11

04 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0eb5a2521d11/ changeset: r5499:0eb5a2521d11 user: jgoecks date: 2011-05-04 16:20:54 summary: Trackster: enable a tool to be run on complete dataset or a visible region. affected #: 3 files (2.0 KB) --- a/lib/galaxy/web/controllers/tracks.py Tue May 03 11:35:21 2011 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Wed May 04 10:20:54 2011 -0400 @@ -645,16 +645,17 @@ return self.tracks_grid( trans, **kwargs ) @web.expose - def run_tool( self, trans, dataset_id, chrom, low, high, tool_id, **kwargs ): + def run_tool( self, trans, dataset_id, tool_id, chrom=None, low=None, high=None, **kwargs ): """ Run a tool on a subset of input data to produce a new output dataset that corresponds to a dataset that a user is currently viewing. """ - # Parameter checks. - if not chrom or not low or not high: - return messages.NO_DATA - low, high = int( low ), int( high ) + # Run tool on region if region is specificied. + run_on_region = False + if chrom and low and high: + run_on_region = True + low, high = int( low ), int( high ) # Dataset check. original_dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) @@ -678,27 +679,23 @@ tool_params = tool.params_from_strings( tool_params, self.app ) # - # Convert input datasets so that region of dataset can be quickly - # extracted. - # TODO: Is it useful/necessary to create data subsets for all input - # datasets or only the original dataset (aka the dataset that the user - # is viewing)? Currently we create data subsets for all input datasets - # because this provides the best performance as the tool runs on small - # datasets. + # If running tool on region, convert input datasets (create indices) so + # that can regions of data can be quickly extracted. # messages_list = [] - for jida in original_job.input_datasets: - input_dataset = jida.dataset - # TODO: put together more robust way to determine if a dataset can be indexed. - if hasattr( input_dataset, 'get_track_type' ): - # Can index dataset. - track_type, data_sources = input_dataset.datatype.get_track_type() - # Convert to datasource that provides 'data' because we need to - # extract the original data. - data_source = data_sources[ 'data' ] - msg = self._convert_dataset( trans, input_dataset, data_source ) - if msg is not None: - messages_list.append( msg ) + if run_on_region: + for jida in original_job.input_datasets: + input_dataset = jida.dataset + # TODO: put together more robust way to determine if a dataset can be indexed. + if hasattr( input_dataset, 'get_track_type' ): + # Can index dataset. + track_type, data_sources = input_dataset.datatype.get_track_type() + # Convert to datasource that provides 'data' because we need to + # extract the original data. + data_source = data_sources[ 'data' ] + msg = self._convert_dataset( trans, input_dataset, data_source ) + if msg is not None: + messages_list.append( msg ) # Return any messages generated during conversions. return_message = _get_highest_priority_msg( messages_list ) @@ -706,41 +703,40 @@ return return_message # - # Set input datasets for tool. Input datasets are subsets of full - # datasets and are based on chrom, low, high. + # Set target history (the history that tool will use for inputs/outputs). + # If user owns dataset, put new data in original dataset's history; if + # user does not own dataset (and hence is accessing dataset via sharing), + # put new data in user's current history. # - - # If user is rerunning own tool, put new data in original dataset's - # history. If another user is running tool, put new data in current - # history. if original_dataset.history.user == trans.user: - working_history = original_dataset.history + target_history = original_dataset.history else: - working_history = trans.get_history( create=True ) - hda_permissions = trans.app.security_agent.history_get_default_permissions( working_history ) - messages_list = [] + target_history = trans.get_history( create=True ) + hda_permissions = trans.app.security_agent.history_get_default_permissions( target_history ) + + # + # Set input datasets for tool. If running on region, extract and use subset + # when possible. + # for jida in original_job.input_datasets: input_dataset = jida.dataset - if hasattr( input_dataset.datatype, 'get_track_type' ): - # - # Dataset can be indexed and hence a subset can be extracted. - # + if run_on_region and hasattr( input_dataset.datatype, 'get_track_type' ): + # Dataset is indexed and hence a subset can be extracted and used + # as input. track_type, data_sources = input_dataset.datatype.get_track_type() data_source = data_sources[ 'data' ] converted_dataset = input_dataset.get_converted_dataset( trans, data_source ) deps = input_dataset.get_converted_dataset_deps( trans, data_source ) - # # Create new HDA for input dataset's subset. - # new_dataset = trans.app.model.HistoryDatasetAssociation( extension=input_dataset.ext, \ - dbkey=input_dataset.dbkey, \ - create_dataset=True, \ - sa_session=trans.sa_session, - name="Subset [%s:%i-%i] of data %i" % \ - ( chrom, low, high, input_dataset.hid ), - visible=False ) - working_history.add_dataset( new_dataset ) + dbkey=input_dataset.dbkey, \ + create_dataset=True, \ + sa_session=trans.sa_session, + name="Subset [%s:%i-%i] of data %i" % \ + ( chrom, low, high, input_dataset.hid ), + visible=False ) + target_history.add_dataset( new_dataset ) trans.sa_session.add( new_dataset ) trans.app.security_agent.set_all_dataset_permissions( new_dataset.dataset, hda_permissions ) @@ -751,7 +747,7 @@ dependencies=deps ) data_provider.write_data_to_file( chrom, low, high, new_dataset.file_name ) - # TODO: size not working. + # TODO: (a) size not working; (b) need to set peek. new_dataset.set_size() new_dataset.info = "Data subset for trackster" new_dataset.set_dataset_state( trans.app.model.Dataset.states.OK ) @@ -761,18 +757,21 @@ tool_params[ jida.name ] = new_dataset # - # Start tool and handle outputs. + # Execute tool and handle outputs. # try: - subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=working_history ) + subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=target_history ) except Exception, e: # Lots of things can go wrong when trying to execute tool. return to_json_string( { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } ) - for output in subset_job_outputs.values(): - output.visible = False - trans.sa_session.flush() - + if run_on_region: + for output in subset_job_outputs.values(): + output.visible = False + trans.sa_session.flush() + + # # Return new track that corresponds to the original dataset. + # output_name = None for joda in original_job.output_datasets: if joda.dataset == original_dataset: @@ -784,9 +783,9 @@ return self.add_track_async( trans, output_dataset.id ) - # + # ----------------- # Helper methods. - # + # ----------------- def _check_dataset_state( self, trans, dataset ): """ --- a/static/scripts/packed/trackster.js Tue May 03 11:35:21 2011 -0400 +++ b/static/scripts/packed/trackster.js Wed May 04 10:20:54 2011 -0400 @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,T){var o=f("class").extend,q=f("slotting"),I=f("painters");var Z=function(aa,ab){this.document=aa;this.default_font=ab!==undefined?ab:"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")};o(Z.prototype,{load_pattern:function(aa,ae){var ab=this.patterns,ac=this.dummy_context,ad=new Image();ad.src=image_path+ae;ad.onload=function(){ab[aa]=ac.createPattern(ad,"repeat")}},get_pattern:function(aa){return this.patterns[aa]},new_canvas:function(){var aa=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(aa)}aa.manager=this;return aa}});var C=function(aa,ab){aa.bind("drag",{handle:ab,relative:true},function(af,ag){var ae=$(this).parent();var ad=ae.children();var ac;for(ac=0;ac<ad.length;ac++){if(ag.offsetY<$(ad.get(ac)).position().top){break}}if(ac===ad.length){if(this!==ad.get(ac-1)){ae.append(this)}}else{if(this!==ad.get(ac)){$(this).insertBefore(ad.get(ac))}}})};T.sortable=C;var h=function(ac,aa){var ab=aa-ac;return(ab<=2?0.01:(ab<=100?1:(ab<=1000?5:10)))};var D=9,A=10,O=D+2,x=100,F=12000,M=200,t=10,H=5000,u=100,n="There was an error in indexing this dataset. ",G="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",B="No data for this chrom/contig.",r="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",d=10,s=5,z=5;function v(aa){return Math.round(aa*1000)/1000}var c=function(aa){this.num_elements=aa;this.clear()};o(c.prototype,{get:function(ab){var aa=this.key_ary.indexOf(ab);if(aa!==-1){this.move_key_to_end(ab,aa)}return this.obj_cache[ab]},set:function(ab,ac){if(!this.obj_cache[ab]){if(this.key_ary.length>=this.num_elements){var aa=this.key_ary.shift();delete this.obj_cache[aa]}this.key_ary.push(ab)}this.obj_cache[ab]=ac;return ac},move_key_to_end:function(ab,aa){this.key_ary.splice(aa,1);this.key_ary.push(ab)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var N=function(ab,aa,ac){c.call(this,ab);this.track=aa;this.subset=(ac!==undefined?ac:true)};o(N.prototype,c.prototype,{load_data:function(ai,aj,ae,ah,ab,ag){var 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Y=function(aa,ad,ac,ab,ae){this.container=aa;this.chrom=null;this.vis_id=ac;this.dbkey=ab;this.title=ad;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ae);this.canvas_manager=new Z(aa.get(0).ownerDocument);this.reset()};o(Y.prototype,{init:function(ad){var ac=this.container,aa=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ac);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ac);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ac);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown below").hide();this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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=$("<a href='javascript:void(0);'>Close Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ab=function(ae){if(ae.type==="focusout"||(ae.keyCode||ae.which)===13||(ae.keyCode||ae.which)===27){if((ae.keyCode||ae.which)!==27){aa.go_to($(this).val())}$(this).hide();$(this).val("");aa.location_span.show();aa.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ab).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){aa.location_span.hide();aa.chrom_select.hide();aa.nav_input.val(aa.chrom+":"+aa.low+"-"+aa.high);aa.nav_input.css("display","inline-block");aa.nav_input.select();aa.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){aa.zoom_out();aa.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){aa.zoom_in();aa.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ad);this.chrom_select.bind("change",function(){aa.change_chrom(aa.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ae){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ae){aa.zoom_in(ae.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ae,af){this.current_x=af.offsetX}).bind("drag",function(ae,ag){var ah=ag.offsetX-this.current_x;this.current_x=ag.offsetX;var af=Math.round(ah/aa.viewport_container.width()*(aa.max_high-aa.max_low));aa.move_delta(-af)});this.overview_close.bind("click",function(){for(var af=0,ae=aa.tracks.length;af<ae;af++){aa.tracks[af].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",aa.overview_box.height());aa.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ae,af){if(ae.clientX>aa.viewport_container.width()-16){return false}}).bind("dragstart",function(ae,af){af.original_low=aa.low;af.current_height=ae.clientY;af.current_x=af.offsetX}).bind("drag",function(ag,ai){var ae=$(this);var aj=ai.offsetX-ai.current_x;var af=ae.scrollTop()-(ag.clientY-ai.current_height);ae.scrollTop(af);ai.current_height=ag.clientY;ai.current_x=ai.offsetX;var ah=Math.round(aj/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}).bind("mousewheel",function(ag,ai,af,ae){if(af){var ah=Math.round(-af/aa.viewport_container.width()*(aa.high-aa.low));aa.move_delta(ah)}});this.top_labeltrack.bind("dragstart",function(ae,af){return $("<div />").css({height:aa.content_div.height()+aa.top_labeltrack.height()+aa.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ai,aj){$(aj.proxy).css({left:Math.min(ai.pageX,aj.startX),width:Math.abs(ai.pageX-aj.startX)});var af=Math.min(ai.pageX,aj.startX)-aa.container.offset().left,ae=Math.max(ai.pageX,aj.startX)-aa.container.offset().left,ah=(aa.high-aa.low),ag=aa.viewport_container.width();aa.update_location(Math.round(af/ag*ah)+aa.low,Math.round(ae/ag*ah)+aa.low)}).bind("dragend",function(aj,ak){var af=Math.min(aj.pageX,ak.startX),ae=Math.max(aj.pageX,ak.startX),ah=(aa.high-aa.low),ag=aa.viewport_container.width(),ai=aa.low;aa.low=Math.round(af/ag*ah)+ai;aa.high=Math.round(ae/ag*ah)+ai;$(ak.proxy).remove();aa.redraw()});this.add_label_track(new X(this,this.top_labeltrack));this.add_label_track(new X(this,this.nav_labeltrack));$(window).bind("resize",function(){aa.resize_window()});$(document).bind("redraw",function(){aa.redraw()});this.reset();$(window).trigger("resize")},update_location:function(aa,ab){this.location_span.text(commatize(aa)+" - "+commatize(ab));this.nav_input.val(this.chrom+":"+commatize(aa)+"-"+commatize(ab))},load_chroms:function(ab,ac){ab.num=u;$.extend(ab,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var aa=this;$.ajax({url:chrom_url,data:ab,dataType:"json",success:function(ae){if(ae.chrom_info.length===0){alert("Invalid chromosome: "+ab.chrom);return}if(ae.reference){aa.add_label_track(new y(aa))}aa.chrom_data=ae.chrom_info;var ah='<option value="">Select Chrom/Contig</option>';for(var ag=0,ad=aa.chrom_data.length;ag<ad;ag++){var af=aa.chrom_data[ag].chrom;ah+='<option value="'+af+'">'+af+"</option>"}if(ae.prev_chroms){ah+='<option value="previous">Previous '+u+"</option>"}if(ae.next_chroms){ah+='<option value="next">Next '+u+"</option>"}aa.chrom_select.html(ah);if(ac){ac()}aa.chrom_start_index=ae.start_index},error:function(){alert("Could not load chroms for this dbkey:",aa.dbkey)}})},change_chrom:function(ae,ab,ag){if(!ae||ae==="None"){return}var ad=this;if(ae==="previous"){ad.load_chroms({low:this.chrom_start_index-u});return}if(ae==="next"){ad.load_chroms({low:this.chrom_start_index+u});return}var af=$.grep(ad.chrom_data,function(ai,aj){return ai.chrom===ae})[0];if(af===undefined){ad.load_chroms({chrom:ae},function(){ad.change_chrom(ae,ab,ag)});return}else{if(ae!==ad.chrom){ad.chrom=ae;if(!ad.chrom){ad.intro_div.show()}else{ad.intro_div.hide()}ad.chrom_select.val(ad.chrom);ad.max_high=af.len-1;ad.reset();ad.redraw(true);for(var ah=0,aa=ad.tracks.length;ah<aa;ah++){var ac=ad.tracks[ah];if(ac.init){ac.init()}}}if(ab!==undefined&&ag!==undefined){ad.low=Math.max(ab,0);ad.high=Math.min(ag,ad.max_high)}ad.reset_overview();ad.redraw()}},go_to:function(ae){var ai=this,aa,ad,ab=ae.split(":"),ag=ab[0],ah=ab[1];if(ah!==undefined){try{var af=ah.split("-");aa=parseInt(af[0].replace(/,/g,""),10);ad=parseInt(af[1].replace(/,/g,""),10)}catch(ac){return false}}ai.change_chrom(ag,aa,ad)},move_fraction:function(ac){var aa=this;var ab=aa.high-aa.low;this.move_delta(ac*ab)},move_delta:function(ac){var aa=this;var ab=aa.high-aa.low;if(aa.low-ac<aa.max_low){aa.low=aa.max_low;aa.high=aa.max_low+ab}else{if(aa.high-ac>aa.max_high){aa.high=aa.max_high;aa.low=aa.max_high-ab}else{aa.high-=ac;aa.low-=ac}}aa.redraw()},add_track:function(aa){aa.view=this;aa.track_id=this.track_id_counter;this.tracks.push(aa);if(aa.init){aa.init()}aa.container_div.attr("id","track_"+aa.track_id);C(aa.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(aa){aa.view=this;this.label_tracks.push(aa)},remove_track:function(aa){this.has_changes=true;aa.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(aa)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ah){var ag=this.high-this.low,af=this.low,ab=this.high;if(af<this.max_low){af=this.max_low}if(ab>this.max_high){ab=this.max_high}if(this.high!==0&&ag<this.min_separation){ab=af+this.min_separation}this.low=Math.floor(af);this.high=Math.ceil(ab);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/M)/Math.LN10));this.zoom_res=Math.pow(t,Math.max(0,Math.ceil(Math.log(this.resolution,t)/Math.log(t))));var aa=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ae=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=13;this.overview_box.css({left:aa,width:Math.max(ai,ae)}).show();if(ae<ai){this.overview_box.css("left",aa-(ai-ae)/2)}if(this.overview_highlight){this.overview_highlight.css({left:aa,width:ae})}this.update_location(this.low,this.high);if(!ah){for(var ac=0,ad=this.tracks.length;ac<ad;ac++){if(this.tracks[ac]&&this.tracks[ac].enabled){this.tracks[ac].draw()}}for(ac=0,ad=this.label_tracks.length;ac<ad;ac++){this.label_tracks[ac].draw()}}},zoom_in:function(ab,ac){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ad=this.high-this.low,ae=ad/2+this.low,aa=(ad/this.zoom_factor)/2;if(ab){ae=ab/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ae-aa);this.high=Math.round(ae+aa);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var ab=this.high-this.low,ac=ab/2+this.low,aa=(ab*this.zoom_factor)/2;this.low=Math.round(ac-aa);this.high=Math.round(ac+aa);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var p=function(ab,ae){this.track=ab;this.name=ae.name;this.params=[];var am=ae.params;for(var ac=0;ac<am.length;ac++){var ah=am[ac],aa=ah.name,al=ah.label,ad=unescape(ah.html),aj=ah.type;if(aj==="number"){this.params[this.params.length]=new g(aa,al,ad,ah.min,ah.max)}else{if(aj=="select"){this.params[this.params.length]=new K(aa,al,ad)}else{console.log("WARNING: unrecognized tool parameter type:",aa,aj)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(ao){ao.stopPropagation()}).bind("click",function(ao){ao.stopPropagation()}).bind("dblclick",function(ao){ao.stopPropagation()});var ak=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ai=this.params;var af=this;$.each(this.params,function(ap,at){var ar=$("<div>").addClass("param-row").appendTo(af.parent_div);var ao=$("<div>").addClass("param-label").text(at.label).appendTo(ar);var aq=$("<div/>").addClass("slider").html(at.html).appendTo(ar);$("<div style='clear: both;'/>").appendTo(ar)});this.parent_div.find("input").click(function(){$(this).select()});var an=$("<div>").addClass("slider-row").appendTo(this.parent_div);var ag=$("<input type='submit'>").attr("value","Run").appendTo(an);var af=this;ag.click(function(){af.run()})};o(p.prototype,{get_param_values_dict:function(){var aa={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();aa[ab]=JSON.stringify(ac)});return aa},get_param_values:function(){var ab=[];var aa={};this.parent_div.find(":input").each(function(){var ac=$(this).attr("name"),ad=$(this).val();if(ac){ab[ab.length]=ad}});return ab},run:function(){var ab={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name};$.extend(ab,this.get_param_values_dict());var ad=this.track,ac=ab.tool_id+ad.tool_region_and_parameters_str(ab.chrom,ab.low,ab.high),ae;if(ad.track_type==="FeatureTrack"){ae=new Q(ac,view,ad.hda_ldda,undefined,{},{},ad)}this.track.add_track(ae);ae.content_div.text("Starting job.");var aa=function(){$.getJSON(run_tool_url,ab,function(af){if(af==="no converter"){ae.container_div.addClass("error");ae.content_div.text(G)}else{if(af.error){ae.container_div.addClass("error");ae.content_div.text(w+af.message)}else{if(af==="pending"){ae.container_div.addClass("pending");ae.content_div.text("Converting input data so that it can be easily reused.");setTimeout(aa,2000)}else{ae.dataset_id=af.dataset_id;ae.content_div.text("Running job.");ae.init()}}}})};aa()}});var K=function(ab,aa,ac){this.name=ab;this.label=aa;this.html=ac};var g=function(ac,ab,ae,ad,aa){K.call(this,ac,ab,ae);this.min=ad;this.max=aa};var j=function(ab,aa,ac){this.name=ab;this.index=aa;this.value=ac};var R=function(ab,aa){this.name=ab;this.index=aa;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};o(R.prototype,{applies_to:function(aa){if(aa.length>this.index){return true}return false},keep:function(aa){if(!this.applies_to(aa)){return true}var ab=parseInt(aa[this.index]);return(isNaN(ab)||(ab>=this.low&&ab<=this.high))},update_attrs:function(ab){var aa=false;if(!this.applies_to(ab)){return aa}if(ab[this.index]<this.min){this.min=Math.floor(ab[this.index]);aa=true}if(ab[this.index]>this.max){this.max=Math.ceil(ab[this.index]);aa=true}return aa},update_ui_elt:function(){var ab=this.slider.slider("option","min"),aa=this.slider.slider("option","max");if(this.min<ab||this.max>aa){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",h(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var W=function(ac,ai){this.track=ac;this.filters=[];for(var ae=0;ae<ai.length;ae++){var aa=ai[ae];var ab=aa.name,ah=aa.type,af=aa.index;if(ah==="int"||ah==="float"){this.filters[ae]=new R(ab,af)}else{this.filters[ae]=new j(ab,af,ah)}}var ag=function(aj,ak,al){aj.click(function(){var am=ak.text();max=parseFloat(al.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(al.slider("option","values")){input_size=2*input_size+1;multi_value=true}ak.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",am).appendTo(ak).focus().select().click(function(an){an.stopPropagation()}).blur(function(){$(this).remove();ak.text(am)}).keyup(function(ar){if(ar.keyCode===27){$(this).trigger("blur")}else{if(ar.keyCode===13){var ap=al.slider("option","min"),an=al.slider("option","max"),aq=function(at){return(isNaN(at)||at>an||at<ap)},ao=$(this).val();if(!multi_value){ao=parseFloat(ao);if(aq(ao)){alert("Parameter value must be in the range ["+ap+"-"+an+"]");return $(this)}}else{ao=ao.split("-");ao=[parseFloat(ao[0]),parseFloat(ao[1])];if(aq(ao[0])||aq(ao[1])){alert("Parameter value must be in the range ["+ap+"-"+an+"]");return $(this)}}al.slider((multi_value?"values":"value"),ao)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(aj){aj.stopPropagation()}).bind("click",function(aj){aj.stopPropagation()}).bind("dblclick",function(aj){aj.stopPropagation()});var ad=this;$.each(this.filters,function(ap,ak){var am=$("<div/>").addClass("slider-row").appendTo(ad.parent_div);var aj=$("<div/>").addClass("slider-label").appendTo(am);var ar=$("<span/>").addClass("slider-name").text(ak.name+" ").appendTo(aj);var al=$("<span/>");var an=$("<span/>").addClass("slider-value").appendTo(aj).append("[").append(al).append("]");var aq=$("<div/>").addClass("slider").appendTo(am);ak.control_element=$("<div/>").attr("id",ak.name+"-filter-control").appendTo(aq);var ao=[0,0];ak.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(at,au){ao=au.values;al.text(au.values[0]+"-"+au.values[1]);setTimeout(function(){if(au.values[0]==ao[0]&&au.values[1]==ao[1]){var av=au.values;al.text(av[0]+"-"+av[1]);ak.low=av[0];ak.high=av[1];ad.track.draw(true,true)}},50)},change:function(at,au){ak.control_element.slider("option","slide").call(ak.control_element,at,au)}});ak.slider=ak.control_element;ak.slider_label=al;ag(an,al,ak.control_element);$("<div style='clear: both;'/>").appendTo(am)})};var V=function(aa){this.track=aa.track;this.params=aa.params;this.values={};if(aa.saved_values){this.restore_values(aa.saved_values)}this.onchange=aa.onchange};o(V.prototype,{restore_values:function(aa){var ab=this;$.each(this.params,function(ac,ad){if(aa[ad.key]!==undefined){ab.values[ad.key]=aa[ad.key]}else{ab.values[ad.key]=ad.default_value}})},build_form:function(){var ab=this;var aa=$("<div />");$.each(this.params,function(af,ad){if(!ad.hidden){var ac="param_"+af;var ak=$("<div class='form-row' />").appendTo(aa);ak.append($("<label />").attr("for",ac).text(ad.label+":"));if(ad.type==="bool"){ak.append($('<input type="checkbox" />').attr("id",ac).attr("name",ac).attr("checked",ab.values[ad.key]))}else{if(ad.type==="color"){var ah=ab.values[ad.key];var ag=$("<input />").attr("id",ac).attr("name",ac).val(ah);var ai=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ae=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ai);var aj=$("<div/>").appendTo(ae).farbtastic({width:100,height:100,callback:ag,color:ah});$("<div />").append(ag).append(ai).appendTo(ak).bind("click",function(al){ai.css({left:$(this).position().left+($(ag).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ai.hide();$(document).unbind("click.color-picker")});al.stopPropagation()})}else{ak.append($("<input />").attr("id",ac).attr("name",ac).val(ab.values[ad.key]))}}}});return aa},update_from_form:function(aa){var ac=this;var ab=false;$.each(this.params,function(ad,af){if(!af.hidden){var ag="param_"+ad;var ae=aa.find("#"+ag).val();if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae)}else{if(af.type==="bool"){ae=aa.find("#"+ag).is(":checked")}}}if(ae!==ac.values[af.key]){ac.values[af.key]=ae;ab=true}}});if(ab){this.onchange()}}});var b=function(ac,ab,aa){this.index=ac;this.resolution=ab;this.canvas=$("<div class='track-tile'/>").append(aa)};var m=function(ac,ab,aa,ad){b.call(this,ac,ab,aa);this.max_val=ad};var L=function(ac,ab,aa){b.call(this,ac,ab,aa)};var k=function(ab,aa,ae,ac,ad){this.name=ab;this.view=aa;this.parent_element=ae;this.data_url=(ac?ac:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ad?ad:H);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};o(k.prototype,{init:function(){var aa=this;aa.enabled=false;aa.tile_cache.clear();aa.data_cache.clear();aa.initial_canvas=undefined;aa.content_div.css("height","auto");aa.container_div.removeClass("nodata error pending");if(!aa.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id,chrom:aa.view.chrom},function(ab){if(!ab||ab==="error"||ab.kind==="error"){aa.container_div.addClass("error");aa.content_div.text(n);if(ab.message){var ad=aa.view.tracks.indexOf(aa);var ac=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+ab.message+"</pre>",{Close:hide_modal})});aa.content_div.append(ac)}}else{if(ab==="no converter"){aa.container_div.addClass("error");aa.content_div.text(G)}else{if(ab==="no data"||(ab.data!==undefined&&(ab.data===null||ab.data.length===0))){aa.container_div.addClass("nodata");aa.content_div.text(B)}else{if(ab==="pending"){aa.container_div.addClass("pending");aa.content_div.text(r);setTimeout(function(){aa.init()},aa.data_query_wait)}else{if(ab.status==="data"){if(ab.valid_chroms){aa.valid_chroms=ab.valid_chroms;aa.make_name_popup_menu()}aa.content_div.text(U);if(aa.view.chrom){aa.content_div.text("");aa.content_div.css("height",aa.height_px+"px");aa.enabled=true;$.when(aa.predraw_init()).done(function(){aa.container_div.removeClass("nodata error pending");aa.draw()})}}}}}}})},predraw_init:function(){},update_name:function(aa){this.old_name=this.name;this.name=aa;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var J=function(ai,ag,aj){var ab=this,ak=ab.view;this.filters_manager=(ai!==undefined?new W(this,ai):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(ag!==undefined&&obj_length(ag)>0?new p(this,ag):undefined);this.parent_track=aj;this.child_tracks=[];if(ab.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}ab.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();ab.container_div.append(ab.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ab.display_modes!==undefined){if(ab.mode_div===undefined){ab.mode_div=$("<div class='right-float menubutton popup' />").appendTo(ab.header_div);var ad=(ab.track_config&&ab.track_config.values.mode?ab.track_config.values.mode:ab.display_modes[0]);ab.mode=ad;ab.mode_div.text(ad);var ac=function(al){ab.mode_div.text(al);ab.mode=al;ab.track_config.values.mode=al;ab.tile_cache.clear();ab.draw()};var aa={};for(var ae=0,ah=ab.display_modes.length;ae<ah;ae++){var af=ab.display_modes[ae];aa[af]=function(al){return function(){ac(al)}}(af)}make_popupmenu(ab.mode_div,aa)}else{ab.mode_div.hide()}}this.make_name_popup_menu()};o(J.prototype,k.prototype,{make_name_popup_menu:function(){var ab=this;var aa={};aa["Edit configuration"]=function(){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ab.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure Track",ab.track_config.build_form(),{Cancel:ah,OK:af})};if(ab.filters_available>0){var ae=(ab.filters_div.is(":visible")?"Hide filters":"Show filters");aa[ae]=function(){ab.filters_visible=(ab.filters_div.is(":visible"));ab.filters_div.toggle();ab.make_name_popup_menu()}}if(ab.tool){var ae=(ab.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");aa[ae]=function(){if(!ab.dynamic_tool_div.is(":visible")){ab.update_name(ab.name+ab.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ab.revert_name()}ab.dynamic_tool_div.toggle();ab.make_name_popup_menu()}}if(ab.valid_chroms){aa["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+ab.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ac=view;var ad=function(){$("#no-tracks").show()};if(this.parent_track){ac=this.parent_track;ad=function(){}}aa.Remove=function(){ac.remove_track(ab);if(ac.num_tracks===0){ad()}};make_popupmenu(ab.name_div,aa)},draw:function(aa,ac){var au=this.view.low,ag=this.view.high,ai=ag-au,ak=this.view.container.width(),ae=ak/ai,al=this.view.resolution,ad=$("<div style='position: relative;'></div>"),am=function(aw,ax,av){return aw+"_"+ax+"_"+av};if(!ac){this.content_div.children().remove()}this.content_div.append(ad);this.max_height=0;var ao=Math.floor(au/al/M);var af=[];var ap=0;while((ao*M*al)<ag){var at=am(ak,ae,ao);var ah=this.tile_cache.get(at);var aq=ao*M*this.view.resolution;var ab=aq+M*this.view.resolution;if(!aa&&ah){af[af.length]=ah;this.show_tile(ah,ad,aq,ae)}else{this.delayed_draw(aa,at,ao,al,ad,ae,af)}ao+=1;ap++}var aj=this;var ar=setInterval(function(){if(af.length===ap){clearInterval(ar);if(ac){var ay=aj.content_div.children();var az=false;for(var ax=ay.length-1,aD=0;ax>=aD;ax--){var aw=$(ay[ax]);if(az){aw.remove()}else{if(aw.children().length!==0){az=true}}}}if(aj.track_type=="FeatureTrack"&&aj.mode=="Histogram"){var aC=-1;for(var ax=0;ax<af.length;ax++){var aF=af[ax].max_val;if(aF>aC){aC=aF}}for(var ax=0;ax<af.length;ax++){if(af[ax].max_val!==aC){var aE=af[ax];aE.canvas.remove();aj.delayed_draw(true,am(ak,ae,aE.index),aE.index,aE.resolution,ad,ae,[],{max:aC})}}}if(aj.filters_manager){var av=aj.filters_manager.filters;for(var aB=0;aB<av.length;aB++){av[aB].update_ui_elt()}var aA=false;if(aj.example_feature){for(var aB=0;aB<av.length;aB++){if(av[aB].applies_to(aj.example_feature)){aA=true;break}}}if(aj.filters_available!==aA){aj.filters_available=aA;if(!aj.filters_available){aj.filters_div.hide()}aj.make_name_popup_menu()}}}},50);for(var an=0;an<this.child_tracks.length;an++){this.child_tracks[an].draw(aa,ac)}},delayed_draw:function(ab,ai,ac,ae,aj,am,ak,af){var ad=this,ag=ac*M*ae,al=ag+M*ae;var ah=function(av,an,ap,ao,at,au,aq){var ar=ad.draw_tile(an,ap,ao,au,aq);ad.tile_cache.set(ai,ar);ad.show_tile(ar,at,ag,au);ak[ak.length]=ar};var aa=setTimeout(function(){if(ag<=ad.view.high&&al>=ad.view.low){var an=(ab?undefined:ad.tile_cache.get(ai));if(an){ad.show_tile(an,aj,ag,am);ak[ak.length]=an}else{$.when(ad.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,ad.data_url_extra_params)).then(function(ao){o(ao,af);if(view.reference_track&&am>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,ag,al,ad.mode,ae,view.reference_track.data_url_extra_params)).then(function(ap){ah(aa,ao,ae,ac,aj,am,ap)})}else{ah(aa,ao,ae,ac,aj,am)}})}}},50)},show_tile:function(ad,ag,ae,ah){var ab=this;var ac=this.view.high-this.view.low,af=(ae-this.view.low)*ah;if(this.left_offset){af-=this.left_offset}var aa=ad.canvas;aa.css({position:"absolute",top:0,left:af,height:""});ag.append(aa);ab.max_height=Math.max(ab.max_height,aa.height());ab.content_div.css("height",ab.max_height+"px");ag.children().css("height",ab.max_height+"px")},set_overview:function(){var aa=this.view;if(this.initial_canvas&&this.is_overview){aa.overview_close.show();aa.overview_viewport.append(this.initial_canvas);aa.overview_highlight.show().height(this.initial_canvas.height());aa.overview_viewport.height(this.initial_canvas.height()+aa.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ac,aa,ad){var ab=this,ae=(ac!==undefined&&aa!==undefined&&ad!==undefined?ac+":"+aa+"-"+ad:"all");return" - region=["+ae+"], parameters=["+ab.tool.get_param_values().join(", ")+"]"},add_track:function(aa){aa.track_id=this.track_id+"_"+this.child_tracks.length;aa.container_div.attr("id","track_"+aa.track_id);this.child_tracks_container.append(aa.container_div);C(aa.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(aa);this.view.has_changes=true},remove_track:function(aa){aa.container_div.fadeOut("slow",function(){$(this).remove()})}});var X=function(aa,ab){this.track_type="LabelTrack";this.hidden=true;k.call(this,null,aa,ab);this.container_div.addClass("label-track")};o(X.prototype,k.prototype,{draw:function(){var ac=this.view,ad=ac.high-ac.low,ag=Math.floor(Math.pow(10,Math.floor(Math.log(ad)/Math.log(10)))),aa=Math.floor(ac.low/ag)*ag,ae=this.view.container.width(),ab=$("<div style='position: relative; height: 1.3em;'></div>");while(aa<ac.high){var af=(aa-ac.low)/ad*ae;ab.append($("<div class='label'>"+commatize(aa)+"</div>").css({position:"absolute",left:af-1}));aa+=ag}this.content_div.children(":first").remove();this.content_div.append(ab)}});var y=function(aa){this.track_type="ReferenceTrack";this.hidden=true;k.call(this,null,aa,aa.top_labeltrack);J.call(this);aa.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:aa.dbkey};this.data_cache=new E(z,this,false);this.tile_cache=new c(s)};o(y.prototype,J.prototype,{draw_tile:function(ai,af,ab,ak){var ae=this,ac=M*af;if(ak>this.view.canvas_manager.char_width_px){if(ai===null){ae.content_div.css("height","0px");return}var ad=this.view.canvas_manager.new_canvas();var aj=ad.getContext("2d");ad.width=Math.ceil(ac*ak+ae.left_offset);ad.height=ae.height_px;aj.font=aj.canvas.manager.default_font;aj.textAlign="center";for(var ag=0,ah=ai.length;ag<ah;ag++){var aa=Math.round(ag*ak);aj.fillText(ai[ag],aa+ae.left_offset,10)}return new b(ab,af,ad)}this.content_div.css("height","0px")}});var l=function(ae,ac,af,aa,ad){var ab=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";k.call(this,ae,ac,ac.viewport_container);J.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=af;this.dataset_id=aa;this.original_dataset_id=aa;this.data_cache=new N(z,this);this.tile_cache=new c(s);this.track_config=new V({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:ad,onchange:function(){ab.vertical_range=ab.prefs.max_value-ab.prefs.min_value;$("#linetrack_"+ab.track_id+"_minval").text(ab.prefs.min_value);$("#linetrack_"+ab.track_id+"_maxval").text(ab.prefs.max_value);ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};o(l.prototype,J.prototype,{add_resize_handle:function(){var aa=this;var ad=false;var ac=false;var ab=$("<div class='track-resize'>");$(aa.container_div).hover(function(){ad=true;ab.show()},function(){ad=false;if(!ac){ab.hide()}});ab.hide().bind("dragstart",function(ae,af){ac=true;af.original_height=$(aa.content_div).height()}).bind("drag",function(af,ag){var ae=Math.min(Math.max(ag.original_height+ag.deltaY,aa.min_height_px),aa.max_height_px);$(aa.content_div).css("height",ae);aa.height_px=ae;aa.draw(true)}).bind("dragend",function(ae,af){aa.tile_cache.clear();ac=false;if(!ad){ab.hide()}aa.track_config.values.height=aa.height_px}).appendTo(aa.container_div)},predraw_init:function(){var aa=this,ab=aa.view.tracks.indexOf(aa);aa.vertical_range=undefined;return $.getJSON(aa.data_url,{stats:true,chrom:aa.view.chrom,low:null,high:null,hda_ldda:aa.hda_ldda,dataset_id:aa.dataset_id},function(ac){aa.container_div.addClass("line-track");var ae=ac.data;if(isNaN(parseFloat(aa.prefs.min_value))||isNaN(parseFloat(aa.prefs.max_value))){aa.prefs.min_value=ae.min;aa.prefs.max_value=ae.max;$("#track_"+ab+"_minval").val(aa.prefs.min_value);$("#track_"+ab+"_maxval").val(aa.prefs.max_value)}aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;aa.total_frequency=ae.total_frequency;aa.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_minval").text(v(aa.prefs.min_value));var ad=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ab+"_maxval").text(v(aa.prefs.max_value));ad.css({position:"absolute",top:"24px",left:"10px"});ad.prependTo(aa.container_div);af.css({position:"absolute",bottom:"2px",left:"10px"});af.prependTo(aa.container_div)})},draw_tile:function(ak,ae,ab,aj){if(this.vertical_range===undefined){return}var af=ab*M*ae,ad=M*ae,aa=Math.ceil(ad*aj),ah=this.height_px;var ac=this.view.canvas_manager.new_canvas();ac.width=aa,ac.height=ah;var ai=ac.getContext("2d");var ag=new I.LinePainter(ak.data,af,af+ad,this.prefs,this.mode);ag.draw(ai,aa,ah);return new b(ad,ae,ac)}});var e=function(aa,af,ae,ai,ah,ac,ad,ag){var ab=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ah,onchange:function(){ab.tile_cache.clear();ab.draw()}});this.prefs=this.track_config.values;k.call(this,aa,af,af.viewport_container);J.call(this,ac,ad,ag);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ae;this.dataset_id=ai;this.original_dataset_id=ai;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new N(20,this);this.left_offset=200;this.painter=I.LinkedFeaturePainter};o(e.prototype,J.prototype,{update_auto_mode:function(aa){if(this.mode=="Auto"){if(aa=="no_detail"){aa="feature spans"}else{if(aa=="summary_tree"){aa="coverage histogram"}}this.mode_div.text("Auto ("+aa+")")}},incremental_slots:function(ae,ab,ad){var ac=this.view.canvas_manager.dummy_context,aa=this.inc_slots[ae];if(!aa||(aa.mode!==ad)){aa=new (q.FeatureSlotter)(ae,ad==="Pack",x,function(af){return ac.measureText(af)});aa.mode=ad;this.inc_slots[ae]=aa}return aa.slot_features(ab)},get_summary_tree_data:function(ae,ah,ac,ap){if(ap>ac-ah){ap=ac-ah}var al=Math.floor((ac-ah)/ap),ao=[],ad=0;var af=0,ag=0,ak,an=0,ai=[],am,aj;var ab=function(at,ar,au,aq){at[0]=ar+au*aq;at[1]=ar+(au+1)*aq};while(an<ap&&af!==ae.length){var aa=false;for(;an<ap&&!aa;an++){ab(ai,ah,an,al);for(ag=af;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){aa=true;break}}if(aa){break}}data_start_index=ag;ao[ao.length]=am=[ai[0],0];for(;ag<ae.length;ag++){ak=ae[ag].slice(1,3);if(is_overlap(ak,ai)){am[1]++}else{break}}if(am[1]>ad){ad=am[1]}an++}return{max:ad,delta:al,data:ao}},draw_tile:function(an,aw,aA,aj,ad){var at=this,aC=aA*M*aw,ab=(aA+1)*M*aw,ap=ab-aC,au=Math.ceil(ap*aj),ar=this.mode,aG=25,ae=this.left_offset,ao,af;if(ar==="Auto"){if(an.dataset_type==="summary_tree"){ar=an.dataset_type}else{if(an.extra_info==="no_detail"){ar="no_detail"}else{var aF=an.data;if(this.view.high-this.view.low>F){ar="Squish"}else{ar="Pack"}}}this.update_auto_mode(ar)}if(ar==="summary_tree"||ar==="Histogram"){af=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var aa=$("<div />").addClass("yaxislabel");aa.text(an.max);aa.css({position:"absolute",top:"22px",left:"10px"});aa.prependTo(this.container_div);var ac=this.view.canvas_manager.new_canvas();ac.width=au+ae;ac.height=af+O;if(an.dataset_type!="summary_tree"){var ak=this.get_summary_tree_data(an.data,aC,ab,200);if(an.max){ak.max=an.max}an=ak}var aD=new I.SummaryTreePainter(an,aC,ab,this.prefs);var av=ac.getContext("2d");av.translate(ae,O);aD.draw(av,au,af);return new m(aA,aw,ac,an.max)}var ao,ah=1;if(ar==="no_detail"||ar==="Squish"||ar==="Pack"){ah=this.incremental_slots(aj,an.data,ar);ao=this.inc_slots[aj].slots}var ai=[];if(an.data){var al=this.filters_manager.filters;for(var ax=0,az=an.data.length;ax<az;ax++){var ag=an.data[ax];var ay=false;var am;for(var aB=0,aE=al.length;aB<aE;aB++){am=al[aB];am.update_attrs(ag);if(!am.keep(ag)){ay=true;break}}if(!ay){ai.push(ag)}}}var aD=new (this.painter)(ai,aC,ab,this.prefs,ar,ad);var af=aD.get_required_height(ah)+A;var ac=this.view.canvas_manager.new_canvas();ac.width=au+ae;ac.height=af;var av=ac.getContext("2d");av.fillStyle=this.prefs.block_color;av.font=av.canvas.manager.default_font;av.textAlign="right";this.container_div.find(".yaxislabel").remove();if(an.message){$(ac).css({"border-top":"1px solid red"});av.fillStyle="red";av.textAlign="left";var aq=av.textBaseline;av.textBaseline="top";av.fillText(an.message,ae,0);av.textBaseline=aq;if(!an.data){return new b(aA,aw,ac,af)}}this.example_feature=(an.data.length?an.data[0]:undefined);av.translate(ae,A);aD.draw(av,au,af,ao);return new L(aA,aw,ac)}});var P=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_type="VcfTrack";this.painter=I.VariantPainter};o(P.prototype,J.prototype,e.prototype);var S=function(ad,ab,af,aa,ac,ae){e.call(this,ad,ab,af,aa,ac,ae);this.track_config=new V({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ac,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=I.ReadPainter;this.make_name_popup_menu()};o(S.prototype,J.prototype,e.prototype);var Q=function(ae,ac,ag,aa,ad,af,ab){e.call(this,ae,ac,ag,aa,ad,af,{},ab);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};o(Q.prototype,J.prototype,e.prototype,{predraw_init:function(){var ab=this;var aa=function(){if(ab.data_cache.size()===0){setTimeout(aa,300)}else{ab.data_url=default_data_url;ab.data_query_wait=H;ab.dataset_state_url=converted_datasets_state_url;$.getJSON(ab.dataset_state_url,{dataset_id:ab.dataset_id,hda_ldda:ab.hda_ldda},function(ac){})}};aa()}});T.View=Y;T.LineTrack=l;T.FeatureTrack=e;T.ReadTrack=S};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(j,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=j;this.include_label=h;this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,s=this.slots,h=this.start_end_dct,y=[],A=[],n=0,z=this.max_rows;for(var w=0,x=m.length;w<x;w++){var l=m[w],o=l[0];if(s[o]!==undefined){n=Math.max(n,s[o]);A.push(s[o])}else{y.push(w)}}var q=function(G,H){for(var F=0;F<=z;F++){var D=false,I=h[F];if(I!==undefined){for(var C=0,E=I.length;C<E;C++){var B=I[C];if(H>B[0]&&G<B[1]){D=true;break}}}if(!D){return F}}return -1};for(var w=0,x=y.length;w<x;w++){var l=m[y[w]],o=l[0],u=l[1],f=l[2],r=l[3],g=Math.floor(u*p),k=Math.ceil(f*p),v=this.measureText(r).width,j;if(r!==undefined&&this.include_label){v+=(d+a);if(g-v>=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var 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c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file +var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var trackster_module=function(f,S){var n=f("class").extend,p=f("slotting"),H=f("painters");var Y=function(Z,aa){this.document=Z;this.default_font=aa!==undefined?aa:"9px Monaco, Lucida Console, 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",F="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",A="No data for this chrom/contig.",q="Currently indexing... please wait",v="Tool cannot be rerun: ",a="Loading data...",T="Ready for display",d=10,r=5,y=5;function u(Z){return Math.round(Z*1000)/1000}var c=function(Z){this.num_elements=Z;this.clear()};n(c.prototype,{get:function(aa){var Z=this.key_ary.indexOf(aa);if(Z!==-1){this.move_key_to_end(aa,Z)}return this.obj_cache[aa]},set:function(aa,ab){if(!this.obj_cache[aa]){if(this.key_ary.length>=this.num_elements){var Z=this.key_ary.shift();delete this.obj_cache[Z]}this.key_ary.push(aa)}this.obj_cache[aa]=ab;return ab},move_key_to_end:function(aa,Z){this.key_ary.splice(Z,1);this.key_ary.push(aa)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var M=function(aa,Z,ab){c.call(this,aa);this.track=Z;this.subset=(ab!==undefined?ab:true)};n(M.prototype,c.prototype,{load_data:function(ah,ai,ad,ag,aa,af){var ac={chrom:ah,low:ai,high:ad,mode:ag,resolution:aa,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ac,af);if(this.track.filters_manager){var aj=[];var Z=this.track.filters_manager.filters;for(var ae=0;ae<Z.length;ae++){aj[aj.length]=Z[ae].name}ac.filter_cols=JSON.stringify(aj)}var ab=this;return $.getJSON(this.track.data_url,ac,function(ak){ab.set_data(ai,ad,ag,ak)})},get_data:function(ab,Z,ae,af,aa,ad){var ac=this.get(this.gen_key(Z,ae,af));if(ac){return ac}ac=this.load_data(ab,Z,ae,af,aa,ad);this.set_data(Z,ae,af,ac);return ac},set_data:function(aa,ab,ac,Z){return this.set(this.gen_key(aa,ab,ac),Z)},gen_key:function(Z,ab,ac){var aa=Z+"_"+ab+"_"+ac;return aa},split_key:function(Z){return Z.split("_")}});var D=function(aa,Z,ab){M.call(this,aa,Z,ab)};n(D.prototype,M.prototype,c.prototype,{load_data:function(ab,Z,ad,ae,aa,ac){if(aa>1){return}return M.prototype.load_data.call(this,ab,Z,ad,ae,aa,ac)}});var X=function(Z,ac,ab,aa,ad){this.container=Z;this.chrom=null;this.vis_id=ab;this.dbkey=aa;this.title=ac;this.tracks=[];this.label_tracks=[];this.max_low=0;this.max_high=0;this.num_tracks=0;this.track_id_counter=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.init(ad);this.canvas_manager=new Y(Z.get(0).ownerDocument);this.reset()};n(X.prototype,{init:function(ac){var ab=this.container,Z=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ab);this.content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ab);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ab);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").addClass("viewport-container").appendTo(this.content_div);this.intro_div=$("<div/>").addClass("intro").text("Select a chrom from the dropdown 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Overview</a>").addClass("overview-close").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var aa=function(ad){if(ad.type==="focusout"||(ad.keyCode||ad.which)===13||(ad.keyCode||ad.which)===27){if((ad.keyCode||ad.which)!==27){Z.go_to($(this).val())}$(this).hide();$(this).val("");Z.location_span.show();Z.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",aa).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").appendTo(this.nav_controls);this.location_span.bind("click",function(){Z.location_span.hide();Z.chrom_select.hide();Z.nav_input.val(Z.chrom+":"+Z.low+"-"+Z.high);Z.nav_input.css("display","inline-block");Z.nav_input.select();Z.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a id='zoom-out' />").click(function(){Z.zoom_out();Z.redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a id='zoom-in' />").click(function(){Z.zoom_in();Z.redraw()}).appendTo(this.nav_controls);this.load_chroms({low:0},ac);this.chrom_select.bind("change",function(){Z.change_chrom(Z.chrom_select.val())});this.intro_div.show();this.content_div.bind("click",function(ad){$(this).find("input").trigger("blur")});this.content_div.bind("dblclick",function(ad){Z.zoom_in(ad.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ad,ae){this.current_x=ae.offsetX}).bind("drag",function(ad,af){var ag=af.offsetX-this.current_x;this.current_x=af.offsetX;var ae=Math.round(ag/Z.viewport_container.width()*(Z.max_high-Z.max_low));Z.move_delta(-ae)});this.overview_close.bind("click",function(){for(var ae=0,ad=Z.tracks.length;ae<ad;ae++){Z.tracks[ae].is_overview=false}$(this).siblings().filter("canvas").remove();$(this).parent().css("height",Z.overview_box.height());Z.overview_highlight.hide();$(this).hide()});this.viewport_container.bind("draginit",function(ad,ae){if(ad.clientX>Z.viewport_container.width()-16){return false}}).bind("dragstart",function(ad,ae){ae.original_low=Z.low;ae.current_height=ad.clientY;ae.current_x=ae.offsetX}).bind("drag",function(af,ah){var ad=$(this);var ai=ah.offsetX-ah.current_x;var ae=ad.scrollTop()-(af.clientY-ah.current_height);ad.scrollTop(ae);ah.current_height=af.clientY;ah.current_x=ah.offsetX;var ag=Math.round(ai/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}).bind("mousewheel",function(af,ah,ae,ad){if(ae){var ag=Math.round(-ae/Z.viewport_container.width()*(Z.high-Z.low));Z.move_delta(ag)}});this.top_labeltrack.bind("dragstart",function(ad,ae){return $("<div />").css({height:Z.content_div.height()+Z.top_labeltrack.height()+Z.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ah,ai){$(ai.proxy).css({left:Math.min(ah.pageX,ai.startX),width:Math.abs(ah.pageX-ai.startX)});var ae=Math.min(ah.pageX,ai.startX)-Z.container.offset().left,ad=Math.max(ah.pageX,ai.startX)-Z.container.offset().left,ag=(Z.high-Z.low),af=Z.viewport_container.width();Z.update_location(Math.round(ae/af*ag)+Z.low,Math.round(ad/af*ag)+Z.low)}).bind("dragend",function(ai,aj){var ae=Math.min(ai.pageX,aj.startX),ad=Math.max(ai.pageX,aj.startX),ag=(Z.high-Z.low),af=Z.viewport_container.width(),ah=Z.low;Z.low=Math.round(ae/af*ag)+ah;Z.high=Math.round(ad/af*ag)+ah;$(aj.proxy).remove();Z.redraw()});this.add_label_track(new W(this,this.top_labeltrack));this.add_label_track(new W(this,this.nav_labeltrack));$(window).bind("resize",function(){Z.resize_window()});$(document).bind("redraw",function(){Z.redraw()});this.reset();$(window).trigger("resize")},update_location:function(Z,aa){this.location_span.text(commatize(Z)+" - "+commatize(aa));this.nav_input.val(this.chrom+":"+commatize(Z)+"-"+commatize(aa))},load_chroms:function(aa,ab){aa.num=t;$.extend(aa,(this.vis_id!==undefined?{vis_id:this.vis_id}:{dbkey:this.dbkey}));var Z=this;$.ajax({url:chrom_url,data:aa,dataType:"json",success:function(ad){if(ad.chrom_info.length===0){alert("Invalid chromosome: "+aa.chrom);return}if(ad.reference){Z.add_label_track(new x(Z))}Z.chrom_data=ad.chrom_info;var ag='<option value="">Select Chrom/Contig</option>';for(var af=0,ac=Z.chrom_data.length;af<ac;af++){var ae=Z.chrom_data[af].chrom;ag+='<option value="'+ae+'">'+ae+"</option>"}if(ad.prev_chroms){ag+='<option value="previous">Previous '+t+"</option>"}if(ad.next_chroms){ag+='<option value="next">Next '+t+"</option>"}Z.chrom_select.html(ag);if(ab){ab()}Z.chrom_start_index=ad.start_index},error:function(){alert("Could not load chroms for this dbkey:",Z.dbkey)}})},change_chrom:function(ad,aa,af){if(!ad||ad==="None"){return}var ac=this;if(ad==="previous"){ac.load_chroms({low:this.chrom_start_index-t});return}if(ad==="next"){ac.load_chroms({low:this.chrom_start_index+t});return}var ae=$.grep(ac.chrom_data,function(ah,ai){return ah.chrom===ad})[0];if(ae===undefined){ac.load_chroms({chrom:ad},function(){ac.change_chrom(ad,aa,af)});return}else{if(ad!==ac.chrom){ac.chrom=ad;if(!ac.chrom){ac.intro_div.show()}else{ac.intro_div.hide()}ac.chrom_select.val(ac.chrom);ac.max_high=ae.len-1;ac.reset();ac.redraw(true);for(var ag=0,Z=ac.tracks.length;ag<Z;ag++){var ab=ac.tracks[ag];if(ab.init){ab.init()}}}if(aa!==undefined&&af!==undefined){ac.low=Math.max(aa,0);ac.high=Math.min(af,ac.max_high)}ac.reset_overview();ac.redraw()}},go_to:function(ad){var ah=this,Z,ac,aa=ad.split(":"),af=aa[0],ag=aa[1];if(ag!==undefined){try{var ae=ag.split("-");Z=parseInt(ae[0].replace(/,/g,""),10);ac=parseInt(ae[1].replace(/,/g,""),10)}catch(ab){return false}}ah.change_chrom(af,Z,ac)},move_fraction:function(ab){var Z=this;var aa=Z.high-Z.low;this.move_delta(ab*aa)},move_delta:function(ab){var Z=this;var aa=Z.high-Z.low;if(Z.low-ab<Z.max_low){Z.low=Z.max_low;Z.high=Z.max_low+aa}else{if(Z.high-ab>Z.max_high){Z.high=Z.max_high;Z.low=Z.max_high-aa}else{Z.high-=ab;Z.low-=ab}}Z.redraw()},add_track:function(Z){Z.view=this;Z.track_id=this.track_id_counter;this.tracks.push(Z);if(Z.init){Z.init()}Z.container_div.attr("id","track_"+Z.track_id);B(Z.container_div,".draghandle");this.track_id_counter+=1;this.num_tracks+=1},add_label_track:function(Z){Z.view=this;this.label_tracks.push(Z)},remove_track:function(Z){this.has_changes=true;Z.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(Z)];this.num_tracks-=1},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},redraw:function(ag){var af=this.high-this.low,ae=this.low,aa=this.high;if(ae<this.max_low){ae=this.max_low}if(aa>this.max_high){aa=this.max_high}if(this.high!==0&&af<this.min_separation){aa=ae+this.min_separation}this.low=Math.floor(ae);this.high=Math.ceil(aa);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/L)/Math.LN10));this.zoom_res=Math.pow(s,Math.max(0,Math.ceil(Math.log(this.resolution,s)/Math.log(s))));var Z=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ad=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ah=13;this.overview_box.css({left:Z,width:Math.max(ah,ad)}).show();if(ad<ah){this.overview_box.css("left",Z-(ah-ad)/2)}if(this.overview_highlight){this.overview_highlight.css({left:Z,width:ad})}this.update_location(this.low,this.high);if(!ag){for(var ab=0,ac=this.tracks.length;ab<ac;ab++){if(this.tracks[ab]&&this.tracks[ab].enabled){this.tracks[ab].draw()}}for(ab=0,ac=this.label_tracks.length;ab<ac;ab++){this.label_tracks[ab].draw()}}},zoom_in:function(aa,ab){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ac=this.high-this.low,ad=ac/2+this.low,Z=(ac/this.zoom_factor)/2;if(aa){ad=aa/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ad-Z);this.high=Math.round(ad+Z);this.redraw()},zoom_out:function(){if(this.max_high===0){return}var aa=this.high-this.low,ab=aa/2+this.low,Z=(aa*this.zoom_factor)/2;this.low=Math.round(ab-Z);this.high=Math.round(ab+Z);this.redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.nav_container.width(this.container.width());this.redraw()},reset_overview:function(){this.overview_viewport.find("canvas").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()}});var o=function(ab,af){this.track=ab;this.name=af.name;this.params=[];var am=af.params;for(var ac=0;ac<am.length;ac++){var ah=am[ac],aa=ah.name,al=ah.label,ad=unescape(ah.html),an=ah.value,aj=ah.type;if(aj==="number"){this.params[this.params.length]=new g(aa,al,ad,an,ah.min,ah.max)}else{if(aj=="select"){this.params[this.params.length]=new J(aa,al,ad,an)}else{console.log("WARNING: unrecognized tool parameter 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ag=this;Z.click(function(){ag.run_on_region()});ae.click(function(){ag.run_on_dataset()})};n(o.prototype,{get_param_values_dict:function(){var Z={};this.parent_div.find(":input").each(function(){var aa=$(this).attr("name"),ab=$(this).val();Z[aa]=JSON.stringify(ab)});return Z},get_param_values:function(){var aa=[];var Z={};this.parent_div.find(":input").each(function(){var ab=$(this).attr("name"),ac=$(this).val();if(ab){aa[aa.length]=ac}});return aa},run_on_dataset:function(){var Z=this;Z.run({dataset_id:this.track.original_dataset_id,tool_id:Z.name},function(aa){show_modal(Z.name+" is Running",Z.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var Z={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ab=this.track,aa=Z.tool_id+ab.tool_region_and_parameters_str(Z.chrom,Z.low,Z.high),ac;if(ab.track_type==="FeatureTrack"){ac=new P(aa,view,ab.hda_ldda,undefined,{},{},ab)}this.track.add_track(ac);ac.content_div.text("Starting job.");this.run(Z,function(ad){ac.dataset_id=ad.dataset_id;ac.content_div.text("Running job.");ac.init()})},run:function(aa,ab){$.extend(aa,this.get_param_values_dict());var Z=function(){$.getJSON(run_tool_url,aa,function(ac){if(ac==="no converter"){new_track.container_div.addClass("error");new_track.content_div.text(F)}else{if(ac.error){new_track.container_div.addClass("error");new_track.content_div.text(v+ac.message)}else{if(ac==="pending"){new_track.container_div.addClass("pending");new_track.content_div.text("Converting input data so that it can be easily reused.");setTimeout(Z,2000)}else{ab(ac)}}}})};Z()}});var J=function(aa,Z,ab,ac){this.name=aa;this.label=Z;this.html=ab;this.value=ac};var g=function(ab,aa,ad,ae,ac,Z){J.call(this,ab,aa,ad,ae);this.min=ac;this.max=Z};var h=function(aa,Z,ab){this.name=aa;this.index=Z;this.value=ab};var Q=function(aa,Z){this.name=aa;this.index=Z;this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.slider=null;this.slider_label=null};n(Q.prototype,{applies_to:function(Z){if(Z.length>this.index){return true}return false},keep:function(Z){if(!this.applies_to(Z)){return true}var aa=parseInt(Z[this.index]);return(isNaN(aa)||(aa>=this.low&&aa<=this.high))},update_attrs:function(aa){var Z=false;if(!this.applies_to(aa)){return Z}if(aa[this.index]<this.min){this.min=Math.floor(aa[this.index]);Z=true}if(aa[this.index]>this.max){this.max=Math.ceil(aa[this.index]);Z=true}return Z},update_ui_elt:function(){var ab=function(ae,ac){var ad=ac-ae;return(ad<=2?0.01:1)};var aa=this.slider.slider("option","min"),Z=this.slider.slider("option","max");if(this.min<aa||this.max>Z){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ab(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var V=function(ab,ah){this.track=ab;this.filters=[];for(var ad=0;ad<ah.length;ad++){var Z=ah[ad];var aa=Z.name,ag=Z.type,ae=Z.index;if(ag==="int"||ag==="float"){this.filters[ad]=new Q(aa,ae)}else{this.filters[ad]=new h(aa,ae,ag)}}var af=function(ai,aj,ak){ai.click(function(){var al=aj.text();max=parseFloat(ak.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(ak.slider("option","values")){input_size=2*input_size+1;multi_value=true}aj.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",al).appendTo(aj).focus().select().click(function(am){am.stopPropagation()}).blur(function(){$(this).remove();aj.text(al)}).keyup(function(aq){if(aq.keyCode===27){$(this).trigger("blur")}else{if(aq.keyCode===13){var ao=ak.slider("option","min"),am=ak.slider("option","max"),ap=function(ar){return(isNaN(ar)||ar>am||ar<ao)},an=$(this).val();if(!multi_value){an=parseFloat(an);if(ap(an)){alert("Parameter value must be in the range ["+ao+"-"+am+"]");return $(this)}}else{an=an.split("-");an=[parseFloat(an[0]),parseFloat(an[1])];if(ap(an[0])||ap(an[1])){alert("Parameter value must be in the range ["+ao+"-"+am+"]");return $(this)}}ak.slider((multi_value?"values":"value"),an)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(ai){ai.stopPropagation()}).bind("click",function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).bind("keydown",function(ai){ai.stopPropagation()});var ac=this;$.each(this.filters,function(ao,aj){var al=$("<div/>").addClass("slider-row").appendTo(ac.parent_div);var ai=$("<div/>").addClass("slider-label").appendTo(al);var aq=$("<span/>").addClass("slider-name").text(aj.name+" ").appendTo(ai);var ak=$("<span/>");var am=$("<span/>").addClass("slider-value").appendTo(ai).append("[").append(ak).append("]");var ap=$("<div/>").addClass("slider").appendTo(al);aj.control_element=$("<div/>").attr("id",aj.name+"-filter-control").appendTo(ap);var an=[0,0];aj.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(ar,at){an=at.values;ak.text(at.values[0]+"-"+at.values[1]);setTimeout(function(){if(at.values[0]==an[0]&&at.values[1]==an[1]){var au=at.values;ak.text(au[0]+"-"+au[1]);aj.low=au[0];aj.high=au[1];ac.track.draw(true,true)}},50)},change:function(ar,at){aj.control_element.slider("option","slide").call(aj.control_element,ar,at)}});aj.slider=aj.control_element;aj.slider_label=ak;af(am,ak,aj.control_element);$("<div style='clear: both;'/>").appendTo(al)})};var U=function(Z){this.track=Z.track;this.params=Z.params;this.values={};if(Z.saved_values){this.restore_values(Z.saved_values)}this.onchange=Z.onchange};n(U.prototype,{restore_values:function(Z){var aa=this;$.each(this.params,function(ab,ac){if(Z[ac.key]!==undefined){aa.values[ac.key]=Z[ac.key]}else{aa.values[ac.key]=ac.default_value}})},build_form:function(){var aa=this;var Z=$("<div />");$.each(this.params,function(ae,ac){if(!ac.hidden){var ab="param_"+ae;var aj=$("<div class='form-row' />").appendTo(Z);aj.append($("<label />").attr("for",ab).text(ac.label+":"));if(ac.type==="bool"){aj.append($('<input type="checkbox" />').attr("id",ab).attr("name",ab).attr("checked",aa.values[ac.key]))}else{if(ac.type==="color"){var ag=aa.values[ac.key];var af=$("<input />").attr("id",ab).attr("name",ab).val(ag);var ah=$("<div class='tipsy tipsy-north' style='position: absolute;' />").hide();var ad=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(ah);var ai=$("<div/>").appendTo(ad).farbtastic({width:100,height:100,callback:af,color:ag});$("<div />").append(af).append(ah).appendTo(aj).bind("click",function(ak){ah.css({left:$(this).position().left+($(af).width()/2)-60,top:$(this).position().top+$(this.height)}).show();$(document).bind("click.color-picker",function(){ah.hide();$(document).unbind("click.color-picker")});ak.stopPropagation()})}else{aj.append($("<input />").attr("id",ab).attr("name",ab).val(aa.values[ac.key]))}}}});return Z},update_from_form:function(Z){var ab=this;var aa=false;$.each(this.params,function(ac,ae){if(!ae.hidden){var af="param_"+ac;var ad=Z.find("#"+af).val();if(ae.type==="float"){ad=parseFloat(ad)}else{if(ae.type==="int"){ad=parseInt(ad)}else{if(ae.type==="bool"){ad=Z.find("#"+af).is(":checked")}}}if(ad!==ab.values[ae.key]){ab.values[ae.key]=ad;aa=true}}});if(aa){this.onchange()}}});var b=function(ab,aa,Z){this.index=ab;this.resolution=aa;this.canvas=$("<div class='track-tile'/>").append(Z)};var l=function(ab,aa,Z,ac){b.call(this,ab,aa,Z);this.max_val=ac};var K=function(ab,aa,Z){b.call(this,ab,aa,Z)};var j=function(aa,Z,ad,ab,ac){this.name=aa;this.view=Z;this.parent_element=ad;this.data_url=(ab?ab:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ac?ac:G);this.dataset_check_url=converted_datasets_state_url;this.container_div=$("<div />").addClass("track").css("position","relative");if(!this.hidden){this.header_div=$("<div class='track-header' />").appendTo(this.container_div);if(this.view.editor){this.drag_div=$("<div class='draghandle' />").appendTo(this.header_div)}this.name_div=$("<div class='menubutton popup' />").appendTo(this.header_div);this.name_div.text(this.name);this.name_div.attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase())}this.content_div=$("<div class='track-content'>").appendTo(this.container_div);this.parent_element.append(this.container_div)};n(j.prototype,{init:function(){var Z=this;Z.enabled=false;Z.tile_cache.clear();Z.data_cache.clear();Z.initial_canvas=undefined;Z.content_div.css("height","auto");Z.container_div.removeClass("nodata error pending");if(!Z.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id,chrom:Z.view.chrom},function(aa){if(!aa||aa==="error"||aa.kind==="error"){Z.container_div.addClass("error");Z.content_div.text(m);if(aa.message){var ac=Z.view.tracks.indexOf(Z);var ab=$(" <a href='javascript:void(0);'></a>").text("View error").bind("click",function(){show_modal("Trackster Error","<pre>"+aa.message+"</pre>",{Close:hide_modal})});Z.content_div.append(ab)}}else{if(aa==="no converter"){Z.container_div.addClass("error");Z.content_div.text(F)}else{if(aa==="no data"||(aa.data!==undefined&&(aa.data===null||aa.data.length===0))){Z.container_div.addClass("nodata");Z.content_div.text(A)}else{if(aa==="pending"){Z.container_div.addClass("pending");Z.content_div.text(q);setTimeout(function(){Z.init()},Z.data_query_wait)}else{if(aa.status==="data"){if(aa.valid_chroms){Z.valid_chroms=aa.valid_chroms;Z.make_name_popup_menu()}Z.content_div.text(T);if(Z.view.chrom){Z.content_div.text("");Z.content_div.css("height",Z.height_px+"px");Z.enabled=true;$.when(Z.predraw_init()).done(function(){Z.container_div.removeClass("nodata error pending");Z.draw()})}}}}}}})},predraw_init:function(){},update_name:function(Z){this.old_name=this.name;this.name=Z;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)}});var I=function(ah,af,ai){var aa=this,aj=aa.view;this.filters_manager=(ah!==undefined?new V(this,ah):undefined);this.filters_available=false;this.filters_visible=false;this.tool=(af!==undefined&&obj_length(af)>0?new o(this,af):undefined);this.parent_track=ai;this.child_tracks=[];if(aa.hidden){return}if(this.parent_track){this.header_div.find(".draghandle").removeClass("draghandle").addClass("child-track-icon").addClass("icon-button");this.parent_element.addClass("child-track");this.tool=undefined}aa.child_tracks_container=$("<div/>").addClass("child-tracks-container").hide();aa.container_div.append(aa.child_tracks_container);if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(aa.display_modes!==undefined){if(aa.mode_div===undefined){aa.mode_div=$("<div class='right-float menubutton popup' />").appendTo(aa.header_div);var ac=(aa.track_config&&aa.track_config.values.mode?aa.track_config.values.mode:aa.display_modes[0]);aa.mode=ac;aa.mode_div.text(ac);var ab=function(ak){aa.mode_div.text(ak);aa.mode=ak;aa.track_config.values.mode=ak;aa.tile_cache.clear();aa.draw()};var Z={};for(var ad=0,ag=aa.display_modes.length;ad<ag;ad++){var ae=aa.display_modes[ad];Z[ae]=function(ak){return function(){ab(ak)}}(ae)}make_popupmenu(aa.mode_div,Z)}else{aa.mode_div.hide()}}this.make_name_popup_menu()};n(I.prototype,j.prototype,{make_name_popup_menu:function(){var aa=this;var Z={};Z["Edit configuration"]=function(){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){aa.track_config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure Track",aa.track_config.build_form(),{Cancel:ag,OK:ae})};if(aa.filters_available>0){var ad=(aa.filters_div.is(":visible")?"Hide filters":"Show filters");Z[ad]=function(){aa.filters_visible=(aa.filters_div.is(":visible"));aa.filters_div.toggle();aa.make_name_popup_menu()}}if(aa.tool){var ad=(aa.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");Z[ad]=function(){if(!aa.dynamic_tool_div.is(":visible")){aa.update_name(aa.name+aa.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";aa.revert_name()}aa.dynamic_tool_div.toggle();aa.make_name_popup_menu()}}if(aa.valid_chroms){Z["List chrom/contigs with data"]=function(){show_modal("Chrom/contigs with data","<p>"+aa.valid_chroms.join("<br/>")+"</p>",{Close:function(){hide_modal()}})}}var ab=view;var ac=function(){$("#no-tracks").show()};if(this.parent_track){ab=this.parent_track;ac=function(){}}Z.Remove=function(){ab.remove_track(aa);if(ab.num_tracks===0){ac()}};make_popupmenu(aa.name_div,Z)},draw:function(Z,ab){var at=this.view.low,af=this.view.high,ah=af-at,aj=this.view.container.width(),ad=aj/ah,ak=this.view.resolution,ac=$("<div style='position: relative;'></div>"),al=function(av,aw,au){return av+"_"+aw+"_"+au};if(!ab){this.content_div.children().remove()}this.content_div.append(ac);this.max_height=0;var an=Math.floor(at/ak/L);var ae=[];var ao=0;while((an*L*ak)<af){var ar=al(aj,ad,an);var ag=this.tile_cache.get(ar);var ap=an*L*this.view.resolution;var aa=ap+L*this.view.resolution;if(!Z&&ag){ae[ae.length]=ag;this.show_tile(ag,ac,ap,ad)}else{this.delayed_draw(Z,ar,an,ak,ac,ad,ae)}an+=1;ao++}var ai=this;var aq=setInterval(function(){if(ae.length===ao){clearInterval(aq);if(ab){var ax=ai.content_div.children();var ay=false;for(var aw=ax.length-1,aC=0;aw>=aC;aw--){var av=$(ax[aw]);if(ay){av.remove()}else{if(av.children().length!==0){ay=true}}}}if(ai.track_type=="FeatureTrack"&&ai.mode=="Histogram"){var aB=-1;for(var aw=0;aw<ae.length;aw++){var aE=ae[aw].max_val;if(aE>aB){aB=aE}}for(var aw=0;aw<ae.length;aw++){if(ae[aw].max_val!==aB){var aD=ae[aw];aD.canvas.remove();ai.delayed_draw(true,al(aj,ad,aD.index),aD.index,aD.resolution,ac,ad,[],{max:aB})}}}if(ai.filters_manager){var au=ai.filters_manager.filters;for(var aA=0;aA<au.length;aA++){au[aA].update_ui_elt()}var az=false;if(ai.example_feature){for(var aA=0;aA<au.length;aA++){if(au[aA].applies_to(ai.example_feature)){az=true;break}}}if(ai.filters_available!==az){ai.filters_available=az;if(!ai.filters_available){ai.filters_div.hide()}ai.make_name_popup_menu()}}}},50);for(var am=0;am<this.child_tracks.length;am++){this.child_tracks[am].draw(Z,ab)}},delayed_draw:function(aa,ah,ab,ad,ai,al,aj,ae){var ac=this,af=ab*L*ad,ak=af+L*ad;var ag=function(au,am,ao,an,ar,at,ap){var aq=ac.draw_tile(am,ao,an,at,ap);ac.tile_cache.set(ah,aq);if(aq===undefined){return}ac.show_tile(aq,ar,af,at);aj[aj.length]=aq};var Z=setTimeout(function(){if(af<=ac.view.high&&ak>=ac.view.low){var am=(aa?undefined:ac.tile_cache.get(ah));if(am){ac.show_tile(am,ai,af,al);aj[aj.length]=am}else{$.when(ac.data_cache.get_data(view.chrom,af,ak,ac.mode,ad,ac.data_url_extra_params)).then(function(an){n(an,ae);if(view.reference_track&&al>view.canvas_manager.char_width_px){$.when(view.reference_track.data_cache.get_data(view.chrom,af,ak,ac.mode,ad,view.reference_track.data_url_extra_params)).then(function(ao){ag(Z,an,ad,ab,ai,al,ao)})}else{ag(Z,an,ad,ab,ai,al)}})}}},50)},show_tile:function(ac,af,ad,ag){var aa=this;var ab=this.view.high-this.view.low,ae=(ad-this.view.low)*ag;if(this.left_offset){ae-=this.left_offset}var Z=ac.canvas;Z.css({position:"absolute",top:0,left:ae,height:""});af.append(Z);aa.max_height=Math.max(aa.max_height,Z.height());aa.content_div.css("height",aa.max_height+"px");af.children().css("height",aa.max_height+"px")},set_overview:function(){var Z=this.view;if(this.initial_canvas&&this.is_overview){Z.overview_close.show();Z.overview_viewport.append(this.initial_canvas);Z.overview_highlight.show().height(this.initial_canvas.height());Z.overview_viewport.height(this.initial_canvas.height()+Z.overview_box.height())}$(window).trigger("resize")},tool_region_and_parameters_str:function(ab,Z,ac){var aa=this,ad=(ab!==undefined&&Z!==undefined&&ac!==undefined?ab+":"+Z+"-"+ac:"all");return" - region=["+ad+"], parameters=["+aa.tool.get_param_values().join(", ")+"]"},add_track:function(Z){Z.track_id=this.track_id+"_"+this.child_tracks.length;Z.container_div.attr("id","track_"+Z.track_id);this.child_tracks_container.append(Z.container_div);B(Z.container_div,".child-track-icon");if(!$(this.child_tracks_container).is(":visible")){this.child_tracks_container.show()}this.child_tracks.push(Z);this.view.has_changes=true},remove_track:function(Z){Z.container_div.fadeOut("slow",function(){$(this).remove()})}});var W=function(Z,aa){this.track_type="LabelTrack";this.hidden=true;j.call(this,null,Z,aa);this.container_div.addClass("label-track")};n(W.prototype,j.prototype,{draw:function(){var ab=this.view,ac=ab.high-ab.low,af=Math.floor(Math.pow(10,Math.floor(Math.log(ac)/Math.log(10)))),Z=Math.floor(ab.low/af)*af,ad=this.view.container.width(),aa=$("<div style='position: relative; height: 1.3em;'></div>");while(Z<ab.high){var ae=(Z-ab.low)/ac*ad;aa.append($("<div class='label'>"+commatize(Z)+"</div>").css({position:"absolute",left:ae-1}));Z+=af}this.content_div.children(":first").remove();this.content_div.append(aa)}});var x=function(Z){this.track_type="ReferenceTrack";this.hidden=true;j.call(this,null,Z,Z.top_labeltrack);I.call(this);Z.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:Z.dbkey};this.data_cache=new D(y,this,false);this.tile_cache=new c(r)};n(x.prototype,I.prototype,{draw_tile:function(ah,ae,aa,aj){var ad=this,ab=L*ae;if(aj>this.view.canvas_manager.char_width_px){if(ah===null){ad.content_div.css("height","0px");return}var ac=this.view.canvas_manager.new_canvas();var ai=ac.getContext("2d");ac.width=Math.ceil(ab*aj+ad.left_offset);ac.height=ad.height_px;ai.font=ai.canvas.manager.default_font;ai.textAlign="center";for(var af=0,ag=ah.length;af<ag;af++){var Z=Math.round(af*aj);ai.fillText(ah[af],Z+ad.left_offset,10)}return new b(aa,ae,ac)}this.content_div.css("height","0px")}});var k=function(ad,ab,ae,Z,ac){var aa=this;this.track_type="LineTrack";this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";j.call(this,ad,ab,ab.viewport_container);I.call(this);this.min_height_px=16;this.max_height_px=400;this.height_px=80;this.hda_ldda=ae;this.dataset_id=Z;this.original_dataset_id=Z;this.data_cache=new M(y,this);this.tile_cache=new c(r);this.track_config=new U({track:this,params:[{key:"color",label:"Color",type:"color",default_value:"black"},{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:this.height_px,hidden:true}],saved_values:ac,onchange:function(){aa.vertical_range=aa.prefs.max_value-aa.prefs.min_value;$("#linetrack_"+aa.track_id+"_minval").text(aa.prefs.min_value);$("#linetrack_"+aa.track_id+"_maxval").text(aa.prefs.max_value);aa.tile_cache.clear();aa.draw()}});this.prefs=this.track_config.values;this.height_px=this.track_config.values.height;this.vertical_range=this.track_config.values.max_value-this.track_config.values.min_value;this.add_resize_handle()};n(k.prototype,I.prototype,{add_resize_handle:function(){var Z=this;var ac=false;var ab=false;var aa=$("<div class='track-resize'>");$(Z.container_div).hover(function(){ac=true;aa.show()},function(){ac=false;if(!ab){aa.hide()}});aa.hide().bind("dragstart",function(ad,ae){ab=true;ae.original_height=$(Z.content_div).height()}).bind("drag",function(ae,af){var ad=Math.min(Math.max(af.original_height+af.deltaY,Z.min_height_px),Z.max_height_px);$(Z.content_div).css("height",ad);Z.height_px=ad;Z.draw(true)}).bind("dragend",function(ad,ae){Z.tile_cache.clear();ab=false;if(!ac){aa.hide()}Z.track_config.values.height=Z.height_px}).appendTo(Z.container_div)},predraw_init:function(){var Z=this,aa=Z.view.tracks.indexOf(Z);Z.vertical_range=undefined;return $.getJSON(Z.data_url,{stats:true,chrom:Z.view.chrom,low:null,high:null,hda_ldda:Z.hda_ldda,dataset_id:Z.dataset_id},function(ab){Z.container_div.addClass("line-track");var ad=ab.data;if(isNaN(parseFloat(Z.prefs.min_value))||isNaN(parseFloat(Z.prefs.max_value))){Z.prefs.min_value=ad.min;Z.prefs.max_value=ad.max;$("#track_"+aa+"_minval").val(Z.prefs.min_value);$("#track_"+aa+"_maxval").val(Z.prefs.max_value)}Z.vertical_range=Z.prefs.max_value-Z.prefs.min_value;Z.total_frequency=ad.total_frequency;Z.container_div.find(".yaxislabel").remove();var ae=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+aa+"_minval").text(u(Z.prefs.min_value));var ac=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+aa+"_maxval").text(u(Z.prefs.max_value));ac.css({position:"absolute",top:"24px",left:"10px"});ac.prependTo(Z.container_div);ae.css({position:"absolute",bottom:"2px",left:"10px"});ae.prependTo(Z.container_div)})},draw_tile:function(aj,ad,aa,ai){if(this.vertical_range===undefined){return}var ae=aa*L*ad,ac=L*ad,Z=Math.ceil(ac*ai),ag=this.height_px;var ab=this.view.canvas_manager.new_canvas();ab.width=Z,ab.height=ag;var ah=ab.getContext("2d");var af=new H.LinePainter(aj.data,ae,ae+ac,this.prefs,this.mode);af.draw(ah,Z,ag);return new b(ac,ad,ab)}});var e=function(Z,ae,ad,ah,ag,ab,ac,af){var aa=this;this.track_type="FeatureTrack";this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];this.track_config=new U({track:this,params:[{key:"block_color",label:"Block color",type:"color",default_value:"#444"},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ag,onchange:function(){aa.tile_cache.clear();aa.draw()}});this.prefs=this.track_config.values;j.call(this,Z,ae,ae.viewport_container);I.call(this,ab,ac,af);this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ad;this.dataset_id=ah;this.original_dataset_id=ah;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.tile_cache=new c(d);this.data_cache=new M(20,this);this.left_offset=200;this.painter=H.LinkedFeaturePainter};n(e.prototype,I.prototype,{update_auto_mode:function(Z){if(this.mode=="Auto"){if(Z=="no_detail"){Z="feature spans"}else{if(Z=="summary_tree"){Z="coverage histogram"}}this.mode_div.text("Auto ("+Z+")")}},incremental_slots:function(ad,aa,ac){var ab=this.view.canvas_manager.dummy_context,Z=this.inc_slots[ad];if(!Z||(Z.mode!==ac)){Z=new (p.FeatureSlotter)(ad,ac==="Pack",w,function(ae){return ab.measureText(ae)});Z.mode=ac;this.inc_slots[ad]=Z}return Z.slot_features(aa)},get_summary_tree_data:function(ad,ag,ab,ao){if(ao>ab-ag){ao=ab-ag}var ak=Math.floor((ab-ag)/ao),an=[],ac=0;var ae=0,af=0,aj,am=0,ah=[],al,ai;var aa=function(ar,aq,at,ap){ar[0]=aq+at*ap;ar[1]=aq+(at+1)*ap};while(am<ao&&ae!==ad.length){var Z=false;for(;am<ao&&!Z;am++){aa(ah,ag,am,ak);for(af=ae;af<ad.length;af++){aj=ad[af].slice(1,3);if(is_overlap(aj,ah)){Z=true;break}}if(Z){break}}data_start_index=af;an[an.length]=al=[ah[0],0];for(;af<ad.length;af++){aj=ad[af].slice(1,3);if(is_overlap(aj,ah)){al[1]++}else{break}}if(al[1]>ac){ac=al[1]}am++}return{max:ac,delta:ak,data:an}},draw_tile:function(am,av,az,ai,ac){var ar=this,aB=az*L*av,aa=(az+1)*L*av,ao=aa-aB,at=Math.ceil(ao*ai),aq=this.mode,aF=25,ad=this.left_offset,an,ae;if(aq==="Auto"){if(am.dataset_type==="summary_tree"){aq=am.dataset_type}else{if(am.extra_info==="no_detail"){aq="no_detail"}else{var aE=am.data;if(this.view.high-this.view.low>E){aq="Squish"}else{aq="Pack"}}}this.update_auto_mode(aq)}if(aq==="summary_tree"||aq==="Histogram"){ae=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var Z=$("<div />").addClass("yaxislabel");Z.text(am.max);Z.css({position:"absolute",top:"22px",left:"10px",color:this.prefs.label_color});Z.prependTo(this.container_div);var ab=this.view.canvas_manager.new_canvas();ab.width=at+ad;ab.height=ae+N;if(am.dataset_type!="summary_tree"){var aj=this.get_summary_tree_data(am.data,aB,aa,200);if(am.max){aj.max=am.max}am=aj}var aC=new H.SummaryTreePainter(am,aB,aa,this.prefs);var au=ab.getContext("2d");au.translate(ad,N);aC.draw(au,at,ae);return new l(az,av,ab,am.max)}var an,ag=1;if(aq==="no_detail"||aq==="Squish"||aq==="Pack"){ag=this.incremental_slots(ai,am.data,aq);an=this.inc_slots[ai].slots}var ah=[];if(am.data){var ak=this.filters_manager.filters;for(var aw=0,ay=am.data.length;aw<ay;aw++){var af=am.data[aw];var ax=false;var al;for(var aA=0,aD=ak.length;aA<aD;aA++){al=ak[aA];al.update_attrs(af);if(!al.keep(af)){ax=true;break}}if(!ax){ah.push(af)}}}var aC=new (this.painter)(ah,aB,aa,this.prefs,aq,ac);var ae=aC.get_required_height(ag)+z;var ab=this.view.canvas_manager.new_canvas();ab.width=at+ad;ab.height=ae;var au=ab.getContext("2d");au.fillStyle=this.prefs.block_color;au.font=au.canvas.manager.default_font;au.textAlign="right";this.container_div.find(".yaxislabel").remove();if(am.message){$(ab).css({"border-top":"1px solid red"});au.fillStyle="red";au.textAlign="left";var ap=au.textBaseline;au.textBaseline="top";au.fillText(am.message,ad,0);au.textBaseline=ap;if(!am.data){return new 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counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:ab,onchange:function(){this.track.tile_cache.clear();this.track.draw()}});this.prefs=this.track_config.values;this.track_type="ReadTrack";this.painter=H.ReadPainter;this.make_name_popup_menu()};n(R.prototype,I.prototype,e.prototype);var P=function(ad,ab,af,Z,ac,ae,aa){e.call(this,ad,ab,af,Z,ac,ae,{},aa);this.track_type="ToolDataFeatureTrack";this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url};n(P.prototype,I.prototype,e.prototype,{predraw_init:function(){var aa=this;var Z=function(){if(aa.data_cache.size()===0){setTimeout(Z,300)}else{aa.data_url=default_data_url;aa.data_query_wait=G;aa.dataset_state_url=converted_datasets_state_url;$.getJSON(aa.dataset_state_url,{dataset_id:aa.dataset_id,hda_ldda:aa.hda_ldda},function(ab){})}};Z()}});S.View=X;S.LineTrack=k;S.FeatureTrack=e;S.ReadTrack=R};var slotting_module=function(c,b){var 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S=1;if(S===0&&C-Q.measureText(I).width<0){Q.textAlign="left";Q.fillText(I,E+k-N,B+8)}else{Q.textAlign="right";Q.fillText(I,C-k-N,B+8)}Q.fillStyle=U}}});w.SummaryTreePainter=u;w.LinePainter=c;w.LinkedFeaturePainter=q;w.ReadPainter=s;w.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file --- a/static/scripts/trackster.js Tue May 03 11:35:21 2011 -0400 +++ b/static/scripts/trackster.js Wed May 04 10:20:54 2011 -0400 @@ -885,11 +885,15 @@ this.parent_div.find("input").click(function() { $(this).select() }); // Add 'Go' button. - var run_tool_row = $("<div>").addClass("slider-row").appendTo(this.parent_div); - var run_tool_button = $("<input type='submit'>").attr("value", "Run").appendTo(run_tool_row); + var run_tool_row = $("<div>").addClass("param-row").appendTo(this.parent_div); + var run_on_dataset_button = $("<input type='submit'>").attr("value", "Run on complete dataset").appendTo(run_tool_row); + var run_on_region_button = $("<input type='submit'>").attr("value", "Run on visible region").css("margin-left", "3em").appendTo(run_tool_row); var tool = this; - run_tool_button.click( function() { - tool.run(); + run_on_region_button.click( function() { + tool.run_on_region(); + }); + run_on_dataset_button.click( function() { + tool.run_on_dataset(); }); }; extend(Tool.prototype, { @@ -920,51 +924,87 @@ return param_values; }, /** - * Run tool. This creates a new child track, runs tool, and places tool's output in the new track. + * Run tool on dataset. Output is placed in dataset's history and no changes to viz are made. */ - run: function() { - // Put together params for running tool. - var url_params = { - dataset_id: this.track.original_dataset_id, - chrom: this.track.view.chrom, - low: this.track.view.low, - high: this.track.view.high, - tool_id: this.name - }; - $.extend(url_params, this.get_param_values_dict()); + run_on_dataset: function() { + var tool = this; + tool.run( + // URL params. + { + dataset_id: this.track.original_dataset_id, + tool_id: tool.name + }, + // Success callback. + function(track_data) { + show_modal(tool.name + " is Running", + tool.name + " is running on the complete dataset. Tool outputs are in dataset's history.", + { "Close" : hide_modal } ); + } + ); + }, + /** + * Run dataset on visible region. This creates a new track and sets the track's contents + * to the tool's output. + */ + run_on_region: function() { // // Create track for tool's output immediately to provide user feedback. // var + url_params = + { + dataset_id: this.track.original_dataset_id, + chrom: this.track.view.chrom, + low: this.track.view.low, + high: this.track.view.high, + tool_id: this.name + }, current_track = this.track, // Set name of track to include tool name, parameters, and region used. track_name = url_params.tool_id + current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high), new_track; + // Create and add track. // TODO: add support for other kinds of tool data tracks. if (current_track.track_type === 'FeatureTrack') { new_track = new ToolDataFeatureTrack(track_name, view, current_track.hda_ldda, undefined, {}, {}, current_track); } - this.track.add_track(new_track); new_track.content_div.text("Starting job."); // Run tool. + this.run(url_params, + // Success callback. + function(track_data) { + new_track.dataset_id = track_data.dataset_id; + new_track.content_div.text("Running job."); + new_track.init(); + } + ); + }, + /** + * Run tool using a set of URL params and a success callback. + */ + run: function(url_params, success_callback) { + // Add tool params to URL params. + $.extend(url_params, this.get_param_values_dict()); + + // Run tool. var json_run_tool = function() { - $.getJSON(run_tool_url, url_params, function(track_data) { - if (track_data === "no converter") { + $.getJSON(run_tool_url, url_params, function(response) { + if (response === "no converter") { // No converter available for input datasets, so cannot run tool. new_track.container_div.addClass("error"); new_track.content_div.text(DATA_NOCONVERTER); } - else if (track_data.error) { + else if (response.error) { // General error. new_track.container_div.addClass("error"); - new_track.content_div.text(DATA_CANNOT_RUN_TOOL + track_data.message); + new_track.content_div.text(DATA_CANNOT_RUN_TOOL + response.message); } - else if (track_data === "pending") { + else if (response === "pending") { // Converting/indexing input datasets; show message and try again. new_track.container_div.addClass("pending"); new_track.content_div.text("Converting input data so that it can be easily reused."); @@ -972,9 +1012,7 @@ } else { // Job submitted and running. - new_track.dataset_id = track_data.dataset_id; - new_track.content_div.text("Running job."); - new_track.init(); + success_callback(response); } }); }; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Add unspecified build validators to dataset inputs for Cufflinks/compare/diff wrappers.
by Bitbucket 03 May '11

03 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0094ba8f1c0a/ changeset: r5497:0094ba8f1c0a user: jgoecks date: 2011-05-03 16:31:14 summary: Add unspecified build validators to dataset inputs for Cufflinks/compare/diff wrappers. affected #: 3 files (545 bytes) --- a/tools/ngs_rna/cuffcompare_wrapper.xml Tue May 03 09:45:40 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Tue May 03 10:31:14 2011 -0400 @@ -33,9 +33,13 @@ #end for </command><inputs> - <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/> + <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""> + <validator type="unspecified_build" /> + </param><repeat name="input_files" title="Additional GTF Input Files"> - <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/> + <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""> + <validator type="unspecified_build" /> + </param></repeat><conditional name="annotation"><param name="use_ref_annotation" type="select" label="Use Reference Annotation"> --- a/tools/ngs_rna/cuffdiff_wrapper.xml Tue May 03 09:45:40 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Tue May 03 10:31:14 2011 -0400 @@ -68,7 +68,9 @@ </command><inputs> - <param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/> + <param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."> + <validator type="unspecified_build" /> + </param><conditional name="group_analysis"><param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group."><option value="No">No</option> @@ -78,13 +80,19 @@ <repeat name="groups" title="Group"><param name="group" title="Group name" type="text" label="Group name (no spaces or commas)"/><repeat name="files" title="Replicate"> - <param name="file" label="Add file" type="data" format="sam,bam"/> + <param name="file" label="Add file" type="data" format="sam,bam"> + <validator type="unspecified_build" /> + </param></repeat></repeat></when><when value="No"> - <param format="sam,bam" name="aligned_reads1" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> - <param format="sam,bam" name="aligned_reads2" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> + <param format="sam,bam" name="aligned_reads1" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""> + <validator type="unspecified_build" /> + </param> + <param format="sam,bam" name="aligned_reads2" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""> + <validator type="unspecified_build" /> + </param></when></conditional> --- a/tools/ngs_rna/cufflinks_wrapper.xml Tue May 03 09:45:40 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Tue May 03 10:31:14 2011 -0400 @@ -41,7 +41,9 @@ #end if </command><inputs> - <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/> + <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""> + <validator type="unspecified_build" /> + </param><param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help=""/><param name="min_isoform_fraction" type="float" value="0.05" min="0" max="1" label="Min Isoform Fraction" help=""/><param name="pre_mrna_fraction" type="float" value="0.05" min="0" max="1" label="Pre MRNA Fraction" help=""/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Fix bug in 'Filter GTF data by attribute values list' tool.
by Bitbucket 03 May '11

03 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/a0165dfc5664/ changeset: r5496:a0165dfc5664 user: jgoecks date: 2011-05-03 15:45:40 summary: Fix bug in 'Filter GTF data by attribute values list' tool. affected #: 1 file (41 bytes) --- a/tools/filters/gff/gtf_filter_by_attribute_values_list.py Mon May 02 17:35:06 2011 -0400 +++ b/tools/filters/gff/gtf_filter_by_attribute_values_list.py Tue May 03 09:45:40 2011 -0400 @@ -54,7 +54,7 @@ for line in open( gff_file ): fields = line.split( '\t' ) attributes = parse_gff_attributes( fields[8] ) - if attributes[ attribute_name ] in ids_dict: + if ( attribute_name in attributes ) and ( attributes[ attribute_name ] in ids_dict ): output.write( line ) output.close() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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