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github.com/GMOD/jbrowse
/ functions
Functions
557 in github.com/GMOD/jbrowse
⨍
Functions
557
◇
Types & classes
41
↓ 1 callers
Function
renderFreqTable
( table, level )
src/JBrowse/View/Track/_VariantDetailMixin.js:202
↓ 1 callers
Function
replaceAt
( str, offset, replacement )
src/JBrowse/Store/SeqFeature.js:301
↓ 1 callers
Function
rgbToHex
(rgb)
plugins/NeatCanvasFeatures/js/View/FeatureGlyph/Box.js:136
↓ 1 callers
Method
scroll_around
( self )
tests/selenium_tests/volvox_REST_names_test.py:43
↓ 1 callers
Method
search_f15
( self )
tests/selenium_tests/volvox_biodb_test.py:230
↓ 1 callers
Method
search_track
( self )
tests/selenium_tests/volvox_biodb_test.py:249
↓ 1 callers
Method
search_yal024c
( self )
tests/selenium_tests/yeast_biodb_test.py:74
↓ 1 callers
Method
sequence
( self )
tests/selenium_tests/yeast_biodb_test.py:58
↓ 1 callers
Method
sequence
( self )
tests/selenium_tests/volvox_biodb_test.py:173
↓ 1 callers
Method
setAllFilled
(data)
src/JBrowse/View/GranularRectLayout.js:33
↓ 1 callers
Function
start_server
()
tests/selenium_tests/name_server.py:65
↓ 1 callers
Method
stat
()
src/JBrowse/Model/BlobFilehandleWrapper.js:21
↓ 1 callers
Function
tilingIsComplete
( regions, start, end )
src/JBrowse/Store/SeqFeature/REST.js:106
↓ 1 callers
Method
track_menu_click
( self, track_name, item_name )
tests/selenium_tests/jbrowse_selenium/JBrowseTest.py:178
↓ 1 callers
Method
trackpane_rubberband
Executes a rubberband gesture from start_pct to end_pct in the main track pane
tests/selenium_tests/jbrowse_selenium/JBrowseTest.py:200
↓ 1 callers
Function
union
( start1, end1, start2, end2 )
src/JBrowse/View/Track/HTMLFeatures.js:783
↓ 1 callers
Method
vcf
( self )
tests/selenium_tests/volvox_biodb_test.py:102
↓ 1 callers
Method
wait_for_dialog_appearance
( self, t=5)
tests/selenium_tests/jbrowse_selenium/JBrowseTest.py:168
↓ 1 callers
Method
wait_until_one_track
(self)
tests/selenium_tests/jbrowse_selenium/JBrowseTest.py:231
↓ 1 callers
Function
xit
(desc, func)
tests/js_tests/lib/jasmine-1.2.0/jasmine.js:499
Function
Animation
* @class
src/JBrowse/View/Animation.js:6
Function
ArrayRepr
* @class JBrowse.Model.ArrayRepr * @constructor * * @description * * Class for operating on indexed array representations of objects. * * For e
src/JBrowse/Model/ArrayRepr.js:99
Function
BehaviorManager
* Stores, applies, and removes a named set of behaviors. A behavior * is a set of event handlers that need to be connected and then * disconnected
src/JBrowse/BehaviorManager.js:37
Function
DataView
()
src/JBrowse/Model/DataView.js:13
Function
DotObject
(seperator, override, useArray)
src/JBrowse/Util/dot-object.js:57
Function
FromBytes
(args)
src/JBrowse/Util/TextIterator.js:10
Function
InfBlocks
(z, checkfn, w)
src/JBrowse/Util/jszlib.js:2379
Function
InfCodes
()
src/JBrowse/Util/jszlib.js:3063
Function
InfTree
()
src/JBrowse/Util/jszlib.js:3694
Function
Inflate
()
src/JBrowse/Util/jszlib.js:2045
Function
Ka
(a)
tests/drupal/jquery.js:17
Function
LazyArray
(lazyArrayParams, baseUrl)
src/JBrowse/Store/LazyArray.js:20
Function
NCList
Nested containment list. @class After <pre> Alekseyenko, A., and Lee, C. (2007). Nested Containment List (NCList): A new algorithm for accelerat
src/JBrowse/Store/NCList.js:34
Function
NCList_v0
* Legacy-compatible NCList for 1.2.1 backward compatibility. * @lends JBrowse.Store.NCList_v0 * @constructs
src/JBrowse/Store/NCList_v0.js:9
Function
Oa
(a,b)
tests/drupal/jquery.js:21
Function
Ruler
* Ruler, with ticks and numbers, drawn with HTML elements. Can be * stretched to any length. * * @class * @constructor * * @param {Number} args.
src/JBrowse/View/Ruler.js:26
Function
Slider
* @class
src/JBrowse/View/Animation/Slider.js:7
Function
U
()
tests/drupal/jquery.js:17
Function
Ya
(a)
tests/drupal/jquery.js:56
Function
Z
(a,b)
tests/drupal/jquery.js:71
Function
ZStream
()
src/JBrowse/Util/jszlib.js:1905
Function
Zoomer
* @class
src/JBrowse/View/Animation/Zoomer.js:7
Method
__init__
(self, browser,time_dilation)
tests/selenium_tests/jbrowse_selenium/track_selectors.py:4
Function
_addRectToBitmap
(rect, data)
src/JBrowse/View/GranularRectLayout.js:332
Function
_applyTopLevelFeaturesTransform
* Apply the topLevelFeatures configuration to possibly extract * subfeature from this feature, and run the given callback on * each of the n
src/JBrowse/Store/SeqFeature.js:258
Function
_autovivifyRow
* make a subarray if it does not exist * @private
src/JBrowse/View/GranularRectLayout.js:323
Function
_bamRecordToFeature
(record, refName)
src/JBrowse/Store/SeqFeature/BAM.js:436
Function
_collides
(rect, top)
src/JBrowse/View/GranularRectLayout.js:301
Function
_cramReadFeaturesToMismatches
(feature, readFeatures)
src/JBrowse/Store/SeqFeature/_MismatchesMixin.js:358
Function
_cramRecordToFeature
(record)
src/JBrowse/Store/SeqFeature/CRAM.js:346
Function
_defaultConfig
()
src/JBrowse/View/FeatureGlyph/PairedAlignment.js:181
Function
_drawOverlappingMismatches
(context, fRect, mismatches, fstart)
src/JBrowse/View/FeatureGlyph/PairedAlignment.js:139
Function
_estimateGlobalStats
* Fetch a region of the current reference sequence and use it to * estimate the feature density of the store. * @private
src/JBrowse/Store/SeqFeature/IndexedStatsEstimationMixin.js:17
Function
_featureData
(data)
src/JBrowse/Store/SeqFeature/GFF3Tabix.js:260
Function
_filterSubSubpart
( feature )
src/JBrowse/View/FeatureGlyph/Segments.js:116
Function
_filterSubpart
(feature)
src/JBrowse/View/FeatureGlyph/Segments.js:110
Function
_findSubfeaturesWithTypes
* traverse the subfeature hierarchy of the given feature, * return an array of features whose types are in the given list * @param {Array[st
src/JBrowse/Store/SeqFeature.js:273
Function
_formatFeatures
* A GFF3 feature is an arrayref of that feature's locations. Because a single feature could be * in multiple locations. To match that wit
src/JBrowse/Store/SeqFeature/GFF3Tabix.js:308
Function
_get
(field)
src/JBrowse/Model/VCFFeature.js:21
Method
_get
(field)
src/JBrowse/Store/SeqFeature/CRAM.js:63
Function
_getFeatureRectangle
( viewArgs, feature )
src/JBrowse/View/FeatureGlyph/Gene.js:46
Function
_getFeatures
(query, featCallback, endCallback, errorCallback)
src/JBrowse/Store/SeqFeature/BAM.js:349
Function
_getFeatures
( query, featureCallback, finishedCallback, er
src/JBrowse/Store/SeqFeature/GFF3Tabix.js:109
Function
_getFeatures
( query, featureCallback, endCallback, errorCallback )
src/JBrowse/Store/SeqFeature/BigBed.js:30
Function
_getFeatures
( query, featureCallback, finishedCallback, errorCallback )
src/JBrowse/Store/SeqFeature/VCFTabix.js:96
Function
_getFeatures
( query, featureCallback, finishedCallback, errorCallback )
src/JBrowse/Store/SeqFeature/VCFTribble.js:85
Function
_getLayout
()
src/JBrowse/View/Track/Alignments2.js:354
Function
_getRefSeqStore
()
src/JBrowse/Store/SeqFeature/BAM.js:240
Function
_getRefSeqStore
()
src/JBrowse/Store/SeqFeature/CRAM.js:229
Function
_getResponseArrayBuffer
(callback,{buffer})
src/JBrowse/Model/XHRBlob.js:205
Function
_getSubSubparts
( feature )
src/JBrowse/View/FeatureGlyph/Segments.js:105
Function
_getSubparts
( feature )
src/JBrowse/View/FeatureGlyph/Segments.js:100
Method
_get_cramFlags
()
src/JBrowse/Store/SeqFeature/CRAM.js:20
Method
_get_cram_read_features
()
src/JBrowse/Store/SeqFeature/CRAM.js:15
Method
_get_duplicate
()
src/JBrowse/Store/SeqFeature/BAM.js:85
Method
_get_duplicate
()
src/JBrowse/Store/SeqFeature/CRAM.js:27
Method
_get_end
()
src/JBrowse/Store/SeqFeature/CRAM.js:14
Method
_get_flags
()
src/JBrowse/Store/SeqFeature/BAM.js:68
Method
_get_flags
()
src/JBrowse/Store/SeqFeature/CRAM.js:19
Method
_get_id
()
src/JBrowse/Store/SeqFeature/BAM.js:64
Method
_get_id
()
src/JBrowse/Store/SeqFeature/CRAM.js:11
Method
_get_is_paired
()
src/JBrowse/Store/SeqFeature/BAM.js:98
Method
_get_is_paired
()
src/JBrowse/Store/SeqFeature/CRAM.js:37
Method
_get_mapping_quality
()
src/JBrowse/Store/SeqFeature/BAM.js:67
Method
_get_mapping_quality
()
src/JBrowse/Store/SeqFeature/CRAM.js:18
Method
_get_md
()
src/JBrowse/Store/SeqFeature/BAM.js:69
Method
_get_multi_segment_all_aligned
()
src/JBrowse/Store/SeqFeature/BAM.js:90
Method
_get_multi_segment_all_aligned
()
src/JBrowse/Store/SeqFeature/CRAM.js:32
Method
_get_multi_segment_all_correctly_aligned
()
src/JBrowse/Store/SeqFeature/BAM.js:89
Method
_get_multi_segment_all_correctly_aligned
()
src/JBrowse/Store/SeqFeature/CRAM.js:31
Method
_get_multi_segment_first
()
src/JBrowse/Store/SeqFeature/BAM.js:92
Method
_get_multi_segment_first
()
src/JBrowse/Store/SeqFeature/CRAM.js:34
Method
_get_multi_segment_last
()
src/JBrowse/Store/SeqFeature/BAM.js:93
Method
_get_multi_segment_last
()
src/JBrowse/Store/SeqFeature/CRAM.js:35
Method
_get_multi_segment_next_segment_reversed
()
src/JBrowse/Store/SeqFeature/BAM.js:94
Method
_get_multi_segment_next_segment_reversed
()
src/JBrowse/Store/SeqFeature/CRAM.js:36
Method
_get_multi_segment_next_segment_unmapped
()
src/JBrowse/Store/SeqFeature/BAM.js:91
Method
_get_multi_segment_next_segment_unmapped
()
src/JBrowse/Store/SeqFeature/CRAM.js:33
Method
_get_multi_segment_template
()
src/JBrowse/Store/SeqFeature/BAM.js:88
Method
_get_multi_segment_template
()
src/JBrowse/Store/SeqFeature/CRAM.js:30
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