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Analyzed about 1 year ago. based on code collected about 1 year ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Jan 16, 2023 — Jan 16, 2024 Showing page 616 of 617 Search / Filter on:
Commenting-out the preference setting to turn the "control server" off. There is no good reason to turn it off, and users who did so by accident might be confused by the inability of the NetAffx website to communicate with IGB.	Ed Erwin as chyekk	More...				almost 20 years ago
Fixed NullPointerException in ExperimentPivotView by checking for (span != null) when creating glyphs based on SeqSpans.	gregghelt2	More...				almost 20 years ago
Fixing small typo in last commit.	gregghelt2	More...				almost 20 years ago
Taking out old annotation type elements, replacing with "annotation_style" elements where needed.	gregghelt2	More...				almost 20 years ago
Removing or commenting out all preferences in igb_prefs.xml -- want to initialize igb_prefs.xml with no prefs, any that need to be set are already set in igb_default_prefs.xml.	gregghelt2	More...				almost 20 years ago
Using IndexedWrapperSym for modelling sin3 data was causing visualization and selection problems. So until these get resolved, swicthed to a different approach for parsing sin3 that uses IndexedSingletonSyms.	gregghelt2	More...				almost 20 years ago
Removed getScores() and getScoreCount() methods, code that previously called these methods now make direct calls on the IndexedSingletonSym's ScoreContainerSym parent.	gregghelt2	More...				almost 20 years ago
Modified to use IndexedSyms instead of IndexedSingletonSyms.	gregghelt2	More...				almost 20 years ago
Item added to ignoreList	gregghelt2	More...				almost 20 years ago
Passing the IGB.getSymHash() to the parsers that want to know about it, and calling IGB.symHashChanged() when done.	Ed Erwin as chyekk	More...				almost 20 years ago
Added a new directive, example:	Ed Erwin as chyekk	More...				almost 20 years ago
Treat both the default graph pixel height and default coord height as integers. One of these is actually used as a double internally, but we should hide that detail from users since they have no need to know it.	Ed Erwin as chyekk	More...				almost 20 years ago
Registers itself as a listener for SymMapChangeEvents during construction.	Ed Erwin as chyekk	More...				almost 20 years ago
Added event coordination for SymMapChangeEvents	Ed Erwin as chyekk	More...				almost 20 years ago
Implementing SymMapChangeListener	Ed Erwin as chyekk	More...				almost 20 years ago
Listener/Event classes to let IGB tell plugins that the id2sym Map has changed. The AnnotationBrowser in particular needs to know when these changes happen.	Ed Erwin as chyekk	More...				almost 20 years ago
Changed to handle sin3 files using IndexedWrapperSyms.	gregghelt2	More...				almost 20 years ago
Changed to require IndexedSyms as children, rather than IndexedSingletonSyms.	gregghelt2	More...				almost 20 years ago
Changed to implement IndexedSym interface.	gregghelt2	More...				almost 20 years ago
Adding IndexedWrapperSym, an IndexedSym implementation that wraps another symmetry and adds index and parent data.	gregghelt2	More...				almost 20 years ago
Moved methods from IndexedSingletonSym into a new interface, IndexedSym, because need multiple implementations.	gregghelt2	More...				almost 20 years ago
Added the ability to use the first member of a group as the parent of a group, from which the properties are taken. Example: if you have three lines - one transcript and two exons -- with the same transcript_id, then the default behavior is to make all three of those be children of some invented symmetry. But if you turn on the new behavior, the two exons can be grouped under the transcript (as long as the transcript was listed first in the file.)	Ed Erwin as chyekk	More...				almost 20 years ago
Removed an obsolete line for reading the "group" field of GFF1. We already have a mechanism for detecting the difference between GFF1 and GFF2 and dealing with that field.	Ed Erwin as chyekk	More...				almost 20 years ago
Changed use of ScoredIntervalParser to pass in is2sym hash.	gregghelt2	More...				almost 20 years ago
Added partial implementation of sin version 3 parsing.	gregghelt2	More...				almost 20 years ago
Incrementin IGB version.	gregghelt2	More...				almost 20 years ago
Modified prefs to CoverageSummarizerFactory to build CoverageSummarizerGlyphs for annotation types that end with "_tf" (meant to catch transfrags) or that start with "coverage: " (meant to catch syms created in IGB by requesting coverage track generation for an existing track).	gregghelt2	More...				almost 20 years ago
Reimplemented addSymCoverageTier() method so that it uses standard mechanism of adding annotation sym to annotated seq and relying on SeqMapView's use of glyph factories to build the coverage glyph(s)	gregghelt2	More...				almost 20 years ago
Added setting of data model for CoverageSummarizerGlyph.	gregghelt2	More...				almost 20 years ago
Fixed bug that occasionally threw ArrayIndexOutOfBounds exception.	gregghelt2	More...				almost 20 years ago

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