kent: changes by file

branch to review (2010-02-02 to 2010-02-10) v225

• src/hg/hgTracks/bigBedTrack.c
  • 1.5 lines changed: 33, context: html, text, full: html, text
    Hopefully fixing bigBed so that it works in dense mode on a clean cart _and_ it works with custom tracks. Have tested these two anyway.
  • 1.4 lines changed: 12, context: html, text, full: html, text
    Moving bigBedFileOpen to a better place.
• src/hg/hgTracks/simpleTracks.c
  • 1.126 lines changed: 1, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
• src/hg/inc/trackDb.h
  • 1.53 lines changed: 3, context: html, text, full: html, text
    Adding trackDbUpdateOldTag function to convert older format trackDb tags to current format. Specifically converting superTrack, compositeTrack, and subTrack tags to use the new container and parent tags instead.
• src/hg/lib/hdb.c
  • 1.418 lines changed: 2, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
• src/hg/lib/hui.c
  • 1.258 lines changed: 3, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
• src/hg/lib/trackDbCustom.c
  • 1.80 lines changed: 30, context: html, text, full: html, text
    Making hgTracks be backwards compatible with older trackDb tables in case they didn't run hgTrackDb.
  • 1.78 lines changed: 8, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
  • 1.77 lines changed: 12, context: html, text, full: html, text
    Ifdeffing out some of the new code until I finish baking it.
  • 1.76 lines changed: 40, context: html, text, full: html, text
    Adding trackDbUpdateOldTag function to convert older format trackDb tags to current format. Specifically converting superTrack, compositeTrack, and subTrack tags to use the new container and parent tags instead.
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.61 lines changed: 2, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
• src/hg/makeDb/trackDb/README
  • 1.100 lines changed: 6, context: html, text, full: html, text
    Tweaking MATRIX section a bit as per Angie's suggestions.
  • 1.99 lines changed: 47, context: html, text, full: html, text
    Clarifying some view info.
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
• src/hg/oneShot/freen/freen.c
  • 1.97 lines changed: 36, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
• src/hg/oneShot/tdbRewriteViewsToSubtracks1/makefile
  • 1.1 lines changed: 17, context: html, text, full: html, text
    Making a single file rewriter for track in the middle.
• src/hg/oneShot/tdbRewriteViewsToSubtracks1/tdbRewriteViewsToSubtracks1.c
  • 1.1 lines changed: 696, context: html, text, full: html, text
    Making a single file rewriter for track in the middle.
• src/hg/utils/tdbQuery/tdbQuery.c
  • 1.29 lines changed: 3, context: html, text, full: html, text
    Changing 'subTrack' to 'parent' internally. A backwards compatability routine will make it so either tag can be used in a trackDb file.
  • 1.28 lines changed: 3, context: html, text, full: html, text
    Taking out a half-baked change.
  • 1.27 lines changed: 63, context: html, text, full: html, text
    Getting rid of settingsByView stuff. Adding in converter to container/parent syntax. Fix to parent-not-found error message.
• src/hg/utils/tdbQuery/tdbRecord.c
  • 1.7 lines changed: 5, context: html, text, full: html, text
    Getting to compile in Linux.
  • 1.6 lines changed: 75, context: html, text, full: html, text
    Getting rid of settingsByView stuff. Adding in converter to container/parent syntax. Fix to parent-not-found error message.
• src/hg/utils/tdbQuery/tdbRecord.h
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Getting rid of settingsByView stuff. Adding in converter to container/parent syntax. Fix to parent-not-found error message.
• src/inc/bigBed.h
  • 1.18 lines changed: 30, context: html, text, full: html, text
    Removing bigBedFileCreate which is no longer in library.
• src/lib/bigBed.c
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Making bigBedCoverageIntervals() static.
  • 1.26 lines changed: 4, context: html, text, full: html, text
    Fixed memory leaks.