kent: changes by file

branch to review (2010-05-18 to 2010-05-25) v232

• src/hg/hgTables/correlate.c
  • 1.80 lines changed: 0, context: html, text, full: html, text
    Using track in preference to table in a couple of user-visibile strings
• src/hg/hgTables/hgTables.c
  • 1.198 lines changed: 3, context: html, text, full: html, text
    Fixing some problems with mrna and est tracks in table browser.
  • 1.197 lines changed: 6, context: html, text, full: html, text
    Fixing crash on regulation group from container track.
• src/hg/hgTables/hgTables.h
  • 1.146 lines changed: 5, context: html, text, full: html, text
    Fixing some problems with mrna and est tracks in table browser.
• src/hg/hgTables/identifiers.c
  • 1.31 lines changed: 1, context: html, text, full: html, text
    Using track in preference to table in a couple of user-visibile strings
• src/hg/hgTables/mainPage.c
  • 1.151 lines changed: 1, context: html, text, full: html, text
    Fixing some problems with mrna and est tracks in table browser.
• src/hg/hgTables/schema.c
  • 1.65 lines changed: 1, context: html, text, full: html, text
    Using track in preference to table in a couple of user-visibile strings
• src/hg/hgTracks/bedGraph.c
  • 1.24 lines changed: 1, context: html, text, full: html, text
    More track/table changes per Angie's suggestions at code review.
• src/hg/hgTracks/cds.c
  • 1.107 lines changed: 1, context: html, text, full: html, text
    More track/table changes per Angie's suggestions at code review.
• src/hg/hgTracks/container.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Adding parent field to struct track, and filling it in for composite and container subtracks. For supertracks, the existing parent finding at the track (as opposed to trackDb) level is buried enough this is difficult, so putting this off until the mythical day when supertracks are refactored out. Making mrna searches open mrna track in hg19, and in general improving search auto-opening when track and table name are different.
• src/hg/hgTracks/hgTracks.c
  • 1.1648 lines changed: 45, context: html, text, full: html, text
    Adding parent field to struct track, and filling it in for composite and container subtracks. For supertracks, the existing parent finding at the track (as opposed to trackDb) level is buried enough this is difficult, so putting this off until the mythical day when supertracks are refactored out. Making mrna searches open mrna track in hg19, and in general improving search auto-opening when track and table name are different.
• src/hg/hgTracks/hgTracks.h
  • 1.211 lines changed: 1, context: html, text, full: html, text
    Adding parent field to struct track, and filling it in for composite and container subtracks. For supertracks, the existing parent finding at the track (as opposed to trackDb) level is buried enough this is difficult, so putting this off until the mythical day when supertracks are refactored out. Making mrna searches open mrna track in hg19, and in general improving search auto-opening when track and table name are different.
• src/hg/hgTracks/simpleTracks.c
  • 1.141 lines changed: 6, context: html, text, full: html, text
    More track/table changes per Angie's suggestions at code review.
  • 1.140 lines changed: 1, context: html, text, full: html, text
    Adding parent field to struct track, and filling it in for composite and container subtracks. For supertracks, the existing parent finding at the track (as opposed to trackDb) level is buried enough this is difficult, so putting this off until the mythical day when supertracks are refactored out. Making mrna searches open mrna track in hg19, and in general improving search auto-opening when track and table name are different.
• src/hg/hgTracks/wigTrack.c
  • 1.112 lines changed: 5, context: html, text, full: html, text
    Making log transform not crash on negative data values.
  • 1.111 lines changed: 48, context: html, text, full: html, text
    Making it so that whiskers mode only sets each pixel once, so it works better in transparent mode.
  • 1.110 lines changed: 16, context: html, text, full: html, text
    Making variable x to hold x1+xOff.
• src/hg/hgc/hgc.c
  • 1.1634 lines changed: 50, context: html, text, full: html, text
    Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
  • 1.1632 lines changed: 2, context: html, text, full: html, text
    Fixing typo of hTableForTrack when I meant hGetTableForTrack. Fixes problem in mrna/est details display on hg19
  • 1.1629 lines changed: 14, context: html, text, full: html, text
    Making hgc output closing HTML tags that were missing in many cases. Still look to be missing in a few more though. Making a call to printAlignmentsSimple use track rather than table name to keep it like everywhere else.
  • 1.1628 lines changed: 4, context: html, text, full: html, text
    Fixing mrna alignment click bug from recent refactoring. Also making listItemsAssayed cgi variable conform with prefix convention.
  • 1.1627 lines changed: 348, context: html, text, full: html, text
    Making big hgc track dispatch use table instead of track.
• src/hg/hgc/mgcClick.c
  • 1.34 lines changed: 1, context: html, text, full: html, text
    Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
• src/hg/hgc/peakClusters.c
  • 1.6 lines changed: 37, context: html, text, full: html, text
    Writing out table of cell types and single letter abbreviations on factorSource details page. Removing some debugging.
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixing mrna alignment click bug from recent refactoring. Also making listItemsAssayed cgi variable conform with prefix convention.
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Adding end to some peakClusters web pages.
• src/hg/hgc/retroClick.c
  • 1.16 lines changed: 13, context: html, text, full: html, text
    Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
• src/hg/hgc/transMapClick.c
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
• src/hg/hgc/virusClick.c
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Cleared up some more track/table mixups in the details pages involving printAlignments in refGene. I tested on quite a number of the details pages that use printAlignments, and made changes to get the transMap and retroGene stuff to work. It looks like some of the retroGene stuff has not worked in some time actually.
• src/hg/inc/hdb.h
  • 1.171 lines changed: 3, context: html, text, full: html, text
    Adding hGetTableForTrack. Refactoring things so that this and hGetTrackForTable share the same settings hash.
  • 1.170 lines changed: 3, context: html, text, full: html, text
    Adding hGetTrackForTable()
• src/hg/inc/hgFind.h
  • 1.21 lines changed: 4, context: html, text, full: html, text
    Renaming carefulTrackOpenVis to hCarefulTrackUpenVis and making it global.
• src/hg/inc/hui.h
  • 1.153 lines changed: 4, context: html, text, full: html, text
    Exposing metadataToggle function as compositeMetadataToggle. Adding support for showSubtrackColorOnUi tag.
• src/hg/inc/trackDb.h
  • 1.60 lines changed: 5, context: html, text, full: html, text
    Exposing trackDbSettingsFromString and using it in place of raFromString.
• src/hg/lib/cart.c
  • 1.120 lines changed: 3, context: html, text, full: html, text
    Making cartWebStart included jquery.js and utils.js. The function that does this already gaurds against multiple inclusion, so this should work.
• src/hg/lib/hdb.c
  • 1.431 lines changed: 4, context: html, text, full: html, text
    Making makeTrackSettingsHash use tableName from database rather than track from settings as key, for slightly better backwards compatibility.
  • 1.430 lines changed: 6, context: html, text, full: html, text
    Making findTdbForTable use hTrackForTable before it searches for track. Fixes missing all_mrna table in table browser correlate page.
  • 1.429 lines changed: 65, context: html, text, full: html, text
    Adding hGetTableForTrack. Refactoring things so that this and hGetTrackForTable share the same settings hash.
  • 1.428 lines changed: 49, context: html, text, full: html, text
    Adding hGetTrackForTable()
• src/hg/lib/hgFind.c
  • 1.229 lines changed: 23, context: html, text, full: html, text
    Further work adapting hgFind to separate track and table names.
  • 1.228 lines changed: 3, context: html, text, full: html, text
    Renaming carefulTrackOpenVis to hCarefulTrackUpenVis and making it global.
• src/hg/lib/hui.c
  • 1.291 lines changed: 3, context: html, text, full: html, text
    Simplifying wording around transparent overlay in user interface.
  • 1.290 lines changed: 18, context: html, text, full: html, text
    Exposing metadataToggle function as compositeMetadataToggle. Adding support for showSubtrackColorOnUi tag.
• src/hg/lib/trackDbCustom.c
  • 1.90 lines changed: 2, context: html, text, full: html, text
    Exposing trackDbSettingsFromString and using it in place of raFromString.
  • 1.89 lines changed: 1, context: html, text, full: html, text
    Fixing reference to nonexistant function in comment.
• src/hg/lib/web.c
  • 1.173 lines changed: 3, context: html, text, full: html, text
    Fixed indentation a little
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.25 lines changed: 1, context: html, text, full: html, text
    Adding showSubtrackColorOnUi
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Fixing typo in comment
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.975 lines changed: 11, context: html, text, full: html, text
    Tweaking settings for regulatory track.
• src/utils/wigSetSpanOrStep/expectedFixed.wig
  • 1.1 lines changed: 106, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....
• src/utils/wigSetSpanOrStep/expectedVar.wig
  • 1.1 lines changed: 25, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....
• src/utils/wigSetSpanOrStep/inFixed.wig
  • 1.1 lines changed: 106, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....
• src/utils/wigSetSpanOrStep/inVar.wig
  • 1.1 lines changed: 25, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....
• src/utils/wigSetSpanOrStep/makefile
  • 1.1 lines changed: 24, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....
• src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c
  • 1.1 lines changed: 112, context: html, text, full: html, text
    Made utility to fix spans or steps in a wig file. About 100x faster than sed is the motivation....