kent: changes by commit

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

• 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/container.c 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c 1.1648 - lines changed: 45, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h 1.211 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.140 - lines changed: 1, context: html, text, full: html, text
• Fixing reference to nonexistant function in comment.
  • src/hg/lib/trackDbCustom.c 1.89 - lines changed: 1, context: html, text, full: html, text
• Adding hGetTrackForTable()
  • src/hg/inc/hdb.h 1.170 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/hdb.c 1.428 - lines changed: 49, context: html, text, full: html, text
• Renaming carefulTrackOpenVis to hCarefulTrackUpenVis and making it global.
  • src/hg/inc/hgFind.h 1.21 - lines changed: 4, context: html, text, full: html, text
  • src/hg/lib/hgFind.c 1.228 - lines changed: 3, context: html, text, full: html, text
• Further work adapting hgFind to separate track and table names.
  • src/hg/lib/hgFind.c 1.229 - lines changed: 23, context: html, text, full: html, text
• Making big hgc track dispatch use table instead of track.
  • src/hg/hgc/hgc.c 1.1627 - lines changed: 348, context: html, text, full: html, text
• Adding end to some peakClusters web pages.
  • src/hg/hgc/peakClusters.c 1.4 - lines changed: 2, context: html, text, full: html, text
• Adding hGetTableForTrack. Refactoring things so that this and hGetTrackForTable share the same settings hash.
  • src/hg/inc/hdb.h 1.171 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/hdb.c 1.429 - lines changed: 65, context: html, text, full: html, text
• Exposing trackDbSettingsFromString and using it in place of raFromString.
  • src/hg/inc/trackDb.h 1.60 - lines changed: 5, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c 1.90 - lines changed: 2, context: html, text, full: html, text
• Fixing mrna alignment click bug from recent refactoring. Also making listItemsAssayed cgi variable conform with prefix convention.
  • src/hg/hgc/hgc.c 1.1628 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgc/peakClusters.c 1.5 - lines changed: 1, context: html, text, full: html, text
• Fixing crash on regulation group from container track.
  • src/hg/hgTables/hgTables.c 1.197 - lines changed: 6, context: html, text, full: html, text
• Fixing some problems with mrna and est tracks in table browser.
  • src/hg/hgTables/hgTables.c 1.198 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.146 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c 1.151 - lines changed: 1, context: html, text, full: html, text
• Fixing typo in comment
  • src/hg/makeDb/trackDb/tagTypes.tab 1.24 - lines changed: 1, context: html, text, full: html, text
• Fixed indentation a little
  • src/hg/lib/web.c 1.173 - 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/cart.c 1.120 - lines changed: 3, context: html, text, full: html, text
• Exposing metadataToggle function as compositeMetadataToggle. Adding support for showSubtrackColorOnUi tag.
  • src/hg/inc/hui.h 1.153 - lines changed: 4, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.290 - lines changed: 18, 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.
  • src/hg/hgc/hgc.c 1.1629 - lines changed: 14, context: html, text, full: html, text
• Writing out table of cell types and single letter abbreviations on factorSource details page. Removing some debugging.
  • src/hg/hgc/peakClusters.c 1.6 - lines changed: 37, context: html, text, full: html, text
• Adding showSubtrackColorOnUi
  • src/hg/makeDb/trackDb/tagTypes.tab 1.25 - lines changed: 1, context: html, text, full: html, text
• Tweaking settings for regulatory track.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.975 - lines changed: 11, 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.
  • src/hg/lib/hdb.c 1.430 - lines changed: 6, context: html, text, full: html, text
• Using track in preference to table in a couple of user-visibile strings
  • src/hg/hgTables/correlate.c 1.80 - lines changed: 0, context: html, text, full: html, text
  • src/hg/hgTables/identifiers.c 1.31 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/schema.c 1.65 - lines changed: 1, context: html, text, full: html, text
• Making makeTrackSettingsHash use tableName from database rather than track from settings as key, for slightly better backwards compatibility.
  • src/hg/lib/hdb.c 1.431 - lines changed: 4, context: html, text, full: html, text
• Making variable x to hold x1+xOff.
  • src/hg/hgTracks/wigTrack.c 1.110 - lines changed: 16, context: html, text, full: html, text
• More track/table changes per Angie's suggestions at code review.
  • src/hg/hgTracks/bedGraph.c 1.24 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/cds.c 1.107 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.141 - lines changed: 6, context: html, text, full: html, text
• Simplifying wording around transparent overlay in user interface.
  • src/hg/lib/hui.c 1.291 - lines changed: 3, context: html, text, full: html, text
• Making it so that whiskers mode only sets each pixel once, so it works better in transparent mode.
  • src/hg/hgTracks/wigTrack.c 1.111 - lines changed: 48, context: html, text, full: html, text
• Fixing typo of hTableForTrack when I meant hGetTableForTrack. Fixes problem in mrna/est details display on hg19
  • src/hg/hgc/hgc.c 1.1632 - lines changed: 2, context: html, text, full: html, text
• Making log transform not crash on negative data values.
  • src/hg/hgTracks/wigTrack.c 1.112 - lines changed: 5, 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/expectedFixed.wig 1.1 - lines changed: 106, context: html, text, full: html, text
  • src/utils/wigSetSpanOrStep/expectedVar.wig 1.1 - lines changed: 25, context: html, text, full: html, text
  • src/utils/wigSetSpanOrStep/inFixed.wig 1.1 - lines changed: 106, context: html, text, full: html, text
  • src/utils/wigSetSpanOrStep/inVar.wig 1.1 - lines changed: 25, context: html, text, full: html, text
  • src/utils/wigSetSpanOrStep/makefile 1.1 - lines changed: 24, context: html, text, full: html, text
  • src/utils/wigSetSpanOrStep/wigSetSpanOrStep.c 1.1 - lines changed: 112, 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/hgc.c 1.1634 - lines changed: 50, context: html, text, full: html, text
  • src/hg/hgc/mgcClick.c 1.34 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgc/retroClick.c 1.16 - lines changed: 13, context: html, text, full: html, text
  • src/hg/hgc/transMapClick.c 1.14 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgc/virusClick.c 1.9 - lines changed: 3, context: html, text, full: html, text