angie: changes by file

review to branch (2009-03-17 to 2009-03-31) v203

• src/hg/hgTracks/cds.c
  • 1.90 lines changed: 41, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgTracks/cds.h
  • 1.20 lines changed: 5, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgTracks/hgTracks.c
  • 1.1562 lines changed: 15, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgTracks/hgTracks.h
  • 1.182 lines changed: 4, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgTracks/pslTrack.c
  • 1.30 lines changed: 94, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgTracks/simpleTracks.c
  • 1.73 lines changed: 34, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgc/hgdpClick.c
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Added links to population key images.
• src/hg/hgc/hgcData/hgdpGeoMap.eps
  • 1.4 lines changed: 53, context: html, text, full: html, text
    Added title for attribution to HGDP.
• src/hg/makeDb/doc/hgdpGeo.txt
  • 1.2 lines changed: 7, context: html, text, full: html, text
    Made a population key image (thanks b0b for suggestion).
• src/hg/mouseStuff/netFilter/netFilter.c
  • 1.21 lines changed: 8, context: html, text, full: html, text
    Check -minSize{Q,T} only for fills, not for gaps -- discarding gaps makes the parent fill incorrectly appear gapless. I think it's odd that we discard all of a fill's gap's children when the fill is disqualified because it's possible for some lower-level nets to pass a filter that excludes a higher-level net, but will leave that as-is for now.
• src/hg/qa/apacheMonitor.c
  • 1.16 lines changed: 4, context: html, text, full: html, text
    Added date and time to output of error-500 details query.
• src/hg/utils/automation/makePushQSql.pl
  • 1.23 lines changed: 3, context: html, text, full: html, text
    Use hgofbeta instead of hgwbeta as the mysql server for qapushq.
• src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Tweaking name of output file to avoid clobbering the main one if there's a problem upstream or downstream.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
  • 1.8 lines changed: 2, context: html, text, full: html, text
    customFactoryTestExistence requires new arg (db).
• src/test/buildTableDescriptions.pl
  • 1.42 lines changed: 15, context: html, text, full: html, text
    Added support for db.host in hgConf, and properly set HGDB_CONF when -hgConf is given so hgsql uses it too.
  • 1.41 lines changed: 1, context: html, text, full: html, text
    Added another duplicate .as to %autoSqlIgnore.
• src/test/perllib/HgConf.pm
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Use HGDB_CONF environment variable if defined.
• src/test/perllib/TrackDb.pm
  • 1.4 lines changed: 16, context: html, text, full: html, text
    Added proper HgConf usage including db.host, since we can no longer assume localhost etc.