mikep: changes by file

branch to review (2009-05-26 to 2009-06-02) v207

• java/src/edu/ucsc/genome/qa/cgiCheck/TrackCheck.java
  • 1.13 lines changed: 4, context: html, text, full: html, text
    disable JavaScript on the rest of the pages
• java/src/edu/ucsc/genome/qa/lib/HgTracks.java
  • 1.17 lines changed: 9, context: html, text, full: html, text
    disable JavaScript on the rest of the pages
• src/hg/encode/DAFs/AffyRnaChip.daf
  • 1.5 lines changed: 2, context: html, text, full: html, text
    shortened view names
• src/hg/hgTables/joining.c
  • 1.55 lines changed: 1, context: html, text, full: html, text
    no, we do not, the type of a track is its type no need to consult parent
• src/hg/hgTables/wiggle.c
  • 1.74 lines changed: 1, context: html, text, full: html, text
    no, we do not, the type of a track is its type no need to consult parent
• src/hg/hgTracks/bedTrack.c
  • 1.13 lines changed: 33, context: html, text, full: html, text
    make colorByStrand work for ordinary beds (item is a bed) and for sequences where basecoloring is done (item is a linkedFeature)
  • 1.12 lines changed: 4, context: html, text, full: html, text
    make colorByStrand independent of baseColor
• src/hg/hgTracks/cds.c
  • 1.99 lines changed: 8, context: html, text, full: html, text
    adding option to replace default 'red' tickmarks with contrasting or lighter color ones similar to the color in zoomed in base view
  • 1.98 lines changed: 12, context: html, text, full: html, text
    choose a contrasting color for tick marks when drawgin differnt bases
• src/hg/hgc/bigBedClick.c
  • 1.5 lines changed: 13, context: html, text, full: html, text
    show seq1,seq2 columns (non-standard bed cols 7+8) for pairedTagAlign. This is not very nice way to deal with it, asking Jim for other suggestion.
  • 1.4 lines changed: 1, context: html, text, full: html, text
    dont print the full record if all the fields are already nicely formatted above
• src/hg/hgc/hgc.c
  • 1.1547 lines changed: 4, context: html, text, full: html, text
    show seq1,seq2 columns (non-standard bed cols 7+8) for pairedTagAlign
• src/hg/makeDb/trackDb/README
  • 1.75 lines changed: 6, context: html, text, full: html, text
    adding option to replace default 'red' tickmarks with contrasting or lighter color ones similar to the color in zoomed in base view
  • 1.74 lines changed: 5, context: html, text, full: html, text
    choose a contrasting color for tick marks when drawgin differnt bases
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.323 lines changed: 20, context: html, text, full: html, text
    adding option to replace default 'red' tickmarks with contrasting or lighter color ones similar to the color in zoomed in base view
  • 1.321 lines changed: 590, context: html, text, full: html, text
    adding 4 new AffyRnaChip submissions, removing old duplicated metadata settings, adding a missing metadata line
  • 1.319 lines changed: 48, context: html, text, full: html, text
    fix up FilteredRawSignal View name to be shorter FiltRawSignal for mysql table names
  • 1.318 lines changed: 47, context: html, text, full: html, text
    rename view to FiltTransfrags to ensure MySQL tablenames shorter than 65
  • 1.312 lines changed: 4, context: html, text, full: html, text
    turn off the base display until we have a better visualization
  • 1.311 lines changed: 5, context: html, text, full: html, text
    showing diffBases for Helicos until we can find an alignment format
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.22 lines changed: 1, context: html, text, full: html, text
    removign /cluster/hive even from comment in case it causes confusion
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.61 lines changed: 2, context: html, text, full: html, text
    v208 preview