kent: changes by file

review to branch (2010-05-11 to 2010-05-18) v231

• src/hg/hgGenome/import.c
  • 1.20 lines changed: 18, context: html, text, full: html, text
    Getting rid of some special cases no longer needed for mrna track.
• src/hg/hgTables/custom.c
  • 1.48 lines changed: 6, context: html, text, full: html, text
    Refactoring a bit so can pass a table string rather than a track struct to eliminate a track/table potential blending of things.
• src/hg/hgTables/hgTables.c
  • 1.196 lines changed: 8, context: html, text, full: html, text
    Refactoring a bit so can pass a table string rather than a track struct to eliminate a track/table potential blending of things.
  • 1.195 lines changed: 13, context: html, text, full: html, text
    Making show schema link work when track != table.
• src/hg/hgTables/hgTables.h
  • 1.145 lines changed: 1, context: html, text, full: html, text
    Refactoring a bit so can pass a table string rather than a track struct to eliminate a track/table potential blending of things.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.525 lines changed: 10, context: html, text, full: html, text
    More noodling getting multiWig UI page to work, mostly by pretending to be composite.
• src/hg/hgTracks/container.c
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Making click on multi-wig bring up trackUi page.
• src/hg/hgTracks/container.h
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Making click on multi-wig bring up trackUi page.
• src/hg/hgTracks/imageV2.c
  • 1.29 lines changed: 4, context: html, text, full: html, text
    improving layout of comment
• src/hg/hgTracks/multiWig.c
  • 1.4 lines changed: 22, context: html, text, full: html, text
    Making click on multi-wig bring up trackUi page.
  • 1.3 lines changed: 74, context: html, text, full: html, text
    Making it so that multi-wigs can draw without overlay as well.
• src/hg/hgTracks/wigTrack.c
  • 1.109 lines changed: 0, context: html, text, full: html, text
    Making it so that multi-wigs can draw without overlay as well.
• src/hg/hgc/encodeClick.c
  • 1.16 lines changed: 52, context: html, text, full: html, text
    Working on details pages for DNase Clusters and Txn Factor ChIP tracks.
• src/hg/hgc/hgc.c
  • 1.1625 lines changed: 5, context: html, text, full: html, text
    Putting in page that shows all tracks that could contribute items to a cluster. Link to this page at the end of items in cluster table.
  • 1.1624 lines changed: 4, context: html, text, full: html, text
    Working on details pages for DNase Clusters and Txn Factor ChIP tracks.
  • 1.1623 lines changed: 4, context: html, text, full: html, text
    Adding handler for clustered-peaks like wgEncodeRegDnaseClustered
  • 1.1622 lines changed: 28, context: html, text, full: html, text
    Starting a generic click handler for containers. Not really useful now though since decided to just go straight to hgTrackUi for multiWigs.
• src/hg/hgc/hgc.h
  • 1.54 lines changed: 6, context: html, text, full: html, text
    Putting in page that shows all tracks that could contribute items to a cluster. Link to this page at the end of items in cluster table.
  • 1.53 lines changed: 7, context: html, text, full: html, text
    Working on details pages for DNase Clusters and Txn Factor ChIP tracks.
  • 1.52 lines changed: 3, context: html, text, full: html, text
    Adding handler for clustered-peaks like wgEncodeRegDnaseClustered
• src/hg/hgc/makefile
  • 1.67 lines changed: 4, context: html, text, full: html, text
    Adding handler for clustered-peaks like wgEncodeRegDnaseClustered
• src/hg/hgc/peakClusters.c
  • 1.3 lines changed: 119, context: html, text, full: html, text
    Putting in page that shows all tracks that could contribute items to a cluster. Link to this page at the end of items in cluster table.
  • 1.2 lines changed: 180, context: html, text, full: html, text
    Working on details pages for DNase Clusters and Txn Factor ChIP tracks.
  • 1.1 lines changed: 200, context: html, text, full: html, text
    Adding handler for clustered-peaks like wgEncodeRegDnaseClustered
• src/hg/inc/hui.h
  • 1.152 lines changed: 11, context: html, text, full: html, text
    implementing compositeGroupLabel and compositeGroupId functions, and exposing existing static function as compositeLabelWithVocabLink
  • 1.151 lines changed: 2, context: html, text, full: html, text
    Removing sum and product type aggregates from UI since they aren't implemented now, and may not be soon.
  • 1.150 lines changed: 6, context: html, text, full: html, text
    Adding stuff for aggregate/overlay dropdown.
• src/hg/inc/wiggle.h
  • 1.91 lines changed: 1, context: html, text, full: html, text
    Adding stuff for aggregate/overlay dropdown.
• src/hg/lib/hdb.c
  • 1.427 lines changed: 1, context: html, text, full: html, text
    Fixing sprung-loose visibilities.
• src/hg/lib/hui.c
  • 1.288 lines changed: 39, context: html, text, full: html, text
    implementing compositeGroupLabel and compositeGroupId functions, and exposing existing static function as compositeLabelWithVocabLink
  • 1.286 lines changed: 4, context: html, text, full: html, text
    Removing sum and product type aggregates from UI since they aren't implemented now, and may not be soon.
  • 1.285 lines changed: 35, context: html, text, full: html, text
    Adding stuff for aggregate/overlay dropdown.
• src/hg/lib/trackDbCustom.c
  • 1.88 lines changed: 59, context: html, text, full: html, text
    Making overrides apply to settings rather than fields. Fields are recalculated from settings later by another routine.
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • 1.70 lines changed: 1, context: html, text, full: html, text
    Fixing a ->table that should be a ->track. Thanks Angie for spotting this.
  • 1.69 lines changed: 1, context: html, text, full: html, text
    Fixing composite tag search that should have been compositeTrack search.
  • 1.68 lines changed: 26, context: html, text, full: html, text
    Removing old code.
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.23 lines changed: 3, context: html, text, full: html, text
    Adding factorSource to inputTracks*
  • 1.22 lines changed: 23, context: html, text, full: html, text
    Adding setting that are used by customTracks to reserve them, and hopefully avoid conflicts in the figure like we had with 'dataUrl' which had to be renamed at some cost to 'bigDataUrl'
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.631 lines changed: 1, context: html, text, full: html, text
    Adjusting some visibilities
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.534 lines changed: 1, context: html, text, full: html, text
    Adjusting some visibilities
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.487 lines changed: 170, context: html, text, full: html, text
    Moving wgEncodeReg track and subtracks to hg18/trackDb.wgEncode.ra from hg18/trackDb.ra. Also starting on a couple of the html descriptions - just a bare start.
  • 1.486 lines changed: 3, context: html, text, full: html, text
    Adding inputTracks tags to wgEncodeReg DNAse component
  • 1.485 lines changed: 83, context: html, text, full: html, text
    More tinkering on encode regulation track.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.971 lines changed: 3, context: html, text, full: html, text
    Adding inputTracks* tags to another wgEncodeReg track.
  • 1.970 lines changed: 172, context: html, text, full: html, text
    Moving wgEncodeReg track and subtracks to hg18/trackDb.wgEncode.ra from hg18/trackDb.ra. Also starting on a couple of the html descriptions - just a bare start.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegDnaseClustered.html
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Moving wgEncodeReg track and subtracks to hg18/trackDb.wgEncode.ra from hg18/trackDb.ra. Also starting on a couple of the html descriptions - just a bare start.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhancer.html
  • 1.1 lines changed: 3, context: html, text, full: html, text
    Moving wgEncodeReg track and subtracks to hg18/trackDb.wgEncode.ra from hg18/trackDb.ra. Also starting on a couple of the html descriptions - just a bare start.
• src/hg/regulate/regCluster/regCluster.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Putting in something so that multiple peaks in the same cluster from the same source don't get counted twice.
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
  • 1.4 lines changed: 3, context: html, text, full: html, text
    moving literal 6 to variable scoreColIx
• src/inc/obscure.h
  • 1.37 lines changed: 1, context: html, text, full: html, text
    Fixed small typo in parameter name in function prototype.