kent: changes by commit

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

• Making overrides apply to settings rather than fields. Fields are recalculated from settings later by another routine.
  • src/hg/lib/trackDbCustom.c 1.88 - lines changed: 59, context: html, text, full: html, text
• Removing old code.
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c 1.68 - lines changed: 26, context: html, text, full: html, text
• Fixing sprung-loose visibilities.
  • src/hg/lib/hdb.c 1.427 - lines changed: 1, context: html, text, full: html, text
• Making show schema link work when track != table.
  • src/hg/hgTables/hgTables.c 1.195 - lines changed: 13, context: html, text, full: html, text
• Fixing composite tag search that should have been compositeTrack search.
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c 1.69 - 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
  • src/hg/makeDb/trackDb/trackDb.ra 1.631 - lines changed: 1, context: html, text, full: html, text
• Adding stuff for aggregate/overlay dropdown.
  • src/hg/inc/hui.h 1.150 - lines changed: 6, context: html, text, full: html, text
  • src/hg/inc/wiggle.h 1.91 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.285 - lines changed: 35, context: html, text, full: html, text
• More noodling getting multiWig UI page to work, mostly by pretending to be composite.
  • src/hg/hgTrackUi/hgTrackUi.c 1.525 - lines changed: 10, context: html, text, full: html, text
• Making it so that multi-wigs can draw without overlay as well.
  • src/hg/hgTracks/multiWig.c 1.3 - lines changed: 74, context: html, text, full: html, text
  • src/hg/hgTracks/wigTrack.c 1.109 - lines changed: 0, 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.
  • src/hg/inc/hui.h 1.151 - lines changed: 2, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.286 - lines changed: 4, context: html, text, full: html, text
• More tinkering on encode regulation track.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.485 - lines changed: 83, context: html, text, full: html, text
• improving layout of comment
  • src/hg/hgTracks/imageV2.c 1.29 - lines changed: 4, context: html, text, full: html, text
• Making click on multi-wig bring up trackUi page.
  • src/hg/hgTracks/container.c 1.4 - lines changed: 7, context: html, text, full: html, text
  • src/hg/hgTracks/container.h 1.2 - lines changed: 8, context: html, text, full: html, text
  • src/hg/hgTracks/multiWig.c 1.4 - lines changed: 22, 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.c 1.1622 - lines changed: 28, context: html, text, full: html, text
• Getting rid of some special cases no longer needed for mrna track.
  • src/hg/hgGenome/import.c 1.20 - lines changed: 18, context: html, text, full: html, text
• Fixing a ->table that should be a ->track. Thanks Angie for spotting this.
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c 1.70 - 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/hgTables/custom.c 1.48 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c 1.196 - lines changed: 8, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.145 - lines changed: 1, 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/tagTypes.tab 1.22 - lines changed: 23, context: html, text, full: html, text
• Adding inputTracks tags to wgEncodeReg DNAse component
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.486 - lines changed: 3, context: html, text, full: html, text
• Adding handler for clustered-peaks like wgEncodeRegDnaseClustered
  • src/hg/hgc/hgc.c 1.1623 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgc/hgc.h 1.52 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgc/makefile 1.67 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgc/peakClusters.c 1.1 - lines changed: 200, 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/regCluster/regCluster.c 1.4 - lines changed: 4, 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/trackDb.ra 1.487 - lines changed: 170, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.970 - lines changed: 172, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRegDnaseClustered.html 1.1 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhancer.html 1.1 - lines changed: 3, context: html, text, full: html, text
• Fixed small typo in parameter name in function prototype.
  • src/inc/obscure.h 1.37 - lines changed: 1, context: html, text, full: html, text
• moving literal 6 to variable scoreColIx
  • src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c 1.4 - lines changed: 3, context: html, text, full: html, text
• Adding factorSource to inputTracks*
  • src/hg/makeDb/trackDb/tagTypes.tab 1.23 - lines changed: 3, context: html, text, full: html, text
• Adding inputTracks* tags to another wgEncodeReg track.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.971 - lines changed: 3, context: html, text, full: html, text
• implementing compositeGroupLabel and compositeGroupId functions, and exposing existing static function as compositeLabelWithVocabLink
  • src/hg/inc/hui.h 1.152 - lines changed: 11, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.288 - lines changed: 39, context: html, text, full: html, text
• Working on details pages for DNase Clusters and Txn Factor ChIP tracks.
  • src/hg/hgc/encodeClick.c 1.16 - lines changed: 52, context: html, text, full: html, text
  • src/hg/hgc/hgc.c 1.1624 - lines changed: 4, context: html, text, full: html, text
  • src/hg/hgc/hgc.h 1.53 - lines changed: 7, context: html, text, full: html, text
  • src/hg/hgc/peakClusters.c 1.2 - lines changed: 180, 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.
  • src/hg/hgc/hgc.c 1.1625 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgc/hgc.h 1.54 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgc/peakClusters.c 1.3 - lines changed: 119, context: html, text, full: html, text