Commits for kate

v295_preview to v295_preview2 (2014-01-20 to 2014-01-27) v295

• Fix dense mode display of motifs by splitting drawItems into two phases (items, and then motifs)
  • src/hg/hgTracks/factorSource.c - lines changed 56, context: html, text, full: html, text
• 1. Split out motif display code for better modularization. Clean up motif details info (add Name, remove max score for perf reasons)
  • src/hg/hgc/peakClusters.c - lines changed 103, context: html, text, full: html, text
• Make cell abbrev table into a collapsible section to reduce clutter on details page
  • src/hg/hgc/peakClusters.c - lines changed 10, context: html, text, full: html, text
  • src/hg/inc/jsHelper.h - lines changed 6, context: html, text, full: html, text
  • src/hg/inc/web.h - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/jsHelper.c - lines changed 35, context: html, text, full: html, text
  • src/hg/lib/web.c - lines changed 18, context: html, text, full: html, text
• Rename motif tables for consistency
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 26, context: html, text, full: html, text
• 1. Correct bad test for no canonical motif in table (thanks Hiram!). 2. Lose an indent for readability
  • src/hg/hgTracks/factorSource.c - lines changed 13, context: html, text, full: html, text
• Suppress overwrite of factor item labels with motif highlight color. refs #9092.
  • src/hg/hgTracks/factorSource.c - lines changed 14, context: html, text, full: html, text
• Add trackDbsetting 'motifMaxWindow' to suppress display of motifs in large windows
  • src/hg/hgTracks/factorSource.c - lines changed 5, context: html, text, full: html, text
• Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 14, context: html, text, full: html, text
  • src/hg/hgTracks/factorSource.c - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text
• Add motif info to ENCODE regulation TF ChIP track description.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html - lines changed 85, context: html, text, full: html, text
• Resolve merge conflict
• Format track references.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html - lines changed 28, context: html, text, full: html, text
• Replace ENCODE portal summary graphic with newer version from Mike Pazin, processed with ImageMagick (tnx Hiram) to trim whitespace and convert format:convert -quality 100 -trim -border 30x30 -bordercolor white ENCODEDatatypes2013v6.jpg EncodeDatatypes2013.png
  • src/hg/htdocs/ENCODE/aboutScaleup.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/ENCODE/index.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/images/EncodeDatatypes2013.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Replace per-item SQL query for motifs with single query at load time (trims 500msec from 30K window timing). refs #9092
  • src/hg/hgTracks/factorSource.c - lines changed 59, context: html, text, full: html, text