File Changes for kate

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

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 14, context: html, text, full: html, text
    Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092
• src/hg/hgTracks/factorSource.c
  • lines changed 56, context: html, text, full: html, text
    Fix dense mode display of motifs by splitting drawItems into two phases (items, and then motifs)
  • lines changed 13, context: html, text, full: html, text
    1. Correct bad test for no canonical motif in table (thanks Hiram!). 2. Lose an indent for readability
  • lines changed 14, context: html, text, full: html, text
    Suppress overwrite of factor item labels with motif highlight color. refs #9092.
  • lines changed 5, context: html, text, full: html, text
    Add trackDbsetting 'motifMaxWindow' to suppress display of motifs in large windows
  • lines changed 5, context: html, text, full: html, text
    Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092
  • lines changed 59, context: html, text, full: html, text
    Replace per-item SQL query for motifs with single query at load time (trims 500msec from 30K window timing). refs #9092
• src/hg/hgc/peakClusters.c
  • lines changed 103, 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)
  • lines changed 10, context: html, text, full: html, text
    Make cell abbrev table into a collapsible section to reduce clutter on details page
• src/hg/htdocs/ENCODE/aboutScaleup.html
  • lines changed 2, 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/index.html
  • lines changed 2, 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/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 19, context: html, text, full: html, text
    Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092
• src/hg/htdocs/images/EncodeDatatypes2013.png
  • lines changed 0, 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/inc/jsHelper.h
  • lines changed 6, context: html, text, full: html, text
    Make cell abbrev table into a collapsible section to reduce clutter on details page
• src/hg/inc/web.h
  • lines changed 7, context: html, text, full: html, text
    Make cell abbrev table into a collapsible section to reduce clutter on details page
• src/hg/lib/jsHelper.c
  • lines changed 35, context: html, text, full: html, text
    Make cell abbrev table into a collapsible section to reduce clutter on details page
• src/hg/lib/web.c
  • lines changed 18, context: html, text, full: html, text
    Make cell abbrev table into a collapsible section to reduce clutter on details page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 26, context: html, text, full: html, text
    Rename motif tables for consistency
  • lines changed 3, context: html, text, full: html, text
    Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092
  • lines changed 2, context: html, text, full: html, text
    Add motif info to ENCODE regulation TF ChIP track description.
  • lines changed 2, context: html, text, full: html, text
    Format track references.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
  • lines changed 85, context: html, text, full: html, text
    Add motif info to ENCODE regulation TF ChIP track description.
  • lines changed 28, context: html, text, full: html, text
    Format track references.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092