tdreszer: changes by commit

branch to review (2009-12-01 to 2009-12-09) v221

• Added in 2 more experiments for HAIB TFSB
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.693 - lines changed: 81, context: html, text, full: html, text
• Some Rep2 tagAligns were missing.
  • src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt 1.10 - lines changed: 120, context: html, text, full: html, text
• Backlog check-in
  • src/hg/makeDb/doc/encodeDccHg18/uwStam.txt 1.4 - lines changed: 11, context: html, text, full: html, text
• Finally most of Yale's tagAligns have been corrected.
  • src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt 1.12 - lines changed: 306, context: html, text, full: html, text
• Backlog of work needing check-in
  • src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt 1.4 - lines changed: 131, context: html, text, full: html, text
• Removed one file that Richard noticed was replaced with differently named file
  • src/hg/makeDb/doc/encodeDccHg18/uwChIPseq.release1.notes.txt 1.3 - lines changed: 2, context: html, text, full: html, text
• relabel a couple of Yale tracks that should belong to YCD or Stanford
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.695 - lines changed: 4, context: html, text, full: html, text
• Fix bug in imageV2 maps to make them written in creation order
  • src/hg/hgTracks/imageV2.c 1.15 - lines changed: 2, context: html, text, full: html, text
• Renamed 6 cell lines by request from Greg Crawford
  • src/hg/encode/encodeValidate/config/cv.ra 1.149 - lines changed: 12, context: html, text, full: html, text
• Switched Gliobla and Medullo
  • src/hg/encode/encodeValidate/config/cv.ra 1.151 - lines changed: 44, context: html, text, full: html, text
• Fixed poorly worded release 2 note.
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html 1.28 - lines changed: 1, context: html, text, full: html, text
• Fix for bug Katrina found. All plus/minus buttons were failing when no matrix exists
  • src/hg/js/hui.js 1.44 - lines changed: 1, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.251 - lines changed: 1, context: html, text, full: html, text
• Replaced a bunch of viewLimitsMax vars with minLimit and maxLimit. Don't like it but will go along with the current.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.707 - lines changed: 20, context: html, text, full: html, text
• Restored viewLimitsCompositeOverride so that minLimit,maxLimit can be used to prompt range in view level cfg
  • src/hg/lib/wiggleCart.c 1.35 - lines changed: 37, context: html, text, full: html, text
• Created static variable advancedJsEnabled to avoid excessive calls to look it up
  • src/hg/hgTracks/config.c 1.87 - lines changed: 17, context: html, text, full: html, text
• Tie the chrom imnnage drag jump feature to advancedJavascriptFeatures
  • src/hg/hgTracks/cytoBandTrack.c 1.12 - lines changed: 8, context: html, text, full: html, text
• Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
  • src/hg/hgTracks/hgTracks.c 1.1612 - lines changed: 660, context: html, text, full: html, text
  • src/hg/hgTracks/imageV2.c 1.17 - lines changed: 273, context: html, text, full: html, text
  • src/hg/hgTracks/imageV2.h 1.12 - lines changed: 78, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c 1.116 - lines changed: 35, context: html, text, full: html, text
  • src/hg/hgTracks/wigTrack.c 1.99 - lines changed: 5, context: html, text, full: html, text
  • src/hg/js/hgTracks.js 1.48 - lines changed: 156, context: html, text, full: html, text
• cartJustify has been added to clean up _imgOrd settings superceded by changed priorities
  • src/hg/lib/cart.c 1.114 - lines changed: 109, context: html, text, full: html, text
• Added a couple color defines
  • src/inc/cheapcgi.h 1.68 - lines changed: 4, context: html, text, full: html, text
• Keeping the record up to date
  • src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt 1.5 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg18/uwStam.txt 1.5 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt 1.13 - lines changed: 49, context: html, text, full: html, text
• Added protocol for HAIB
  • src/hg/encode/encodeValidate/config/fields.ra 1.23 - lines changed: 5, context: html, text, full: html, text
• Added some treatments and protocols for HAIB
  • src/hg/encode/encodeValidate/config/cv.ra 1.152 - lines changed: 55, context: html, text, full: html, text
• Added protocol and treatment terms
  • src/hg/encode/DAFs/HAIBChIPseq.daf 1.2 - lines changed: 1, context: html, text, full: html, text
• Example with protocol and treatment
  • src/hg/encode/DAFs/HAIBChIPseqExample.ddf 1.1 - lines changed: 9, context: html, text, full: html, text
• Added protocol as another term
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.207 - lines changed: 1, context: html, text, full: html, text
• Added 3 dimensionChecked terms and made subGroup6 allowed on any type
  • src/hg/makeDb/trackDb/tagTypes.tab 1.4 - lines changed: 4, context: html, text, full: html, text
• Added protocol and treatment to HAIB TFBS
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.715 - lines changed: 226, context: html, text, full: html, text