tdreszer: changes by commit

review to branch (2009-05-05 to 2009-05-12) v206

• Added 6 more datasets for Yale and changed the Peak controls
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.284 - lines changed: 395, context: html, text, full: html, text
• Marked the metadata of Yale's datasets that still have problems (peaks and signals)
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.285 - lines changed: 14, context: html, text, full: html, text
• Added simple routine to find a metadata setting
  • src/hg/inc/trackDb.h 1.48 - lines changed: 4, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c 1.64 - lines changed: 22, context: html, text, full: html, text
• Use metadata setting for controlled vocabulary look up and for restriction date lookup
  • src/hg/lib/hui.c 1.191 - lines changed: 37, context: html, text, full: html, text
• Clarified function comment
  • src/hg/inc/hui.h 1.126 - lines changed: 2, context: html, text, full: html, text
• Free memory after restrictionDate lookup
  • src/hg/hgTables/mainPage.c 1.143 - lines changed: 3, context: html, text, full: html, text
• Removed obsolete special case code for ENCODE Gencode linking to VEGA and Ensembl, because this is now done with trackDB.ra url settin. Also made dataVersion and restriction date use metadata
  • src/hg/hgc/hgc.c 1.1533 - lines changed: 27, context: html, text, full: html, text
• Removed NO_VALUE define, as it is defined in the header file. Thanks Hiram
  • src/lib/cheapcgi.c 1.121 - lines changed: 1, context: html, text, full: html, text
• Moved metadata display to separate function to be called from hgc and hgTables
  • src/hg/inc/hui.h 1.127 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.192 - lines changed: 57, context: html, text, full: html, text
• Moved metadata display toggle code to utils to be called from hgc and hgTrackUi
  • src/hg/js/hui.js 1.26 - lines changed: 20, context: html, text, full: html, text
  • src/hg/js/utils.js 1.21 - lines changed: 21, context: html, text, full: html, text
• Added call to show metadata if track is not a composite
  • src/hg/hgTrackUi/hgTrackUi.c 1.486 - lines changed: 5, context: html, text, full: html, text
• Added call to show metadata
  • src/hg/hgc/hgc.c 1.1534 - lines changed: 5, context: html, text, full: html, text
• Removed a lot of obsolete settings - values now in metadata. Should remove all these obsolete settings from non-released tracks
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.286 - lines changed: 841, context: html, text, full: html, text
• Fixed some Yale metadata and make Gencode not a default track (as per Jim)
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.288 - lines changed: 75, context: html, text, full: html, text
• Added the special case Ensembl Transcript Report link back in, due to tRNAs not having Ensembl IDs causing the trackDb.ra url setting to fail
  • src/hg/hgc/hgc.c 1.1535 - lines changed: 11, context: html, text, full: html, text
• Removed the Gencode url setting for auto-annotated track. tRNAs have no Ensembl ID so the link was broken.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.289 - lines changed: 2, context: html, text, full: html, text
• Now the page will be sorted on the defined sort order fields from the metadata.
  • src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl 1.12 - lines changed: 168, context: html, text, full: html, text
• Changed 'Track details..s' to 'Table metadata...'
  • src/hg/hgTrackUi/hgTrackUi.c 1.487 - lines changed: 1, context: html, text, full: html, text
• Temprarily comment out Duke/Unc/Uta RawSignals while they are regenerated
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.290 - lines changed: 460, context: html, text, full: html, text
• Fixed -quick, allow fragLength=0, removed obsolete trackDb.ra settings
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.181 - lines changed: 8, context: html, text, full: html, text
• Added Display Conventions section
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html 1.11 - lines changed: 6, context: html, text, full: html, text
• Added Duke/Uta/Unc Raw signals back in, now that they have been regenerated.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.291 - lines changed: 461, context: html, text, full: html, text
• Had to regen some 1/2 of Yale Raw Signals. Since already release, made alpha/beta tracks.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.292 - lines changed: 518, context: html, text, full: html, text
• Changed the name of some Yale tables to be consistent
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.293 - lines changed: 16, context: html, text, full: html, text
• Added description of scoreFilter and filterBy category
  • src/hg/makeDb/trackDb/README 1.70 - lines changed: 46, context: html, text, full: html, text
• Added API for hgTrackUi and hgc to show schemaLink, Downlaods link and metadata
  • src/hg/inc/hui.h 1.128 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.193 - lines changed: 111, context: html, text, full: html, text
• Call common API for showing downloads, schema and metadata links
  • src/hg/hgTrackUi/hgTrackUi.c 1.488 - lines changed: 11, context: html, text, full: html, text
  • src/hg/hgc/hgc.c 1.1539 - lines changed: 2, context: html, text, full: html, text
• Added a link to help on 'Filter by category' UI
  • src/hg/lib/hui.c 1.194 - lines changed: 3, context: html, text, full: html, text