File Changes for tdreszer

v249_preview2 to v249_base (2011-03-22 to 2011-03-29) v249

• src/hg/encode/encodeExp/encodeExp.c
  • lines changed 12, context: html, text, full: html, text
    Added useful functions to mdb, including encode specific ones. Fixed encodeExp retreival by mdb obj.
  • lines changed 8, context: html, text, full: html, text
    Clarified a message to Kate
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 117, context: html, text, full: html, text
    Made mdb dependent upon cv defines. Made hgEncodeVocab use cv defines.
• src/hg/hgApi/hgApi.c
  • lines changed 5, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 43, context: html, text, full: html, text
    Fixed bug on name/description search and fleshed out wild card and quoted strings in description search
  • lines changed 46, context: html, text, full: html, text
    Now both name and description searches match each word, accept wildcards and respect quotes
  • lines changed 21, context: html, text, full: html, text
    Corrected the about message at the bottom of the page.
  • lines changed 47, context: html, text, full: html, text
    Addressed a bug in description searches and slightly streamlined.
  • lines changed 3, context: html, text, full: html, text
    File search should not advertise support for quoted string search, since new lines, etc. in target tdb->html can result in false negatives.
  • lines changed 13, context: html, text, full: html, text
    Ensure the backgound floret is used but avoid the overhead that hgTracks uses to acheive this.
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 7, context: html, text, full: html, text
    Add navigation link to downloads search
  • lines changed 1, context: html, text, full: html, text
    Katrina prefers 'File Search' to 'Downloads Search'
• src/hg/hgTracks/simpleTracks.c
  • lines changed 23, context: html, text, full: html, text
    redmine 1876. Hopefully fixed. Subtracks were going through limitVisibility() before their items were loaded.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 209, context: html, text, full: html, text
    Added 'files search buttons to downloads pages
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 56, context: html, text, full: html, text
    Added 'files search buttons to downloads pages
• src/hg/htdocs/ENCODE/index.html
  • lines changed 3, context: html, text, full: html, text
    Added page of search options for ENCODE files nad tracks. Also made attempt at using CSS instead of our usual tables within tables within tables to make borders to things.
  • lines changed 1, context: html, text, full: html, text
    Added a left menu search item under mouse too.
• src/hg/htdocs/ENCODE/search.html
  • lines changed 91, context: html, text, full: html, text
    Added page of search options for ENCODE files nad tracks. Also made attempt at using CSS instead of our usual tables within tables within tables to make borders to things.
  • lines changed 1, context: html, text, full: html, text
    Added 'files search buttons to downloads pages
• src/hg/inc/cv.h
  • lines changed 69, context: html, text, full: html, text
    Split out the cv routines into their own lib file, but have yet to rename any of the APIs
  • lines changed 12, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
  • lines changed 16, context: html, text, full: html, text
    Made mdb dependent upon cv defines. Made hgEncodeVocab use cv defines.
• src/hg/inc/encode/encodeExp.h
  • lines changed 1, context: html, text, full: html, text
    Added useful functions to mdb, including encode specific ones. Fixed encodeExp retreival by mdb obj.
  • lines changed 4, context: html, text, full: html, text
    Needed to protext NULLs when inserting into encodeExp table.
• src/hg/inc/mdb.h
  • lines changed 71, context: html, text, full: html, text
    Better management of mdb vars and cv terms string literals in anticilation of splitting out cv lib. Also removed the varType once and for all
  • lines changed 67, context: html, text, full: html, text
    Split out the cv routines into their own lib file, but have yet to rename any of the APIs
  • lines changed 6, context: html, text, full: html, text
    Made mdb dependent upon cv defines. Made hgEncodeVocab use cv defines.
  • lines changed 45, context: html, text, full: html, text
    Added useful functions to mdb, including encode specific ones. Fixed encodeExp retreival by mdb obj.
  • lines changed 4, context: html, text, full: html, text
    Needed to expose mdbVarsFree()
• src/hg/lib/cv.c
  • lines changed 238, context: html, text, full: html, text
    Split out the cv routines into their own lib file, but have yet to rename any of the APIs
  • lines changed 22, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
  • lines changed 24, context: html, text, full: html, text
    Made mdb dependent upon cv defines. Made hgEncodeVocab use cv defines.
• src/hg/lib/encode/encodeExp.c
  • lines changed 1, context: html, text, full: html, text
    Fixed a bug from unremoved older code.
  • lines changed 74, context: html, text, full: html, text
    Added useful functions to mdb, including encode specific ones. Fixed encodeExp retreival by mdb obj.
  • lines changed 44, context: html, text, full: html, text
    Needed to protext NULLs when inserting into encodeExp table.
• src/hg/lib/fileUi.c
  • lines changed 3, context: html, text, full: html, text
    Reduce limit on number of found files to 1000, because 200 takes too long.
  • lines changed 6, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Split out the cv routines into their own lib file, but have yet to rename any of the APIs
• src/hg/lib/mdb.c
  • lines changed 162, context: html, text, full: html, text
    Better management of mdb vars and cv terms string literals in anticilation of splitting out cv lib. Also removed the varType once and for all
  • lines changed 228, context: html, text, full: html, text
    Split out the cv routines into their own lib file, but have yet to rename any of the APIs
  • lines changed 13, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
  • lines changed 14, context: html, text, full: html, text
    Minor change to the experimentifier output as requested by Cricket.
  • lines changed 222, context: html, text, full: html, text
    Added useful functions to mdb, including encode specific ones. Fixed encodeExp retreival by mdb obj.
  • lines changed 28, context: html, text, full: html, text
    Needed to expose mdbVarsFree()
• src/hg/lib/searchTracks.c
  • lines changed 11, context: html, text, full: html, text
    Renamed a bunch of mdbCv APIs to cv APIs.
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 25, context: html, text, full: html, text
    Checking in old and newer doc of broad HMM
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeBroadHmm.release1.notes
  • lines changed 62, context: html, text, full: html, text
    Preparing for pushQ entry
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/makefile
  • lines changed 3, context: html, text, full: html, text
    These old tracks needed metadata lines replaced with mdb table entries
  • lines changed 1, context: html, text, full: html, text
    Moved perhaps the last of the metadata lines from trackDb to metaDb.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 162, context: html, text, full: html, text
    These old tracks needed metadata lines replaced with mdb table entries
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 16, context: html, text, full: html, text
    These old tracks needed metadata lines replaced with mdb table entries
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriNRE.ra
  • lines changed 69, context: html, text, full: html, text
    These old tracks needed metadata lines replaced with mdb table entries
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUmasshaTfbsValid.ra
  • lines changed 17, context: html, text, full: html, text
    Moved perhaps the last of the metadata lines from trackDb to metaDb.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 16, context: html, text, full: html, text
    These old tracks needed metadata lines replaced with mdb table entries
  • lines changed 30, context: html, text, full: html, text
    Moved perhaps the last of the metadata lines from trackDb to metaDb.
  • lines changed 29, context: html, text, full: html, text
    Mistakenly took out metadata lines from beta/public versions. They were already removed from alpha versions.
  • lines changed 185, context: html, text, full: html, text
    Round and round. Split the tracks that are having their metadata lines removed into alpha aand beta,public versions.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra
  • lines changed 104, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra
  • lines changed 44, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
  • lines changed 44, context: html, text, full: html, text
    Mistakenly took out metadata lines from beta/public versions. They were already removed from alpha versions.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.ra
  • lines changed 58, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
  • lines changed 6, context: html, text, full: html, text
    Mistakenly took out metadata lines from beta/public versions. They were already removed from alpha versions.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
  • lines changed 18, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
  • lines changed 18, context: html, text, full: html, text
    Mistakenly took out metadata lines from beta/public versions. They were already removed from alpha versions.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.ra
  • lines changed 6, context: html, text, full: html, text
    More metadata lines removed from trackDb but all of these should already have been in the mdb.
  • lines changed 6, context: html, text, full: html, text
    Mistakenly took out metadata lines from beta/public versions. They were already removed from alpha versions.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 0, context: html, text, full: html, text
    I had let CRLFs seep in while editing in windows.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
  • lines changed 14, context: html, text, full: html, text
    Added text about pooled replicates as per Katrina and Kate request.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
  • lines changed 3, context: html, text, full: html, text
    Standardized the liftOver note as per Katrina's request.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra
  • lines changed 0, context: html, text, full: html, text
    I had let CRLFs seep in while editing in windows.
• src/inc/common.h
  • lines changed 6, context: html, text, full: html, text
    Added respect for quotes in a couple of places.
  • lines changed 1, context: html, text, full: html, text
    Little more robust handling of one case of respect quotes.
• src/lib/common.c
  • lines changed 39, context: html, text, full: html, text
    Added respect for quotes in a couple of places.
  • lines changed 7, context: html, text, full: html, text
    Little more robust handling of one case of respect quotes.
  • lines changed 5, context: html, text, full: html, text
    Fixed bug that Kate found.