File Changes for kent

v245_base to v246_preview (2011-01-04 to 2010-01-11) v246

• src/hg/hgGateway/hgGateway.c
  • lines changed 11, context: html, text, full: html, text
    Adding 'import tracks' button to hgGateway.
  • lines changed 5, context: html, text, full: html, text
    Updating import button to work with changes in main branch.
  • lines changed 2, context: html, text, full: html, text
    Commenting out import button in preparation for merging with main tree.
  • lines changed 2, context: html, text, full: html, text
    Adding back in import button
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 101, context: html, text, full: html, text
    Checking in a skeletal hub connection page.
  • lines changed 56, context: html, text, full: html, text
    Adding genome and assembly to hgHubConnect, and a submit button. Adding dbList to hubConnect table.
  • lines changed 13, context: html, text, full: html, text
    Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
  • lines changed 1, context: html, text, full: html, text
    Fixing it's/its grammar mistake.
• src/hg/hgHubConnect/makefile
  • lines changed 17, context: html, text, full: html, text
    Checking in a skeletal hub connection page.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 24, context: html, text, full: html, text
    Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
  • lines changed 1, context: html, text, full: html, text
    Starting to get trackHub stuff to work with composite tracks. (Using UNC Faire as a test set on hg19.)
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 6, context: html, text, full: html, text
    Redoing dataHub using new trackHub library routines. Still pretty embryonic, but once again is displaying a couple of tracks for me, this time ones that are genuinely remote. Code is activated by having a 'tracksHub' variable in the cart, which currently is only possible by hacking with cartDump.
  • lines changed 2, context: html, text, full: html, text
    Fixing bug where bogus NULL would be returned for bbiFileName.
  • lines changed 1, context: html, text, full: html, text
    Removing some debugging statements.
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 3, context: html, text, full: html, text
    Redoing dataHub using new trackHub library routines. Still pretty embryonic, but once again is displaying a couple of tracks for me, this time ones that are genuinely remote. Code is activated by having a 'tracksHub' variable in the cart, which currently is only possible by hacking with cartDump.
• src/hg/hgTracks/hgTracks.c
  • lines changed 23, context: html, text, full: html, text
    Adding a bunch of debugging stuff.
  • lines changed 12, context: html, text, full: html, text
    Making dataHubs work with oneWig.ra and reducing the debugging.
  • lines changed 32, context: html, text, full: html, text
    Redoing dataHub using new trackHub library routines. Still pretty embryonic, but once again is displaying a couple of tracks for me, this time ones that are genuinely remote. Code is activated by having a 'tracksHub' variable in the cart, which currently is only possible by hacking with cartDump.
  • lines changed 44, context: html, text, full: html, text
    Making hubs appear in group list.
  • lines changed 27, context: html, text, full: html, text
    Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
  • lines changed 4, context: html, text, full: html, text
    Removing some debugging statements.
  • lines changed 11, context: html, text, full: html, text
    Removing debugging statements.
  • lines changed 3, context: html, text, full: html, text
    Starting to get trackHub stuff to work with composite tracks. (Using UNC Faire as a test set on hg19.)
  • lines changed 18, context: html, text, full: html, text
    Fixing subtrack sorting problem in composite tracks in track hub.
• src/hg/hgTracks/hgTracks.h
  • lines changed 2, context: html, text, full: html, text
    Redoing dataHub using new trackHub library routines. Still pretty embryonic, but once again is displaying a couple of tracks for me, this time ones that are genuinely remote. Code is activated by having a 'tracksHub' variable in the cart, which currently is only possible by hacking with cartDump.
  • lines changed 1, context: html, text, full: html, text
    Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
  • lines changed 1, context: html, text, full: html, text
    Fixing redmine issue #2151 where multiWig tracks had to be visibility full in trackDb.ra to _ever_ be seen properly.
• src/hg/hgTracks/multiWig.c
  • lines changed 10, context: html, text, full: html, text
    Making it so system handles missing aggregate tag in multiWig trackDb stanzas.
  • lines changed 1, context: html, text, full: html, text
    Fixing redmine issue #2151 where multiWig tracks had to be visibility full in trackDb.ra to _ever_ be seen properly.
  • lines changed 0, context: html, text, full: html, text
    Removing debugging statements.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 15, context: html, text, full: html, text
    Fixing redmine issue #2151 where multiWig tracks had to be visibility full in trackDb.ra to _ever_ be seen properly.
  • lines changed 2, context: html, text, full: html, text
    Fixing subtrack sorting problem in composite tracks in track hub.
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    Adding trackDbPolishAfterLinkup routine that bundles together a number of other calls, and exposing it for use by data hub trackDb list makers.
• src/hg/inc/hubConnect.h
  • lines changed 15, context: html, text, full: html, text
    Adding hubConnect module to help manage list of hubs that are available.
  • lines changed 2, context: html, text, full: html, text
    Making hubConnect.as and hubConnect.sql. This is _not_ done by autoSql since we just want field-by-field access of this in the code.
  • lines changed 3, context: html, text, full: html, text
    Adding genome and assembly to hgHubConnect, and a submit button. Adding dbList to hubConnect table.
  • lines changed 48, context: html, text, full: html, text
    Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
• src/hg/inc/trackDb.h
  • lines changed 3, context: html, text, full: html, text
    Adding trackDbFromOpenRa entry point.
  • lines changed 10, context: html, text, full: html, text
    Fixing conflicts from merging with master.
  • lines changed 4, context: html, text, full: html, text
    Fixing subtrack sorting problem in composite tracks in track hub.
• src/hg/inc/trackHub.h
  • lines changed 76, context: html, text, full: html, text
    Moving many routines from hubCheck to trackHub.c library file.
  • lines changed 6, context: html, text, full: html, text
    Adding trackHubAddNamePrefix to help give hubs their own name space within cart.
  • lines changed 7, context: html, text, full: html, text
    Making hubs appear in group list.
  • lines changed 3, context: html, text, full: html, text
    Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    Removing some ugly debugging statements.
  • lines changed 16, context: html, text, full: html, text
    Adding trackDbPolishAfterLinkup routine that bundles together a number of other calls, and exposing it for use by data hub trackDb list makers.
  • lines changed 8, context: html, text, full: html, text
    Fixing subtrack sorting problem in composite tracks in track hub.
• src/hg/lib/hubConnect.as
  • lines changed 13, context: html, text, full: html, text
    Making hubConnect.as and hubConnect.sql. This is _not_ done by autoSql since we just want field-by-field access of this in the code.
  • lines changed 2, context: html, text, full: html, text
    Adding genome and assembly to hgHubConnect, and a submit button. Adding dbList to hubConnect table.
• src/hg/lib/hubConnect.c
  • lines changed 24, context: html, text, full: html, text
    Adding hubConnect module to help manage list of hubs that are available.
  • lines changed 2, context: html, text, full: html, text
    Making hubConnect.as and hubConnect.sql. This is _not_ done by autoSql since we just want field-by-field access of this in the code.
  • lines changed 125, context: html, text, full: html, text
    Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
  • lines changed 7, context: html, text, full: html, text
    Making it so only hubs actually turned on are added.
  • lines changed 1, context: html, text, full: html, text
    Removing debugging statements.
• src/hg/lib/hubConnect.sql
  • lines changed 20, context: html, text, full: html, text
    Making hubConnect.as and hubConnect.sql. This is _not_ done by autoSql since we just want field-by-field access of this in the code.
  • lines changed 2, context: html, text, full: html, text
    Adding genome and assembly to hgHubConnect, and a submit button. Adding dbList to hubConnect table.
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving many routines from hubCheck to trackHub.c library file.
  • lines changed 1, context: html, text, full: html, text
    Adding hubConnect module to help manage list of hubs that are available.
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    Making trackDbFromRa() able to take a URL as well as a file name.
  • lines changed 14, context: html, text, full: html, text
    Adding trackDbFromOpenRa entry point.
  • lines changed 62, context: html, text, full: html, text
    Fixing subtrack sorting problem in composite tracks in track hub.
• src/hg/lib/trackHub.c
  • lines changed 281, context: html, text, full: html, text
    Moving many routines from hubCheck to trackHub.c library file.
  • lines changed 57, context: html, text, full: html, text
    Adding trackHubAddNamePrefix to help give hubs their own name space within cart.
  • lines changed 10, context: html, text, full: html, text
    Making hubs appear in group list.
  • lines changed 17, context: html, text, full: html, text
    Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
  • lines changed 1, context: html, text, full: html, text
    Fixing conflicts from merging with master.
  • lines changed 4, context: html, text, full: html, text
    Removing debugging statements.
  • lines changed 4, context: html, text, full: html, text
    Making trackHub tolerate 'on' and 'off' in a parent line in trackDb.ra file.
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 3, context: html, text, full: html, text
    Making system work even when there are tabs rather than spaces in the type, shortLabel, or longLabel fields.
  • lines changed 66, context: html, text, full: html, text
    Fixing subtrack sorting problem in composite tracks in track hub.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Sneaking in a commented out include for testing stuff vs. data hub tracks that do the same thing.
• src/hg/oneShot/freen/freen.c
  • lines changed 30, context: html, text, full: html, text
    Making freen test netLineFileOpen.
  • lines changed 22, context: html, text, full: html, text
    Testing track list.
  • lines changed 17, context: html, text, full: html, text
    Changing freen to test stripRegEx
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 200, context: html, text, full: html, text
    Start version of hub checker.
  • lines changed 23, context: html, text, full: html, text
    Reading tdb list for a given genome for a hub.
  • lines changed 135, context: html, text, full: html, text
    Checking trackDb.ra file to make sure items are containers or have bigDataUrl. Some other checks.
  • lines changed 246, context: html, text, full: html, text
    Moving many routines from hubCheck to trackHub.c library file.
  • lines changed 1, context: html, text, full: html, text
    Adding name parameter to hubOpen call.
• src/hg/utils/hubCheck/makefile
  • lines changed 18, context: html, text, full: html, text
    Start version of hub checker.
  • lines changed 2, context: html, text, full: html, text
    Reading tdb list for a given genome for a hub.
• src/inc/common.h
  • lines changed 5, context: html, text, full: html, text
    Adding catTwoStrings to common library.
• src/inc/filePath.h
  • lines changed 10, context: html, text, full: html, text
    Adding new function pathRelativeToFile
• src/inc/udc.h
  • lines changed 13, context: html, text, full: html, text
    Adding new functions udcFileReadAll and udcWrapShortLineFile
• src/lib/common.c
  • lines changed 13, context: html, text, full: html, text
    Adding catTwoStrings to common library.
• src/lib/filePath.c
  • lines changed 21, context: html, text, full: html, text
    Adding new function pathRelativeToFile
• src/lib/net.c
  • lines changed 8, context: html, text, full: html, text
    Made it so that netUrlOpenSockets (and hence netUrlOpen and netLineFileOpen) can handle a plain unix file name as well as a URL.
• src/lib/udc.c
  • lines changed 31, context: html, text, full: html, text
    Adding new functions udcFileReadAll and udcWrapShortLineFile