Commits for braney

v258_preview2 to v258_base (2011-10-04 to 2011-10-10) v258

• change the relationship between the trackHub structure and the hubConnectStatus structure to be hierarchical. This fixes #4920. We now *always* fetch the URL contents instead of trusting what's in the hubStatus table *unless* there's an error message in the hubStatus table.
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 22, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text
  • src/hg/inc/hubConnect.h - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 207, context: html, text, full: html, text
• oops... need to initialize this
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
• fix blue bug #5571
  • src/hg/hgc/mafClick.c - lines changed 2, context: html, text, full: html, text
• fix a weirdness with the display caused by a pause when the track hubs are collected. The behavior was that the window would paint one way, and then repaint correctly.
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 6, context: html, text, full: html, text
• fix a bug that only showed up in building the CDS FASTA alignments for rn4 RGD genes
  • src/hg/lib/mafGene.c - lines changed 3, context: html, text, full: html, text
• check trackDb.txt files and hub.txt files more closely in hgHubConnect so errors can be discovered ASAP. #4679 and others.
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 28, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 30, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 29, context: html, text, full: html, text
• don't reopen the trackHub's since they get opened when we check the status
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 4, context: html, text, full: html, text
  • src/hg/inc/hubConnect.h - lines changed 5, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 29, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 25, context: html, text, full: html, text
• don't reopen the trackHub since it's already in the hubStatus
  • src/hg/hgTables/hgTables.c - lines changed 7, context: html, text, full: html, text
• v258 final build
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v258
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text