Commits for larrym

v243_base to v244_preview (2010-11-02 to 2010-11-16) v244

• add geneModel option to accomodate using alternate gene models; use nibTwoCache to read DNA sequences (much faster than using hFetchSeqMixed)
  • src/hg/utils/mutationClassifier/mutationClassifier.c - lines changed 55, context: html, text, full: html, text
• start adding support for discovery of de novo binding site mutations
  • src/hg/utils/mutationClassifier/mutationClassifier.c - lines changed 157, context: html, text, full: html, text
• make sure openLink links contain chrom
  • src/hg/js/hgTracks.js - lines changed 5, context: html, text, full: html, text
• add makeImgTag to fix FireFox problem
  • src/hg/js/hgTracks.js - lines changed 19, context: html, text, full: html, text
• strip-out double quotes from description search string
  • src/hg/hgTracks/searchTracks.c - lines changed 1, context: html, text, full: html, text
• support codon numbering in genePred tracks
  • src/hg/hgTracks/cds.c - lines changed 30, context: html, text, full: html, text
  • src/hg/hgTracks/cds.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 5, context: html, text, full: html, text
• add codonColoringChanged
  • src/hg/js/utils.js - lines changed 7, context: html, text, full: html, text
• support codon numbering checkbox in hgTrackUi
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 9, context: html, text, full: html, text
• turn on CONTEXT_MENU
  • src/hg/hgTracks/imageV2.h - lines changed 1, context: html, text, full: html, text
• fix typo
  • src/hg/js/hgTracks.js - lines changed 1, context: html, text, full: html, text