hartera: changes by commit

review to branch (2009-08-25 to 2009-09-02) v214

• Added code to call the vegaGeneUI function if the track is vegaGeneComposite. vegaGenUI() creates radio buttons to select accession, gene name, both or none for track item labels. It also adds a check box to select for noncoding genes not to be shown and the base colouring drop down menu.
  • src/hg/hgTrackUi/hgTrackUi.c 1.498 - lines changed: 13, context: html, text, full: html, text
• Added code to vegaMethods() that calls loadGenePredWithConfiguredName on loading track items to interpret the radio button selections in the track UI.
  • src/hg/hgTracks/simpleTracks.c 1.99 - lines changed: 1, context: html, text, full: html, text
• Added printEnsemblOrVegaCustomUrl() to create URL links like Ensembl for the Vega track details page to link to the Vega gene, transcript and protein reports. Only Vega uses this right now. Need to test for Ensembl.
  • src/hg/hgc/hgc.c 1.1567 - lines changed: 119, context: html, text, full: html, text
• Added code to geneShowPosAndLinks() to write that there is no protein prediction for Vega gene if it is noncoding instead of having the sequence link.
  • src/hg/hgc/hgc.c 1.1568 - lines changed: 5, context: html, text, full: html, text
• Removed the hide noncoding genes option.
  • src/hg/hgTrackUi/hgTrackUi.c 1.499 - lines changed: 2, context: html, text, full: html, text
• Added vegaPep to vegaGeneComposite trackDb entry.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.415 - lines changed: 1, context: html, text, full: html, text