hartera: changes by file

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

• src/hg/hgTrackUi/hgTrackUi.c
  • 1.499 lines changed: 2, context: html, text, full: html, text
    Removed the hide noncoding genes option.
  • 1.498 lines changed: 13, context: html, text, full: html, text
    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/hgTracks/simpleTracks.c
  • 1.99 lines changed: 1, 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/hgc/hgc.c
  • 1.1568 lines changed: 5, 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.
  • 1.1567 lines changed: 119, 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/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.415 lines changed: 1, context: html, text, full: html, text
    Added vegaPep to vegaGeneComposite trackDb entry.