angie: changes by file

branch to review (2009-08-18 to 2009-08-25) v213

• src/ameme/ameme.c
  • 1.15 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/ameme/amemeFloat.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/ameme/fixpAmeme.c
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/gsid/pbGsid/pbGsid.c
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/hgCustom/hgCustom.c
  • 1.131 lines changed: 13, context: html, text, full: html, text
    Added errCatch around customTracksParseCartDetailed (similar to that around customTrackUpdateFromConfig) because bad URL in doc input was causing abort.
• src/hg/hgGene/altSplice.c
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/hgGeneRing/hgGeneRing.c
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/hgGenome/mainPage.c
  • 1.27 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/hgTables/correlatePlot.c
  • 1.16 lines changed: 5, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/hgTracks/bamTrack.c
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Ignore strand -- seems to always be + and BAM inherently adjusts sequence and CIGAR to the positive strand when the alignment was -. Probably should test for inversion cases and make those appear minus strand.
  • 1.6 lines changed: 26, context: html, text, full: html, text
    Removed the hardcoded BAM_MAX_ZOOM -- using trackDb setting maxWindowToDraw now.
• src/hg/hgTracks/hgTracks.c
  • 1.1594 lines changed: 23, context: html, text, full: html, text
    Fixed maxWindowToDraw-handling to support the setting at both composite track and subtrack level. Unfortunately, view-level does not yet work because limitedVisFromComposite overrides the dense limitedVis, so if view default vis is pack then the message is not displayed (clipped, 0 items = 0 height).
  • 1.1593 lines changed: 1, context: html, text, full: html, text
    Use trackDbSettingClosestToHome (not just trackDbSetting) in getMaxWindowToDraw, so subtracks will display the correct size threshold.
  • 1.1592 lines changed: 11, context: html, text, full: html, text
    Handle composite tracks in maxWindowSizeExceeded. (Individual subtracks of a composite track still not supported.)
  • 1.1591 lines changed: 2, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
  • 1.1590 lines changed: 5, context: html, text, full: html, text
    When winEnd-winStart > trackDb setting maxWindowToDraw, inhibit the toggle-link over the message because toggling vis doesn't affect the image.
• src/hg/hgTracks/oneTrack.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/hgc/bamClick.c
  • 1.7 lines changed: 38, context: html, text, full: html, text
    Added bamIgnoreStrand, bamIsRc, bamShowCigarEnglish, bamShowTags. In hgc/bamClick.c, also added showOverlap.
  • 1.6 lines changed: 26, context: html, text, full: html, text
    Added search for paired ends outside window, +- trackDb setting pairSearchRange.
  • 1.5 lines changed: 47, context: html, text, full: html, text
    Added pairing for easy cases (both ends in hgTracks window).
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Use the new ffShowSideBySide to display just the side-by-side read alignments, instead of ffShAliPart which expects to fill a page.
  • 1.3 lines changed: 15, context: html, text, full: html, text
    Use the new bamToFfAli and the old ffShAliPart to display aligned bases.
• src/hg/hgc/hgc.c
  • 1.1566 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/inc/bamFile.h
  • 1.7 lines changed: 14, context: html, text, full: html, text
    Added bamIgnoreStrand, bamIsRc, bamShowCigarEnglish, bamShowTags. In hgc/bamClick.c, also added showOverlap.
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Added bamClone. Fixed bamToFfAli to walk through CIGAR operations backwards when strand is -.
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Added bamToFfAli (for using fuzzyShow display).
• src/hg/inc/hvGfx.h
  • 1.5 lines changed: 11, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/instinct/hgHeatmap/mainPage.c
  • 1.71 lines changed: 3, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.70 lines changed: 12, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/instinct/hgHeatmap2/hgAnnotations.c
  • 1.11 lines changed: 4, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/instinct/hgHeatmap2/hgCircleMaps.c
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/lib/bamFile.c
  • 1.6 lines changed: 89, context: html, text, full: html, text
    Added bamIgnoreStrand, bamIsRc, bamShowCigarEnglish, bamShowTags. In hgc/bamClick.c, also added showOverlap.
  • 1.5 lines changed: 15, context: html, text, full: html, text
    Added bamClone. Fixed bamToFfAli to walk through CIGAR operations backwards when strand is -.
  • 1.4 lines changed: 49, context: html, text, full: html, text
    Added bamToFfAli (for using fuzzyShow display).
• src/hg/lib/hvGfx.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/makeDb/doc/hg18.txt
  • 1.377 lines changed: 29, context: html, text, full: html, text
    Updated snp130 with corrected functional annotations from dbSNP.
• src/hg/makeDb/doc/mm9.txt
  • 1.105 lines changed: 86, context: html, text, full: html, text
    Updates for MGI: RepTranscript, Allele, Phenotype, and IKMC.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.410 lines changed: 1, context: html, text, full: html, text
    Added maxWindowToDraw setting to bamNA12878 so we don't have to rely on hardcoded max in bamTrack.c.
• src/hg/makeDb/trackDb/mouse/jaxAllele.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Added link to file referenced in Methods.
• src/hg/makeDb/trackDb/mouse/jaxPhenotype.html
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Added link to file referenced in Methods.
• src/hg/phyloGif/phyloGif.c
  • 1.22 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/protein/lib/doTracks.c
  • 1.22 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/protein/pbGlobal/pbGlobal.c
  • 1.47 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/protein/pbTracks/pbTracks.c
  • 1.59 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/tutorial/cgiPicture/cgiPicture.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/hg/wikiPlot/wikiPlot.c
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/inc/fuzzyFind.h
  • 1.20 lines changed: 8, context: html, text, full: html, text
    Factored out the side-by-side part of ffShAliPart into ffShowSideBySide.
• src/inc/memgfx.h
  • 1.26 lines changed: 14, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/inc/seqOut.h
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Added bafFlushLineNoHr for more compact side-by-side alignment display.
• src/inc/vGfx.h
  • 1.15 lines changed: 7, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/lib/fuzzyShow.c
  • 1.25 lines changed: 150, context: html, text, full: html, text
    Factored out the side-by-side part of ffShAliPart into ffShowSideBySide.
• src/lib/gifLabel.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/lib/gifwrite.c
  • 1.8 lines changed: 29, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/lib/pngwrite.c
  • 1.2 lines changed: 10, context: html, text, full: html, text
    Used more civilized language in comment & errAbort per Larry's code review feedback. Also corrected terminology: PNG palette images do not have an alpha channel, just a parallel map of opacity values. So useAlpha-->useTransparency.
• src/lib/seqOut.c
  • 1.28 lines changed: 10, context: html, text, full: html, text
    Added bafFlushLineNoHr for more compact side-by-side alignment display.
• src/lib/vGif.c
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/lib/vPng.c
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Corrected terminology: PNG palette images do not have an alpha channel, just a parallel map of opacity values. So useAlpha-->useTransparency.
• src/test/test.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/tracks/tracks.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.
• src/weblet/counter/counter.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Added option to mgSaveToGif and its call stack, to use GIF's Graphic Control Extension to make memgfx's background color (0) transparent. Also corrected terminology for PNG in .h files: useAlpha -> useTransparency.