Package org.broad.igv.sam.AlignmentTrack

Examples of org.broad.igv.sam.AlignmentTrack.ColorOption

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        final byte[] reference = isSoftClipped ? softClippedReference : genome.getSequence(chr, start, end);

        boolean haveBases = (block.hasBases() && block.getLength() > 0);

        ShadeBasesOption shadeBasesOption = renderOptions.shadeBasesOption;
        ColorOption colorOption = renderOptions.getColorOption();

        // Disable showAllBases in bisulfite mode
        boolean showAllBases = renderOptions.showAllBases &&
                !(colorOption == ColorOption.BISULFITE || colorOption == ColorOption.NOMESEQ);
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        Color color = alignment.getColor();
        if(color != null) return color;   // Color has been explicitly set

        Color c = alignment.isSupplementary() ? Color.darkGray : grey1;

        ColorOption colorOption = renderOptions.getColorOption();
        switch (colorOption) {
            case BISULFITE:
                // Just a simple forward/reverse strand color scheme that won't clash with the
                // methylation rectangles.
                c = (alignment.getFirstOfPairStrand() == Strand.POSITIVE) ? bisulfiteColorFw1 : bisulfiteColorRev1;
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Related Classes of org.broad.igv.sam.AlignmentTrack.ColorOption

  • org.broad.igv.sam.AlignmentRenderer
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