Package org.broad.igv.feature

Examples of org.broad.igv.feature.Strand

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                case START:
                    return centerAlignment.getStart();
                case STRAND:
                    return centerAlignment.isNegativeStrand() ? -1 : 1;
                case FIRST_OF_PAIR_STRAND:
                    Strand strand = centerAlignment.getFirstOfPairStrand();
                    int score = 2;
                    if (strand != Strand.NONE) {
                        score = strand == Strand.NEGATIVE ? 1 : -1;
                    }
                    return score;
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                        queryEnd = Integer.parseInt(tokens[queryEndIdx]);
                    }
                    catch (NumberFormatException ne) {
                        throw new RuntimeException("Non-numeric value found in either start or end column");
                    }
                    Strand queryStrand = Strand.NONE;
                    if (!tabblastn) {
                        int str = Integer.parseInt(tokens[queryStrandIdx]);
                        queryStrand = str == 1 ? Strand.POSITIVE : Strand.NEGATIVE;
                    }

                    String subjectChr = tokens[subjectChrIdx];

                    int subjectStart;
                    int subjectEnd;
                    try {
                        subjectStart = Integer.parseInt(tokens[subjectStartIdx]);
                        subjectEnd = Integer.parseInt(tokens[subjectEndIdx]);
                    }
                    catch (NumberFormatException ne) {
                        throw new RuntimeException("Non-numeric value found in " +
                                " either subject start or end column");
                    }
                    Strand subjectStrand = Strand.NONE;
                    if (!tabblastn) {
                        try {
                            int str = Integer.parseInt(tokens[subjectStrandIdx]);
                            subjectStrand = str == 1 ? Strand.POSITIVE : Strand.NEGATIVE;
                        }
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                } else {
                    c = posStrandColor;
                }
                break;
            case FIRST_OF_PAIR_STRAND:
                final Strand fragmentStrand = alignment.getFirstOfPairStrand();
                if (fragmentStrand == Strand.NEGATIVE) {
                    c = negStrandColor;
                } else if (fragmentStrand == Strand.POSITIVE) {
                    c = posStrandColor;
                }
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            end = Integer.parseInt(tokens[col]);
        } catch (NumberFormatException ne) {
            String msg = String.format("Column %d must contain a numeric value. %s", col + 1, ne.getMessage());
            throw new ParserException(msg, -1, line);
        }
        Strand strand = convertStrand(tokens[6]);

        String attributeString = tokens[8];

        MultiMap<String, String> attributes = new MultiMap<String, String>();
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    public Object getHeader() {
        return header;
    }

    private Strand convertStrand(String strandString) {
        Strand strand = Strand.NONE;
        if (strandString.equals("-")) {
            strand = Strand.NEGATIVE;
        } else if (strandString.equals("+")) {
            strand = Strand.POSITIVE;
        }
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            String chrToken = tokens[13];
            String chr = genome == null ? chrToken : genome.getChromosomeAlias(chrToken);
            int start = Integer.parseInt(tokens[15]); // IS PSL 1 or ZERO based,  closed or open?

            String strandString = tokens[8];
            Strand strand = strandString.startsWith("+") ? Strand.POSITIVE : Strand.NEGATIVE;

            boolean gNeg = false;
            if (strandString.length() > 1) {
                gNeg = strandString.charAt(1) == '-';
            }
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Related Classes of org.broad.igv.feature.Strand

  • org.broad.igv.feature.dranger.DRangerParser
  • org.broad.igv.feature.tribble.EMBLTableCodec$EmblRecord
  • org.broad.igv.feature.tribble.GFFCodec
  • org.broad.igv.feature.tribble.PSLCodec
  • org.broad.igv.feature.tribble.UCSCGeneTableCodec
  • org.broad.igv.methyl.BBMethylDataSource$WrappedIterator
  • org.broad.igv.sam.AlignmentPacker
  • org.broad.igv.sam.AlignmentRenderer
  • org.broad.igv.sam.BaseAlignmentCounts
  • org.broad.igv.sam.Row
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