Examples of addExon()

Examples of org.broad.igv.feature.BasicFeature.addExon()

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            feature.setName(emblRecord.getAlias());
        }

        // If this is a "gene part" add the exons
        for (Exon exon : emblRecord.getExons()) {
            feature.addExon(exon);
        }

        return feature;
    }
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Examples of org.broad.igv.feature.PSLRecord.addExon()

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                    if (gNeg) {
                        exonStart = tSize - exonStart - exonSize;
                    }
                    int exonEnd = exonStart + exonSize;
                    Exon exon = new Exon(chr, exonStart, exonEnd, strand);
                    f.addExon(exon);
                }
            } else {
                // TODO -- warn
            }
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Examples of picard.annotation.Gene.Transcript.addExon()

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        final int codingEnd = row.getIntegerField(RefFlatColumns.CDS_END.name());

        final Transcript tx = gene.addTranscript(transcriptName, transcriptionStart, transcriptionEnd, codingStart, codingEnd, exonCount);

        for (int i = 0; i < exonCount; ++i) {
            final Exon e = tx.addExon(Integer.parseInt(exonStarts[i]) + 1, Integer.parseInt(exonEnds[i]));

            if (e.start >= e.end) {
                throw new AnnotationException("Exon has 0 or negative extent for " + transcriptDescription);
            }
            if (i > 0 && tx.exons[i-1].end >= tx.exons[i].start) {
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