Examples of Exon

org.broad.igv.feature.Exon
A sub region of a feature. For example, a Gene exon @author jrobinso
picard.annotation.Gene.Transcript.Exon

Examples of org.broad.igv.feature.Exon


        int[] exonStarts = new int[]{53,351,501};
        int[] exonEnds = new int[]{250,400,550};


        for(int ii= 0; ii < 3; ii++){
            Exon exon = transcript.getExons().get(ii);
            assertEquals(exonStarts[ii] - 1, exon.getStart());
            assertEquals(exonEnds[ii], exon.getEnd());
            String exonFPKM = transcript.getAttributes().get("FPKM");
            assertTrue("Exon FPKM invalid: " + exonFPKM, exonFPKM.startsWith("105"));
            assertTrue(exonFPKM.startsWith("105"));
        }

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Examples of org.broad.igv.feature.Exon

                    if (tmp.length > 1) {
                        exonEnd = Integer.parseInt(tmp[1]);
                    }


                    Strand strand = isNegative ? Strand.NEGATIVE : Strand.POSITIVE;
                    Exon r = new Exon(chromosome, exonStart, exonEnd, strand);
                    start = Math.min(start, exonStart);
                    end = Math.max(end, exonEnd);
                    exons.add(r);

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Examples of org.broad.igv.feature.Exon

            int exonNumber = (strand == Strand.NEGATIVE ? exonCount : 1);


            for (int i = 0; i < startsBuffer.length; i++) {
                int exonStart = Integer.parseInt(startsBuffer[i]);
                int exonEnd = Integer.parseInt(endsBuffer[i]);
                Exon exon = new Exon(chr, exonStart, exonEnd, strand);
                exon.setCodingStart(cdStart);
                exon.setCodingEnd(cdEnd);
                gene.addExon(exon);


                exon.setNumber(exonNumber);
                if (strand == Strand.NEGATIVE) {
                    exonNumber--;
                } else {
                    exonNumber++;
                }


            }
        }


        List<Exon> exons = gene.getExons();


        // Walk through exons setting mRNA start position
        int start = strand == Strand.POSITIVE ? 0 : exonCount - 1;
        int end = strand == Strand.POSITIVE ? exonCount : -1;
        int increment = strand == Strand.POSITIVE ? 1 : -1;


        int mRNABase = 0;
        for (int i = start; i != end; i += increment) {
            Exon exon = exons.get(i);
            exon.setMrnaBase(mRNABase);
            mRNABase += exon.getCodingLength();
        }




        if (type == Type.GENEPRED && tokenCount > 15) {
            try {

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Examples of org.broad.igv.feature.Exon

                //JOptionPane.showMessageDialog(IGV.getInstance(),
                //        "Track panning is not enabled for data tracks.");
                return;
            }


            Exon e = null;
            if (t instanceof FeatureTrack) {
                int center = (int) vc.getCenter();
                FeatureTrack ft = (FeatureTrack) t;
                if (ft.getDisplayMode() == Track.DisplayMode.COLLAPSED ||
                        ft.getSelectedFeatureRowIndex() == FeatureTrack.NO_FEATURE_ROW_SELECTED) {
                    MessageUtils.showMessage(
                            "Exon navigation is only allowed when track is expanded and a single " +
                                    "feature row is selected.");
                    return;
                }
                List<Feature> featureList = ft.getFeaturesAtPositionInFeatureRow(center, ft.getSelectedFeatureRowIndex(), vc);
                Feature feature = featureList != null && featureList.size() > 0 ? featureList.get(0) : null;


                if (feature == null)
                    return;
                if (feature instanceof BasicFeature) {
                    BasicFeature bf = (BasicFeature) feature;
                    java.util.List<Exon> exons = bf.getExons();
                    if (exons == null || exons.isEmpty()) {
                        MessageUtils.showMessage("At least one centered feature does not have exon structure");
                        return;
                    }


                    if (forward) {
                        for (Exon exon : bf.getExons()) {
                            //the "+ 1" here is necessary because the rounding in the recentering method
                            //sometimes places the center one base off.  This should be perfectly safe,
                            //but it does assume no one's abusing the exon datastructure and creating
                            //exons that are right next to each other.
                            if (exon.getStart() > vc.getCenter() + 1) {
                                e = exon;
                                break;
                            }
                        }
                    } else {
                        for (int i = exons.size() - 1; i >= 0; i--) {
                            Exon exon = exons.get(i);
                            if (exon.getEnd() < vc.getCenter()) {
                                e = exon;
                                break;
                            }
                        }
                    }

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Examples of org.broad.igv.feature.Exon

                    int exonStart = Integer.parseInt(startsBuffer[i]);
                    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 org.broad.igv.feature.Exon

                continue;
            } else {
                continue;
            }


            Exon lastExon = exons.get(exons.size() - 1);
            assertEquals(7600, lastExon.getCdEnd());
            assertEquals(lastExon.getCdStart(), lastExon.getStart());
            assertEquals(9000, lastExon.getEnd());


            int midCDSInd = 2;


            if (ident.equals("mRNA00001")) {
                assertEquals(4, bf.getExonCount());
                assertEquals(1201 - 1, exons.get(0).getCdStart());


                Exon secExon = exons.get(1);
                assertWholeExonCoding(secExon);
                assertEquals(3000 - 1, secExon.getStart());
                assertEquals(3902, secExon.getEnd());


            }
            if (ident.equals("mRNA00002")) {
                assertEquals(3, bf.getExonCount());
                assertEquals(1201 - 1, exons.get(0).getCdStart());
                midCDSInd = 1;
            }
            if (ident.equals("mRNA00003")) {
                assertEquals(4, bf.getExonCount());
                boolean passedCdStart = false;
                for (Exon exon : exons) {
                    if (exon.isNonCoding()) {
                        assertEquals("Entire exon is UTR but has coding region: " + exon.getName(), 0, exon.getCodingLength());
                        assertEquals("Entire exon is UTR but has coding region: " + exon.getName(), 0, exon.getCdEnd() - exon.getCdEnd());
                    } else {
                        //There are two coding sequences which differ only in start position
                        if (!passedCdStart) {
                            int cdStart = exon.getCdStart();
                            assertTrue("Exon cdStart not expected, was " + cdStart, mRNA3CdStarts.contains(cdStart));
                            mRNA3CdStarts.remove(cdStart);
                            passedCdStart = true;
                        }
                    }
                    assertTrue(exon.getName().contains("exon0000"));
                }
                assertTrue(passedCdStart);
            }


            Exon midCDS = exons.get(midCDSInd);
            assertEquals(4999, midCDS.getStart());
            assertEquals(5500, midCDS.getEnd());
            assertEquals(midCDS.getStart(), midCDS.getCdStart());
            assertEquals(midCDS.getEnd(), midCDS.getCdEnd());
        }


        assertEquals(0, mRNA3CdStarts.size());


        assertEquals(expmRNAFeats, actmRNAFeats);

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Examples of org.broad.igv.feature.Exon

            } else if (basicFeature.getType().equals("gene")) {
                assertEquals(1, basicFeature.getExonCount());
                assertTrue(basicFeature.getIdentifier().contains("gene"));
                assertTrue(basicFeature.getName().contains("A1S_"));


                Exon exon = basicFeature.getExons().get(0);
                assertTrue("Exon name incorrect: " + exon.getName(), exon.getName().contains("YP_00"));


                assertWholeExonCoding(exon);
                assertEquals(0, exon.getReadingFrame());
            } else {
                throw new AssertionError("Unknown feature type: " + basicFeature.getType());
            }


        }

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Examples of org.broad.igv.feature.Exon

        }


        assertEquals(gene.getIdentifier(), tRNA.getAttributes().get("Parent"));


        assertEquals(1, tRNA.getExonCount());
        Exon exon = tRNA.getExons().get(0);
        assertEquals(tRNA.getIdentifier(), exon.getAttributes().get("Parent"));
        assertWholeExonNonCoding(exon);
    }

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Examples of org.broad.igv.feature.Exon


            BasicFeature feature = (BasicFeature) features.get(0);
            List<Exon> exons = feature.getExons();
            assertEquals(2, exons.size());


            Exon firstExon = exons.get(0);
            assertTrue(firstExon.isNonCoding());
            assertEquals(11783, firstExon.getStart());
            assertEquals(12157, firstExon.getEnd());
            assertEquals(12157, firstExon.getCdStart());


            Exon secondExon = exons.get(1);
            assertFalse(secondExon.isNonCoding());
            assertEquals(12157, secondExon.getCdStart());
            assertEquals(12157, secondExon.getStart());
            assertEquals(12994, secondExon.getEnd());


        } finally {
            if (reader != null) reader.close();
        }
    }

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Examples of picard.annotation.Gene.Transcript.Exon

        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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