public void addSequence(final SAMSequenceRecord sequenceRecord) { if (mSequenceMap.containsKey(sequenceRecord.getSequenceName())) { throw new IllegalArgumentException("Cannot add sequence that already exists in SAMSequenceDictionary: " + sequenceRecord.getSequenceName()); } sequenceRecord.setSequenceIndex(mSequences.size()); mSequences.add(sequenceRecord); mSequenceMap.put(sequenceRecord.getSequenceName(), sequenceRecord); }
public void addSequence(final SAMSequenceRecord sequenceRecord) { if (mSequenceMap.containsKey(sequenceRecord.getSequenceName())) { throw new IllegalArgumentException("Cannot add sequence that already exists in SAMSequenceDictionary: " + sequenceRecord.getSequenceName()); } sequenceRecord.setSequenceIndex(mSequences.size()); mSequences.add(sequenceRecord); mSequenceMap.put(sequenceRecord.getSequenceName(), sequenceRecord); }
public void addSequence(final SAMSequenceRecord sequenceRecord) { if (mSequenceMap.containsKey(sequenceRecord.getSequenceName())) { throw new IllegalArgumentException("Cannot add sequence that already exists in SAMSequenceDictionary: " + sequenceRecord.getSequenceName()); } sequenceRecord.setSequenceIndex(mSequences.size()); mSequences.add(sequenceRecord); mSequenceMap.put(sequenceRecord.getSequenceName(), sequenceRecord); }
/** * Replaces the existing list of SAMSequenceRecords with the given list. * Reset the aliases * * @param list This value is used directly, rather than being copied. */ public void setSequences(final List<SAMSequenceRecord> list) { mSequences = list; mSequenceMap.clear(); int index = 0; for (final SAMSequenceRecord record : list) { record.setSequenceIndex(index++); if (mSequenceMap.put(record.getSequenceName(), record) != null) { throw new IllegalArgumentException("Cannot add sequence that already exists in SAMSequenceDictionary: " + record.getSequenceName()); } } }
/** * Replaces the existing list of SAMSequenceRecords with the given list. * * @param list This value is used directly, rather than being copied. */ public void setSequences(final List<SAMSequenceRecord> list) { mSequences = list; mSequenceMap.clear(); int index = 0; for (final SAMSequenceRecord record : list) { record.setSequenceIndex(index++); if (mSequenceMap.put(record.getSequenceName(), record) != null) { throw new IllegalArgumentException("Cannot add sequence that already exists in SAMSequenceDictionary: " + record.getSequenceName()); } } }
/** * Replaces the existing list of SAMSequenceRecords with the given list. * Reset the aliases * * @param list This value is used directly, rather than being copied. */ public void setSequences(final List<SAMSequenceRecord> list) { mSequences = list; mSequenceMap.clear(); int index = 0; for (final SAMSequenceRecord record : list) { record.setSequenceIndex(index++); if (mSequenceMap.put(record.getSequenceName(), record) != null) { throw new IllegalArgumentException("Cannot add sequence that already exists in SAMSequenceDictionary: " + record.getSequenceName()); } } }
public SAMSequenceRecord getSAMSequenceRecord() { final String lengthString = this.getGenericFieldValue("length"); if (lengthString == null) throw new TribbleException("Contig " + this.getID() + " does not have a length field."); final SAMSequenceRecord record = new SAMSequenceRecord(this.getID(), Integer.valueOf(lengthString)); record.setSequenceIndex(this.contigIndex); return record; }
@Test(dataProvider = "testIsSameSequenceData") public void testIsSameSequence(final SAMSequenceRecord rec1 , final SAMSequenceRecord rec2, final String md5One, final String md5Two, final int index1, final int index2, final boolean isSame) { if (rec2 != null) { rec2.setMd5(md5Two); rec2.setSequenceIndex(index2); } if (rec1 != null) { rec1.setMd5(md5One); rec1.setSequenceIndex(index1); Assert.assertEquals(rec1.isSameSequence(rec2), isSame); } }
public SAMSequenceRecord getSAMSequenceRecord() { final String lengthString = this.getGenericFieldValue("length"); if (lengthString == null) throw new TribbleException("Contig " + this.getID() + " does not have a length field."); final SAMSequenceRecord record = new SAMSequenceRecord(this.getID(), Integer.valueOf(lengthString)); record.setAssembly(this.getGenericFieldValue("assembly")); record.setSequenceIndex(this.contigIndex); return record; }
public SAMSequenceRecord getSAMSequenceRecord() { final String lengthString = this.getGenericFieldValue("length"); if (lengthString == null) throw new TribbleException("Contig " + this.getID() + " does not have a length field."); final SAMSequenceRecord record = new SAMSequenceRecord(this.getID(), Integer.valueOf(lengthString)); record.setAssembly(this.getGenericFieldValue("assembly")); record.setSequenceIndex(this.contigIndex); return record; }