* @return vector of alignment sequences in order of SeqCigar array (but
* missing unfound seqcigars)
*/
- private Vector findAlignmentSequences(AlignmentI jal,
+ private Vector<SequenceI> findAlignmentSequences(AlignmentI jal,
SeqCigar[] sequences)
{
SeqCigar[] tseqs = new SeqCigar[sequences.length];
System.arraycopy(sequences, 0, tseqs, 0, sequences.length);
- Vector alsq = new Vector();
- List<SequenceI> jalsqs;
- synchronized (jalsqs = jal.getSequences())
+ Vector<SequenceI> alsq = new Vector<>();
+ List<SequenceI> jalsqs = jal.getSequences();
+ synchronized (jalsqs)
{
for (SequenceI asq : jalsqs)
{
Integer nindx = (Integer) nodespecs.get(nname);
if (nindx == null)
{
- nindx = new Integer(1);
+ nindx = Integer.valueOf(1);
}
nname = nindx.toString() + " " + nname;
return nname;
String oval = nodespec.substring(0, nodespec.indexOf(' '));
try
{
- occurence = new Integer(oval).intValue();
+ occurence = Integer.valueOf(oval).intValue();
} catch (Exception e)
{
System.err.println("Invalid nodespec '" + nodespec + "'");