/**
* Make a new alignment from an array of SeqCigars
*
- * @param seqs
- * SeqCigar[]
+ * @param alseqs
*/
public Alignment(SeqCigar[] alseqs)
{
return null;
}
+ private static final SequenceGroup[] noGroups = new SequenceGroup[0];
+
+ private ArrayList<SequenceGroup> temp = new ArrayList<>();
+
/*
* (non-Javadoc)
*
@Override
public SequenceGroup[] findAllGroups(SequenceI s)
{
- ArrayList<SequenceGroup> temp = new ArrayList<>();
synchronized (groups)
{
+ temp.clear();
int gSize = groups.size();
+ if (gSize == 0)
+ {
+ return noGroups;
+ }
for (int i = 0; i < gSize; i++)
{
SequenceGroup sg = groups.get(i);