private boolean nucleotide = true;
+ private List<AlignedCodonFrame> codonFrameList;
+
+ private static final SequenceGroup[] noGroups = new SequenceGroup[0];
+
+ /*
+ * persistent object to hold result of findAllGroups(SequenceI)
+ */
+ private List<SequenceGroup> groupsForSequence = new ArrayList<>();
+
public boolean hasRNAStructure = false;
public AlignmentAnnotation[] annotations;
public Hashtable alignmentProperties;
- private List<AlignedCodonFrame> codonFrameList;
-
private void initAlignment(SequenceI[] seqs)
{
groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
return null;
}
- private static final SequenceGroup[] noGroups = new SequenceGroup[0];
-
- private ArrayList<SequenceGroup> temp = new ArrayList<>();
-
/*
* (non-Javadoc)
*
@Override
public SequenceGroup[] findAllGroups(SequenceI s)
{
-
synchronized (groups)
{
int gSize = groups.size();
{
return noGroups;
}
- temp.clear();
+ groupsForSequence.clear();
for (int i = 0; i < gSize; i++)
{
SequenceGroup sg = groups.get(i);
if (sg.getSequences().contains(s))
{
- temp.add(sg);
+ groupsForSequence.add(sg);
}
}
}
- SequenceGroup[] ret = new SequenceGroup[temp.size()];
- return temp.toArray(ret);
+ SequenceGroup[] ret = new SequenceGroup[groupsForSequence.size()];
+ return groupsForSequence.toArray(ret);
}
/** */