-public class SeqGroupIndexVector extends InputType implements
- AlignmentProcessor
+public class SeqGroupIndexVector extends InputType
+ implements AlignmentProcessor
{
public SeqGroupIndexVector()
{
{
public SeqGroupIndexVector()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
/**
}
/**
@@ -76,6+75,7 @@ public class SeqGroupIndexVector extends InputType implements
* - alignment to be processed
* @return al or a new alignment with appropriate attributes/order for input
*/
* - alignment to be processed
* @return al or a new alignment with appropriate attributes/order for input
*/
+ @Override
public AlignmentI prepareAlignment(AlignmentI al)
{
jalview.analysis.AlignmentSorter.sortByGroup(al);
public AlignmentI prepareAlignment(AlignmentI al)
{
jalview.analysis.AlignmentSorter.sortByGroup(al);
@@ -91,16+91,19 @@ public class SeqGroupIndexVector extends InputType implements
AlignmentI al = rj.getAlignmentForInput(token, type);
// assume that alignment is properly ordered so groups form consecutive
// blocks
AlignmentI al = rj.getAlignmentForInput(token, type);
// assume that alignment is properly ordered so groups form consecutive
// blocks
- ArrayList<int[]> gl = new ArrayList<int[]>();
+ ArrayList<int[]> gl = new ArrayList<>();
int p = 0, lowest = al.getHeight(), highest = 0;
int p = 0, lowest = al.getHeight(), highest = 0;
- List<SequenceGroup> sgs;
- synchronized (sgs = al.getGroups())
+ List<SequenceGroup> sgs = al.getGroups();
+ synchronized (sgs)
{
for (SequenceGroup sg : sgs)
{
if (sg.getSize() < minsize)
{
{
for (SequenceGroup sg : sgs)
{
if (sg.getSize() < minsize)
{
- throw new NoValidInputDataException(MessageManager.formatMessage("exception.notvaliddata_group_contains_less_than_min_seqs", new String[]{Integer.valueOf(minsize).toString()}));
+ throw new NoValidInputDataException(MessageManager.formatMessage(