@@ -91,7+92,7 @@ public class SeqGroupIndexVector extends InputType implements
// assume that alignment is properly ordered so groups form consecutive
// blocks
ArrayList<int[]> gl = new ArrayList<int[]>();
// assume that alignment is properly ordered so groups form consecutive
// blocks
ArrayList<int[]> gl = new ArrayList<int[]>();
- 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;
synchronized (sgs = al.getGroups())
{
@@ -99,8+100,7 @@ public class SeqGroupIndexVector extends InputType implements
{
if (sg.getSize() < minsize)
{
{
if (sg.getSize() < minsize)
{
- throw new NoValidInputDataException("Group contains less than "
- + minsize + " sequences.");
+ throw new NoValidInputDataException(MessageManager.formatMessage("exception.notvaliddata_group_contains_less_than_min_seqs", new String[]{Integer.valueOf(minsize).toString()}));
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
@@ -108,13+108,13 @@ public class SeqGroupIndexVector extends InputType implements
for (SequenceI sq : sg.getSequencesInOrder(al))
{
p = al.findIndex(sq);
for (SequenceI sq : sg.getSequencesInOrder(al))
{
p = al.findIndex(sq);
- if (lowest>p)
+ if (lowest > p)
{
{
- lowest=p;
+ lowest = p;
}
}
- if (highest<p)
+ if (highest < p)
{
{
- highest=p;
+ highest = p;
}
if (se == null)
{
}
if (se == null)
{
@@ -139,14+139,15 @@ public class SeqGroupIndexVector extends InputType implements
// remaining group ? - these might be at the start or the end
if (gl.size() > 0)
{
// remaining group ? - these might be at the start or the end