sgs;
synchronized (sgs = al.getGroups())
{
@@ -96,8 +99,12 @@ public class SeqGroupIndexVector extends InputType implements
{
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)
@@ -105,18 +112,17 @@ public class SeqGroupIndexVector extends InputType implements
for (SequenceI sq : sg.getSequencesInOrder(al))
{
p = al.findIndex(sq);
- if (lowest>p)
+ if (lowest > p)
{
- lowest=p;
+ lowest = p;
}
- if (highest 0)
{
- if (lowest-1>minsize)
+ if (lowest - 1 > minsize)
{
- gl.add(0, new int[]
- { 0, lowest-2});
+ gl.add(0, new int[] { 0, lowest - 2 });
}
- if ((al.getHeight()-1-highest)>minsize)
+ if ((al.getHeight() - 1 - highest) > minsize)
{
- gl.add(new int[] { highest+1, al.getHeight()-1});
+ gl.add(new int[] { highest + 1, al.getHeight() - 1 });
}
}
else
{
- gl.add(new int[]
- { 0, al.getHeight() - 1 });
+ gl.add(new int[] { 0, al.getHeight() - 1 });
}
if (min >= 0 && gl.size() < min)
{
@@ -275,8 +279,8 @@ public class SeqGroupIndexVector extends InputType implements
List lst = getBaseOptions();
lst.add(new Option("sep",
"Separator character between elements of vector", true, ",",
- sep, Arrays.asList(new String[]
- { " ", ",", ";", "\t", "|" }), null));
+ sep, Arrays.asList(new String[] { " ", ",", ";", "\t", "|" }),
+ null));
lst.add(new IntegerParameter("minsize",
"Minimum size of partition allowed by service", true, 1,
minsize, 1, 0));