import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.Option;
// 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())
{
{
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)
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)
{
// remaining group ? - these might be at the start or the end
if (gl.size() > 0)
{
- if (lowest-1>minsize)
+ if (lowest - 1 > minsize)
{
gl.add(0, new int[]
- { 0, lowest-2});
+ { 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