/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* @author JimP
*
*/
-public class SeqGroupIndexVector extends InputType implements
- AlignmentProcessor
+public class SeqGroupIndexVector extends InputType
+ implements AlignmentProcessor
{
public SeqGroupIndexVector()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
/**
{
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(
+ "exception.notvaliddata_group_contains_less_than_min_seqs",
+ new String[]
+ { Integer.valueOf(minsize).toString() }));
}
// TODO: refactor to sequenceGroup for efficiency -
// getAlignmentRowInterval(AlignmentI al)
}
if (se == null)
{
- se = new int[]
- { p, p };
+ se = new int[] { p, p };
}
else
{
{
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)
{
- 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)
{
return true;
} catch (Exception x)
{
- warnings.append("Invalid molecule type '" + val
- + "'. Must be one of (");
+ warnings.append(
+ "Invalid molecule type '" + val + "'. Must be one of (");
for (molType v : molType.values())
{
warnings.append(" " + v);