* - 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);
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;
- List<SequenceGroup> sgs;
- synchronized (sgs = al.getGroups())
+ List<SequenceGroup> sgs = al.getGroups();
+ synchronized (sgs)
{
for (SequenceGroup sg : sgs)
{
else
{
if (p < se[0])
+ {
se[0] = p;
+ }
if (p > se[1])
+ {
se[1] = p;
+ }
}
}
if (se != null)
int[][] vals = gl.toArray(new int[gl.size()][]);
int[] srt = new int[gl.size()];
for (int i = 0; i < vals.length; i++)
+ {
srt[i] = vals[i][0];
+ }
jalview.util.QuickSort.sort(srt, vals);
list = false;
int last = vals[0][0] - 1;
@Override
public List<String> getURLEncodedParameter()
{
- ArrayList<String> prms = new ArrayList<String>();
+ ArrayList<String> prms = new ArrayList<>();
super.addBaseParams(prms);
prms.add("minsize='" + minsize + "'");
prms.add("sep='" + sep + "'");
{
minsize = Integer.valueOf(val);
if (minsize >= 0)
+ {
return true;
+ }
} catch (Exception x)
{