*/
package jalview.ws.rest.params;
+import jalview.analysis.AlignmentSorter;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
+import jalview.util.QuickSort;
import jalview.ws.params.OptionI;
import jalview.ws.params.simple.IntegerParameter;
import jalview.ws.params.simple.Option;
*/
public AlignmentI prepareAlignment(AlignmentI al)
{
- jalview.analysis.AlignmentSorter.sortByGroup(al);
+ AlignmentSorter.sortByGroup(al);
return al;
}
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.sortInt(srt, vals);
+ }
+ QuickSort.sortInt(srt, vals);
list = false;
int last = vals[0][0] - 1;
for (int[] range : vals)
{
minsize = Integer.valueOf(val);
if (minsize >= 0)
+ {
return true;
+ }
} catch (Exception x)
{