new sortbyPID for specific start/end region

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index e16e2ab..bb55426 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -79,6 +79,23 @@ public class AlignmentSorter
   public static void sortByPID(AlignmentI align, SequenceI s,
           SequenceI[] tosort)
   {
+    sortByPID(align,s,tosort,0,-1);
+  }
+  /**
+   * Sort by Percentage Identity w.r.t. s
+   * 
+   * @param align
+   *                AlignmentI
+   * @param s
+   *                SequenceI
+   * @param tosort
+   *                sequences from align that are to be sorted.
+   * @param start   start column (0 for beginning 
+   * @param end
+   */
+  public static void sortByPID(AlignmentI align, SequenceI s,
+          SequenceI[] tosort,int start, int end)
+  {
     int nSeq = align.getHeight();
 
     float[] scores = new float[nSeq];