From: jprocter <Jim Procter>
Date: Fri, 19 Dec 2008 15:33:08 +0000 (+0000)
Subject: sort by length
X-Git-Tag: Release_2_5~373
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bc71174b43a00b00e6a5229fc0ae22d4df9fb14e;p=jalview.git

sort by length
---

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index ab1e62d..9353aab 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -64,6 +64,8 @@ public class AlignmentSorter
    */
   private static String lastSortByFeatureScore;
 
+  private static boolean sortLengthAscending;
+
   /**
    * Sort by Percentage Identity w.r.t. s
    * 
@@ -202,6 +204,38 @@ public class AlignmentSorter
 
     sortIdAscending = !sortIdAscending;
   }
+  /**
+   * Sorts by sequence length
+   * 
+   * @param align
+   *                The alignment object to sort
+   */
+  public static void sortByLength(AlignmentI align)
+  {
+    int nSeq = align.getHeight();
+
+    float[] length = new float[nSeq];
+    SequenceI[] seqs = new SequenceI[nSeq];
+    
+    for (int i = 0; i < nSeq; i++)
+    {
+      seqs[i] = align.getSequenceAt(i);
+      length[i] = (float) (seqs[i].getEnd()-seqs[i].getStart());
+    }
+
+    QuickSort.sort(length, seqs);
+
+    if (sortLengthAscending)
+    {
+      setReverseOrder(align, seqs);
+    }
+    else
+    {
+      setOrder(align, seqs);
+    }
+
+    sortLengthAscending = !sortLengthAscending;
+  }
 
   /**
    * Sorts the alignment by size of group. <br>