X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=48dbb6a55cdac0a69c092d705c1a5a27e1c8c127;hb=f6a7e5514230be7ea8c2d4cccb504b4ed95f80ef;hp=3c3feb3a0b352046b623bcccf3e2de44f8c62d8f;hpb=d6509fcf3a8cc90616e18cb22cec97f85c722bb8;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 3c3feb3..48dbb6a 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -253,7 +253,7 @@ public class AlignmentSorter
     for (int i = 0; i < nSeq; i++)
     {
       seqs[i] = align.getSequenceAt(i);
-      length[i] = (float) (seqs[i].getEnd() - seqs[i].getStart());
+      length[i] = (seqs[i].getEnd() - seqs[i].getStart());
     }
 
     QuickSort.sort(length, seqs);
@@ -296,7 +296,7 @@ public class AlignmentSorter
 
     // SORTS GROUPS BY SIZE
     // ////////////////////
-    for (SequenceGroup sg:align.getGroups())
+    for (SequenceGroup sg : align.getGroups())
     {
       for (int j = 0; j < groups.size(); j++)
       {
@@ -365,12 +365,12 @@ public class AlignmentSorter
   /**
    * Select sequences in order from tmp that is present in mask, and any
    * remaining seqeunces in mask not in tmp
-   *
+   * 
    * @param tmp
    *          thread safe collection of sequences
    * @param mask
    *          thread safe collection of sequences
-   *
+   * 
    * @return intersect(tmp,mask)+intersect(complement(tmp),mask)
    */
   private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
@@ -469,8 +469,12 @@ public class AlignmentSorter
 
       if (tmp.size() != nSeq)
       {
-        System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq="
-                + nSeq + " in getOrderByTree - tree contains sequences not in alignment");
+        System.err
+                .println("WARNING: tmp.size()="
+                        + tmp.size()
+                        + " != nseq="
+                        + nSeq
+                        + " in getOrderByTree - tree contains sequences not in alignment");
       }
     }
 
@@ -566,9 +570,11 @@ public class AlignmentSorter
       {
         if (node.element() instanceof SequenceI)
         {
-          if (!tmp.contains(node.element())) //  && (seqset==null || seqset.size()==0 || seqset.contains(tmp)))
+          if (!tmp.contains(node.element())) // && (seqset==null ||
+                                             // seqset.size()==0 ||
+                                             // seqset.contains(tmp)))
           {
-            tmp.addElement((SequenceI) node.element());
+            tmp.addElement(node.element());
           }
         }
       }