X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=d1962c580bec19fa027dbf2dae07ef428f1e90ae;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=3c3feb3a0b352046b623bcccf3e2de44f8c62d8f;hpb=d6509fcf3a8cc90616e18cb22cec97f85c722bb8;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 3c3feb3..d1962c5 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,19 +1,22 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * 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.
- * 
+ * 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 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.analysis;
 
@@ -253,7 +256,7 @@ 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 +299,7 @@ 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 +368,12 @@ 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 +472,12 @@ 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 +573,11 @@ 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());
           }
         }
       }
@@ -748,8 +757,7 @@ public class AlignmentSorter
     if (method != FEATURE_SCORE && method != FEATURE_LABEL
             && method != FEATURE_DENSITY)
     {
-      throw new Error(
-              "Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.");
+      throw new Error(MessageManager.getString("error.implementation_error_sortbyfeature"));
     }
     boolean ignoreScore = method != FEATURE_SCORE;
     StringBuffer scoreLabel = new StringBuffer();
@@ -929,7 +937,7 @@ public class AlignmentSorter
     {
       if (method == FEATURE_LABEL)
       {
-        throw new Error("Not yet implemented.");
+        throw new Error(MessageManager.getString("error.not_yet_implemented"));
       }
     }
     if (lastSortByFeatureScore == null