X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=b7cfbbdb3f1f29b8042e9ca11b1971ea2b0c5389;hb=0616883e9c584c0f8600cfec79d9bf50cde337a4;hp=b84eeaf2d690ece19e1e0e898e411ea19c27dd1a;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index b84eeaf..b7cfbbd 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 2.8.2)
+ * Copyright (C) 2014 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;
 
@@ -146,11 +149,15 @@ public class AlignmentSorter
     }
 
     // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-    for (int i = 0; i < len; i++)
+    List<SequenceI> asq;
+    synchronized (asq = align.getSequences())
     {
-      // SequenceI tmp = seqs[i];
-      align.getSequences().setElementAt(seqs[nSeq - i - 1], i);
-      align.getSequences().setElementAt(seqs[i], nSeq - i - 1);
+      for (int i = 0; i < len; i++)
+      {
+        // SequenceI tmp = seqs[i];
+        asq.set(i, seqs[nSeq - i - 1]);
+        asq.set(nSeq - i - 1, seqs[i]);
+      }
     }
   }
 
@@ -178,24 +185,26 @@ public class AlignmentSorter
   public static void setOrder(AlignmentI align, SequenceI[] seqs)
   {
     // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work
-    Vector algn = align.getSequences();
-    Vector tmp = new Vector();
-
-    for (int i = 0; i < seqs.length; i++)
+    List<SequenceI> algn;
+    synchronized (algn = align.getSequences())
     {
-      if (algn.contains(seqs[i]))
+      List<SequenceI> tmp = new ArrayList<SequenceI>();
+
+      for (int i = 0; i < seqs.length; i++)
       {
-        tmp.addElement(seqs[i]);
+        if (algn.contains(seqs[i]))
+        {
+          tmp.add(seqs[i]);
+        }
       }
-    }
 
-    algn.removeAllElements();
-    // User may have hidden seqs, then clicked undo or redo
-    for (int i = 0; i < tmp.size(); i++)
-    {
-      algn.addElement(tmp.elementAt(i));
+      algn.clear();
+      // User may have hidden seqs, then clicked undo or redo
+      for (int i = 0; i < tmp.size(); i++)
+      {
+        algn.add(tmp.get(i));
+      }
     }
-
   }
 
   /**
@@ -247,7 +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);
@@ -290,7 +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++)
       {
@@ -357,18 +366,20 @@ public class AlignmentSorter
   }
 
   /**
-   * DOCUMENT ME!
+   * Select sequences in order from tmp that is present in mask, and any
+   * remaining seqeunces in mask not in tmp
    * 
    * @param tmp
-   *          DOCUMENT ME!
+   *          thread safe collection of sequences
    * @param mask
-   *          DOCUMENT ME!
+   *          thread safe collection of sequences
    * 
-   * @return DOCUMENT ME!
+   * @return intersect(tmp,mask)+intersect(complement(tmp),mask)
    */
-  private static SequenceI[] vectorSubsetToArray(Vector tmp, Vector mask)
+  private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
+          List<SequenceI> mask)
   {
-    Vector seqs = new Vector();
+    ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
     int i, idx;
     boolean[] tmask = new boolean[mask.size()];
 
@@ -379,12 +390,12 @@ public class AlignmentSorter
 
     for (i = 0; i < tmp.size(); i++)
     {
-      Object sq = tmp.elementAt(i);
+      SequenceI sq = tmp.get(i);
       idx = mask.indexOf(sq);
       if (idx > -1 && tmask[idx])
       {
         tmask[idx] = false;
-        seqs.addElement(sq);
+        seqs.add(sq);
       }
     }
 
@@ -392,11 +403,11 @@ public class AlignmentSorter
     {
       if (tmask[i])
       {
-        seqs.addElement(mask.elementAt(i));
+        seqs.add(mask.get(i));
       }
     }
 
-    return vectorToArray(seqs);
+    return seqs.toArray(new SequenceI[seqs.size()]);
   }
 
   /**
@@ -461,8 +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");
       }
     }
 
@@ -542,7 +557,7 @@ public class AlignmentSorter
    * @return DOCUMENT ME!
    */
   private static Vector _sortByTree(SequenceNode node, Vector tmp,
-          Vector seqset)
+          List<SequenceI> seqset)
   {
     if (node == null)
     {
@@ -558,9 +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());
           }
         }
       }
@@ -740,8 +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();
@@ -921,7 +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