X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=103fbf09c1fc4d6b1cb502763d4ebf1b301f93ec;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=48dbb6a55cdac0a69c092d705c1a5a27e1c8c127;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 48dbb6a..103fbf0 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -1,26 +1,38 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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;
 
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.QuickSort;
 
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Routines for manipulating the order of a multiple sequence alignment TODO:
@@ -117,7 +129,7 @@ public class AlignmentSorter
       seqs[i] = align.getSequenceAt(i);
     }
 
-    QuickSort.sort(scores, 0, scores.length - 1, seqs);
+    QuickSort.sort(scores, seqs);
 
     setReverseOrder(align, seqs);
   }
@@ -166,7 +178,7 @@ public class AlignmentSorter
    * @param tmp
    *          sequences as a vector
    */
-  private static void setOrder(AlignmentI align, Vector tmp)
+  private static void setOrder(AlignmentI align, List<SequenceI> tmp)
   {
     setOrder(align, vectorSubsetToArray(tmp, align.getSequences()));
   }
@@ -282,7 +294,7 @@ public class AlignmentSorter
   {
     // MAINTAINS ORIGNAL SEQUENCE ORDER,
     // ORDERS BY GROUP SIZE
-    Vector groups = new Vector();
+    List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
 
     if (groups.hashCode() != lastGroupHash)
     {
@@ -300,11 +312,11 @@ public class AlignmentSorter
     {
       for (int j = 0; j < groups.size(); j++)
       {
-        SequenceGroup sg2 = (SequenceGroup) groups.elementAt(j);
+        SequenceGroup sg2 = groups.get(j);
 
         if (sg.getSize() > sg2.getSize())
         {
-          groups.insertElementAt(sg, j);
+          groups.add(j, sg);
 
           break;
         }
@@ -312,22 +324,22 @@ public class AlignmentSorter
 
       if (!groups.contains(sg))
       {
-        groups.addElement(sg);
+        groups.add(sg);
       }
     }
 
     // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
     // /////////////////////////////////////////////
-    Vector seqs = new Vector();
+    List<SequenceI> seqs = new ArrayList<SequenceI>();
 
     for (int i = 0; i < groups.size(); i++)
     {
-      SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+      SequenceGroup sg = groups.get(i);
       SequenceI[] orderedseqs = sg.getSequencesInOrder(align);
 
       for (int j = 0; j < orderedseqs.length; j++)
       {
-        seqs.addElement(orderedseqs[j]);
+        seqs.add(orderedseqs[j]);
       }
     }
 
@@ -343,28 +355,8 @@ public class AlignmentSorter
   }
 
   /**
-   * Converts Vector to array. java 1.18 does not have Vector.toArray()
-   * 
-   * @param tmp
-   *          Vector of SequenceI objects
-   * 
-   * @return array of Sequence[]
-   */
-  private static SequenceI[] vectorToArray(Vector tmp)
-  {
-    SequenceI[] seqs = new SequenceI[tmp.size()];
-
-    for (int i = 0; i < tmp.size(); i++)
-    {
-      seqs[i] = (SequenceI) tmp.elementAt(i);
-    }
-
-    return seqs;
-  }
-
-  /**
    * Select sequences in order from tmp that is present in mask, and any
-   * remaining seqeunces in mask not in tmp
+   * remaining sequences in mask not in tmp
    * 
    * @param tmp
    *          thread safe collection of sequences
@@ -376,6 +368,10 @@ public class AlignmentSorter
   private static SequenceI[] vectorSubsetToArray(List<SequenceI> tmp,
           List<SequenceI> mask)
   {
+    // or?
+    // tmp2 = tmp.retainAll(mask);
+    // return tmp2.addAll(mask.removeAll(tmp2))
+
     ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
     int i, idx;
     boolean[] tmask = new boolean[mask.size()];
@@ -418,7 +414,7 @@ public class AlignmentSorter
   public static void sortBy(AlignmentI align, AlignmentOrder order)
   {
     // Get an ordered vector of sequences which may also be present in align
-    Vector tmp = order.getOrder();
+    List<SequenceI> tmp = order.getOrder();
 
     if (lastOrder == order)
     {
@@ -449,11 +445,12 @@ public class AlignmentSorter
    * 
    * @return DOCUMENT ME!
    */
-  private static Vector getOrderByTree(AlignmentI align, NJTree tree)
+  private static List<SequenceI> getOrderByTree(AlignmentI align,
+          NJTree tree)
   {
     int nSeq = align.getHeight();
 
-    Vector tmp = new Vector();
+    List<SequenceI> tmp = new ArrayList<SequenceI>();
 
     tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());
 
@@ -491,7 +488,7 @@ public class AlignmentSorter
    */
   public static void sortByTree(AlignmentI align, NJTree tree)
   {
-    Vector tmp = getOrderByTree(align, tree);
+    List<SequenceI> tmp = getOrderByTree(align, tree);
 
     // tmp should properly permute align with tree.
     if (lastTree != tree)
@@ -519,22 +516,22 @@ public class AlignmentSorter
    * 
    * @param align
    *          DOCUMENT ME!
-   * @param seqs
+   * @param tmp
    *          DOCUMENT ME!
    */
-  private static void addStrays(AlignmentI align, Vector seqs)
+  private static void addStrays(AlignmentI align, List<SequenceI> tmp)
   {
     int nSeq = align.getHeight();
 
     for (int i = 0; i < nSeq; i++)
     {
-      if (!seqs.contains(align.getSequenceAt(i)))
+      if (!tmp.contains(align.getSequenceAt(i)))
       {
-        seqs.addElement(align.getSequenceAt(i));
+        tmp.add(align.getSequenceAt(i));
       }
     }
 
-    if (nSeq != seqs.size())
+    if (nSeq != tmp.size())
     {
       System.err
               .println("ERROR: Size still not right even after addStrays");
@@ -553,8 +550,8 @@ public class AlignmentSorter
    * 
    * @return DOCUMENT ME!
    */
-  private static Vector _sortByTree(SequenceNode node, Vector tmp,
-          List<SequenceI> seqset)
+  private static List<SequenceI> _sortByTree(SequenceNode node,
+          List<SequenceI> tmp, List<SequenceI> seqset)
   {
     if (node == null)
     {
@@ -574,7 +571,7 @@ public class AlignmentSorter
                                              // seqset.size()==0 ||
                                              // seqset.contains(tmp)))
           {
-            tmp.addElement(node.element());
+            tmp.add((SequenceI) node.element());
           }
         }
       }
@@ -721,9 +718,9 @@ public class AlignmentSorter
   public static void sortByFeature(String featureLabel, String groupLabel,
           int start, int stop, AlignmentI alignment, String method)
   {
-    sortByFeature(featureLabel == null ? null : new String[]
-    { featureLabel }, groupLabel == null ? null : new String[]
-    { groupLabel }, start, stop, alignment, method);
+    sortByFeature(featureLabel == null ? null
+            : new String[] { featureLabel }, groupLabel == null ? null
+            : new String[] { groupLabel }, start, stop, alignment, method);
   }
 
   private static boolean containsIgnoreCase(final String lab,
@@ -755,7 +752,8 @@ public class AlignmentSorter
             && method != FEATURE_DENSITY)
     {
       throw new Error(
-              "Implementation Error - sortByFeature method must be one of FEATURE_SCORE, FEATURE_LABEL or FEATURE_DENSITY.");
+              MessageManager
+                      .getString("error.implementation_error_sortbyfeature"));
     }
     boolean ignoreScore = method != FEATURE_SCORE;
     StringBuffer scoreLabel = new StringBuffer();
@@ -783,10 +781,6 @@ public class AlignmentSorter
     for (int i = 0; i < seqs.length; i++)
     {
       SequenceFeature[] sf = seqs[i].getSequenceFeatures();
-      if (sf == null && seqs[i].getDatasetSequence() != null)
-      {
-        sf = seqs[i].getDatasetSequence().getSequenceFeatures();
-      }
       if (sf == null)
       {
         sf = new SequenceFeature[0];
@@ -827,7 +821,7 @@ public class AlignmentSorter
         else
         {
           // or, also take a look at the scores if necessary.
-          if (!ignoreScore && sf[f].getScore() != Float.NaN)
+          if (!ignoreScore && !Float.isNaN(sf[f].getScore()))
           {
             if (seqScores[i] == 0)
             {
@@ -935,7 +929,8 @@ 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