JAL-1115 List rather than vector for sequence groups (minimal additional synchronized...

diff --git a/src/jalview/datamodel/AlignmentView.java b/src/jalview/datamodel/AlignmentView.java
index efb7c4a..2d234fe 100644 (file)
--- a/src/jalview/datamodel/AlignmentView.java
+++ b/src/jalview/datamodel/AlignmentView.java
@@ -24,7 +24,7 @@ import jalview.util.MessageManager;
 import jalview.util.ShiftList;
 
 import java.io.PrintStream;
-import java.util.Enumeration;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Vector;
 
@@ -47,7 +47,7 @@ public class AlignmentView
    * one or more ScGroup objects, which are referenced by each seqCigar's group
    * membership
    */
-  private Vector scGroups;
+  private List<ScGroup> scGroups=null;
 
   private boolean isNa = false;
 
@@ -133,27 +133,24 @@ public class AlignmentView
       selseqs = alignment.getSequencesArray();
     }
 
+    List<List<SequenceI>> seqsets=new ArrayList<List<SequenceI>>();
     // get the alignment's group list and make a copy
-    Vector grps = new Vector();
+    List<SequenceGroup> grps = new ArrayList<SequenceGroup>();
     List<SequenceGroup> gg = alignment.getGroups();
     grps.addAll(gg);
     ScGroup[] sgrps = null;
     boolean addedgps[] = null;
     if (grps != null)
     {
-      SequenceGroup sg;
       if (selection != null && selectedRegionOnly)
       {
         // trim annotation to the region being stored.
         // strip out any groups that do not actually intersect with the
         // visible and selected region
         int ssel = selection.getStartRes(), esel = selection.getEndRes();
-        Vector isg = new Vector();
-        Enumeration en = grps.elements();
-        while (en.hasMoreElements())
+        List<SequenceGroup> isg = new ArrayList<SequenceGroup>();
+        for (SequenceGroup sg : grps)
         {
-          sg = (SequenceGroup) en.nextElement();
-
           if (!(sg.getStartRes() > esel || sg.getEndRes() < ssel))
           {
             // adjust bounds of new group, if necessary.
@@ -168,7 +165,7 @@ public class AlignmentView
             sg.setStartRes(sg.getStartRes() - ssel + 1);
             sg.setEndRes(sg.getEndRes() - ssel + 1);
 
-            isg.addElement(sg);
+            isg.add(sg);
           }
         }
         grps = isg;
@@ -178,13 +175,13 @@ public class AlignmentView
       addedgps = new boolean[grps.size()];
       for (int g = 0; g < sgrps.length; g++)
       {
-        sg = (SequenceGroup) grps.elementAt(g);
+        SequenceGroup sg = grps.get(g);
         sgrps[g] = new ScGroup();
         sgrps[g].sg = new SequenceGroup(sg);
         addedgps[g] = false;
-        grps.setElementAt(sg.getSequences(null), g);
+        seqsets.set(g, sg.getSequences(null));
       }
-      // grps now contains vectors (should be sets) for each group, so we can
+      // seqsets now contains vectors (should be sets) for each group, so we can
       // track when we've done with the group
     }
     int csi = 0;
@@ -198,11 +195,11 @@ public class AlignmentView
           sequences[csi].setGroupMembership(selected);
           selected.addElement(sequences[csi]);
         }
-        if (grps != null)
+        if (seqsets != null)
         {
           for (int sg = 0; sg < sgrps.length; sg++)
           {
-            if (((Vector) grps.elementAt(sg)).contains(selseqs[i]))
+            if ((seqsets.get(sg)).contains(selseqs[i]))
             {
               sequences[csi].setGroupMembership(sgrps[sg]);
               sgrps[sg].sg.deleteSequence(selseqs[i], false);
@@ -211,10 +208,10 @@ public class AlignmentView
               {
                 if (scGroups == null)
                 {
-                  scGroups = new Vector();
+                  scGroups = new ArrayList<ScGroup>();
                 }
                 addedgps[sg] = true;
-                scGroups.addElement(sgrps[sg]);
+                scGroups.add(sgrps[sg]);
               }
             }
           }
@@ -356,7 +353,7 @@ public class AlignmentView
           SequenceGroup[] nsg = new SequenceGroup[nvg];
           for (int g = 0; g < nvg; g++)
           {
-            SequenceGroup sg = ((ScGroup) scGroups.elementAt(g)).sg;
+            SequenceGroup sg = scGroups.get(g).sg;
             if (r)
             {
               if (sg.getStartRes() > gend || sg.getEndRes() < gstart)
@@ -442,7 +439,7 @@ public class AlignmentView
             for (int g = 0; g < nvg; g++)
             {
               if (nsg[g] != null
-                      && sequences[nsq].isMemberOf(scGroups.elementAt(g)))
+                      && sequences[nsq].isMemberOf(scGroups.get(g)))
               {
                 nsg[g].addSequence(aln[nsq], false);
               }
@@ -1038,7 +1035,7 @@ public class AlignmentView
               + " groups defined on the view.");
       for (int g = 0; g < view.scGroups.size(); g++)
       {
-        ScGroup sgr = (ScGroup) view.scGroups.elementAt(g);
+        ScGroup sgr = view.scGroups.get(g);
         os.println("Group " + g + ": Name = " + sgr.sg.getName()
                 + " Contains " + sgr.seqs.size() + " Seqs.");
         os.println("This group runs from " + sgr.sg.getStartRes() + " to "

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 752c6d4..c6b9cbd 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -27,7 +27,6 @@ import jalview.schemes.ResidueProperties;
 
 import java.awt.Color;
 import java.util.ArrayList;
-import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Map;
@@ -63,7 +62,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   /**
    * group members
    */
-  private Vector<SequenceI> sequences = new Vector<SequenceI>();
+  private List<SequenceI> sequences = new ArrayList<SequenceI>();
 
   /**
    * representative sequence for this group (if any)
@@ -136,7 +135,7 @@ public class SequenceGroup implements AnnotatedCollectionI
    * @param end
    *          last column of group
    */
-  public SequenceGroup(Vector sequences, String groupName,
+  public SequenceGroup(List<SequenceI> sequences, String groupName,
           ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
           boolean colourText, int start, int end)
   {
@@ -160,13 +159,8 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     if (seqsel != null)
     {
-      sequences = new Vector();
-      Enumeration<SequenceI> sq = seqsel.sequences.elements();
-      while (sq.hasMoreElements())
-      {
-        sequences.addElement(sq.nextElement());
-      }
-      ;
+      sequences = new ArrayList<SequenceI>();
+      sequences.addAll(seqsel.sequences);
       if (seqsel.groupName != null)
       {
         groupName = new String(seqsel.groupName);
@@ -310,16 +304,15 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     if (hiddenReps == null)
     {
+      // TODO: need a synchronizedCollection here ?
       return sequences;
     }
     else
     {
-      Vector allSequences = new Vector();
-      SequenceI seq;
-      for (int i = 0; i < sequences.size(); i++)
+      List<SequenceI> allSequences = new ArrayList<SequenceI>();
+      for (SequenceI seq : sequences)
       {
-        seq = sequences.elementAt(i);
-        allSequences.addElement(seq);
+        allSequences.add(seq);
         if (hiddenReps.containsKey(seq))
         {
           SequenceCollectionI hsg = hiddenReps.get(seq);
@@ -327,7 +320,7 @@ public class SequenceGroup implements AnnotatedCollectionI
           {
             if (seq2 != seq && !allSequences.contains(seq2))
             {
-              allSequences.addElement(seq2);
+              allSequences.add(seq2);
             }
           }
         }
@@ -471,14 +464,17 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public void addSequence(SequenceI s, boolean recalc)
   {
-    if (s != null && !sequences.contains(s))
+    synchronized (sequences)
     {
-      sequences.addElement(s);
-    }
+      if (s != null && !sequences.contains(s))
+      {
+        sequences.add(s);
+      }
 
-    if (recalc)
-    {
-      recalcConservation();
+      if (recalc)
+      {
+        recalcConservation();
+      }
     }
   }
 
@@ -613,6 +609,8 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public void addOrRemove(SequenceI s, boolean recalc)
   {
+    synchronized (sequences)
+    {
     if (sequences.contains(s))
     {
       deleteSequence(s, recalc);
@@ -620,24 +618,28 @@ public class SequenceGroup implements AnnotatedCollectionI
     else
     {
       addSequence(s, recalc);
+      }
     }
   }
 
   /**
-   * DOCUMENT ME!
+   * remove
    * 
    * @param s
-   *          DOCUMENT ME!
+   *          to be removed
    * @param recalc
-   *          DOCUMENT ME!
+   *          true means recalculate conservation
    */
   public void deleteSequence(SequenceI s, boolean recalc)
   {
-    sequences.removeElement(s);
-
-    if (recalc)
+    synchronized (sequences)
     {
-      recalcConservation();
+      sequences.remove(s);
+
+      if (recalc)
+      {
+        recalcConservation();
+      }
     }
   }
 
@@ -683,9 +685,7 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * @return number of sequences in group
    */
   public int getSize()
   {
@@ -693,23 +693,17 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * DOCUMENT ME!
-   * 
    * @param i
-   *          DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
+   * @return the ith sequence
    */
   public SequenceI getSequenceAt(int i)
   {
-    return sequences.elementAt(i);
+    return sequences.get(i);
   }
 
   /**
-   * DOCUMENT ME!
-   * 
    * @param state
-   *          DOCUMENT ME!
+   *          colourText
    */
   public void setColourText(boolean state)
   {
@@ -769,30 +763,26 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * DOCUMENT ME!
+   * computes the width of current set of sequences and returns it
    * 
    * @return DOCUMENT ME!
    */
   @Override
   public int getWidth()
   {
-    // MC This needs to get reset when characters are inserted and deleted
-    if (sequences.size() > 0)
+    synchronized (sequences)
     {
-      width = sequences.elementAt(0).getLength();
-    }
-
-    for (int i = 1; i < sequences.size(); i++)
-    {
-      SequenceI seq = sequences.elementAt(i);
-
-      if (seq.getLength() > width)
-      {
-        width = seq.getLength();
+      // MC This needs to get reset when characters are inserted and deleted
+      boolean first=true;
+      for (SequenceI seq:sequences) {
+        if (first || seq.getLength() > width)
+        {
+          width = seq.getLength();
+          first = false;
+        }
       }
+      return width;
     }
-
-    return width;
   }
 
   /**
@@ -843,39 +833,42 @@ public class SequenceGroup implements AnnotatedCollectionI
    */
   public SequenceI[] getSequencesInOrder(AlignmentI al, boolean trim)
   {
-    int sSize = sequences.size();
-    int alHeight = al.getHeight();
+    synchronized (sequences)
+    {
+      int sSize = sequences.size();
+      int alHeight = al.getHeight();
 
-    SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
+      SequenceI[] seqs = new SequenceI[(trim) ? sSize : alHeight];
 
-    int index = 0;
-    for (int i = 0; i < alHeight && index < sSize; i++)
-    {
-      if (sequences.contains(al.getSequenceAt(i)))
+      int index = 0;
+      for (int i = 0; i < alHeight && index < sSize; i++)
       {
-        seqs[(trim) ? index : i] = al.getSequenceAt(i);
-        index++;
+        if (sequences.contains(al.getSequenceAt(i)))
+        {
+          seqs[(trim) ? index : i] = al.getSequenceAt(i);
+          index++;
+        }
       }
-    }
-    if (index == 0)
-    {
-      return null;
-    }
-    if (!trim)
-    {
-      return seqs;
-    }
-    if (index < seqs.length)
-    {
-      SequenceI[] dummy = seqs;
-      seqs = new SequenceI[index];
-      while (--index >= 0)
+      if (index == 0)
+      {
+        return null;
+      }
+      if (!trim)
+      {
+        return seqs;
+      }
+      if (index < seqs.length)
       {
-        seqs[index] = dummy[index];
-        dummy[index] = null;
+        SequenceI[] dummy = seqs;
+        seqs = new SequenceI[index];
+        while (--index >= 0)
+        {
+          seqs[index] = dummy[index];
+          dummy[index] = null;
+        }
       }
+      return seqs;
     }
-    return seqs;
   }
 
   /**
@@ -989,23 +982,14 @@ public class SequenceGroup implements AnnotatedCollectionI
   {
     SequenceGroup sgroup = new SequenceGroup(this);
     SequenceI[] insect = getSequencesInOrder(alignment);
-    sgroup.sequences = new Vector();
+    sgroup.sequences = new ArrayList<SequenceI>();
     for (int s = 0; insect != null && s < insect.length; s++)
     {
       if (map == null || map.containsKey(insect[s]))
       {
-        sgroup.sequences.addElement(insect[s]);
+        sgroup.sequences.add(insect[s]);
       }
     }
-    // Enumeration en =getSequences(hashtable).elements();
-    // while (en.hasMoreElements())
-    // {
-    // SequenceI elem = (SequenceI) en.nextElement();
-    // if (alignment.getSequences().contains(elem))
-    // {
-    // sgroup.addSequence(elem, false);
-    // }
-    // }
     return sgroup;
   }
 
@@ -1225,27 +1209,30 @@ public class SequenceGroup implements AnnotatedCollectionI
     // TODO add in other methods like 'getAlignmentAnnotation(String label),
     // etc'
     ArrayList<AlignmentAnnotation> annot = new ArrayList<AlignmentAnnotation>();
-    for (SequenceI seq : sequences)
+    synchronized (sequences)
     {
-      AlignmentAnnotation[] aa = seq.getAnnotation();
-      if (aa != null)
+      for (SequenceI seq : sequences)
       {
-        for (AlignmentAnnotation al : aa)
+        AlignmentAnnotation[] aa = seq.getAnnotation();
+        if (aa != null)
         {
-          if (al.groupRef == this)
+          for (AlignmentAnnotation al : aa)
           {
-            annot.add(al);
+            if (al.groupRef == this)
+            {
+              annot.add(al);
+            }
           }
         }
       }
-    }
-    if (consensus != null)
-    {
-      annot.add(consensus);
-    }
-    if (conservation != null)
-    {
-      annot.add(conservation);
+      if (consensus != null)
+      {
+        annot.add(consensus);
+      }
+      if (conservation != null)
+      {
+        annot.add(conservation);
+      }
     }
     return annot.toArray(new AlignmentAnnotation[0]);
   }
@@ -1310,7 +1297,10 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public void clear()
   {
-    sequences.clear();
+    synchronized (sequences)
+    {
+      sequences.clear();
+    }
   }
 
   private AnnotatedCollectionI context;