javatidy

[jalview.git] / src / jalview / datamodel / HiddenSequences.java

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 21dcce1..2a6b601 100755 (executable)
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,22 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
  *
- * This program is free software; you can redistribute it and/or
+ * 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 2
- * 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.
  *
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
-
 package jalview.datamodel;
 
 import java.util.*;
@@ -27,6 +25,7 @@ public class HiddenSequences
    * holds a list of hidden sequences associated with an alignment.
    */
   public SequenceI[] hiddenSequences;
+
   AlignmentI alignment;
 
   public HiddenSequences(AlignmentI al)
@@ -57,7 +56,8 @@ public class HiddenSequences
     int width = 0;
     for (int i = 0; i < hiddenSequences.length; i++)
     {
-      if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width)
+      if (hiddenSequences[i] != null
+              && hiddenSequences[i].getLength() > width)
       {
         width = hiddenSequences[i].getLength();
       }
@@ -67,8 +67,7 @@ public class HiddenSequences
   }
 
   /**
-   * Call this method if sequences are removed from the
-   * main alignment
+   * Call this method if sequences are removed from the main alignment
    */
   public void adjustHeightSequenceDeleted(int seqIndex)
   {
@@ -104,8 +103,8 @@ public class HiddenSequences
   }
 
   /**
-   * Call this method if sequences are added to or removed from the
-   * main alignment
+   * Call this method if sequences are added to or removed from the main
+   * alignment
    */
   public void adjustHeightSequenceAdded()
   {
@@ -141,14 +140,15 @@ public class HiddenSequences
     alignment.deleteSequence(sequence);
   }
 
-  public Vector showAll(Hashtable hiddenReps)
+  public Vector showAll(
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     Vector revealedSeqs = new Vector();
     for (int i = 0; i < hiddenSequences.length; i++)
     {
       if (hiddenSequences[i] != null)
       {
-        Vector tmp = showSequence(i, hiddenReps);
+        Vector tmp = showSequence(i, hiddenRepSequences);
         for (int t = 0; t < tmp.size(); t++)
         {
           revealedSeqs.addElement(tmp.elementAt(t));
@@ -158,15 +158,15 @@ public class HiddenSequences
     return revealedSeqs;
   }
 
-  public Vector showSequence(int alignmentIndex, Hashtable hiddenReps)
+  public Vector showSequence(int alignmentIndex,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     Vector revealedSeqs = new Vector();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
-    if (repSequence != null &&
-        hiddenReps != null
-        && hiddenReps.containsKey(repSequence))
+    if (repSequence != null && hiddenRepSequences != null
+            && hiddenRepSequences.containsKey(repSequence))
     {
-      hiddenReps.remove(repSequence);
+      hiddenRepSequences.remove(repSequence);
       revealedSeqs.addElement(repSequence);
     }
 
@@ -177,24 +177,29 @@ public class HiddenSequences
       end = hiddenSequences.length - 1;
     }
 
-    for (int index = end; index > start; index--)
+    List<SequenceI> asequences;
+    synchronized (asequences = alignment.getSequences())
     {
-      SequenceI seq = hiddenSequences[index];
-      hiddenSequences[index] = null;
-
-      if (seq != null)
+      for (int index = end; index > start; index--)
       {
-        if (seq.getLength() > 0)
-        {
-          revealedSeqs.addElement(seq);
-          alignment.getSequences().insertElementAt(seq, alignmentIndex);
-        }
-        else
+        SequenceI seq = hiddenSequences[index];
+        hiddenSequences[index] = null;
+
+        if (seq != null)
         {
-          System.out.println(seq.getName() + " has been deleted whilst hidden");
+          if (seq.getLength() > 0)
+          {
+            revealedSeqs.addElement(seq);
+            asequences.add(alignmentIndex, seq);
+          }
+          else
+          {
+            System.out.println(seq.getName()
+                    + " has been deleted whilst hidden");
+          }
         }
-      }
 
+      }
     }
 
     return revealedSeqs;