X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=9a7afd2fe31e7ebca8c951218880cc7604c4907a;hb=c41fb5c4448bb657b7478cef551d3377aa290b88;hp=c53568495944cf69118481fe45eb0a56258da943;hpb=a6e190fbc74751c783edfa6ff7f6cd1a08f3e80d;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index c535684..9a7afd2 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -36,6 +36,19 @@ public class HiddenSequences
     return hiddenSequences == null ? 0 : hiddenSequences.size();
   }
 
+  public int getWidth()
+  {
+    Enumeration en = hiddenSequences.elements();
+    int width = 0;
+    while(en.hasMoreElements())
+    {
+      SequenceI seq = (SequenceI)en.nextElement();
+      if(seq.getLength()>width)
+        width = seq.getLength();
+    }
+    return width;
+  }
+
   public void hideSequence(SequenceI sequence)
   {
     if(hiddenSequences==null)
@@ -49,14 +62,21 @@ public class HiddenSequences
     alignment.deleteSequence(sequence);
   }
 
-  public void showAll()
+  public Vector showAll()
   {
+   Vector revealedSeqs = new Vector();
    for(int i=0; i<alignment.getHeight()+hiddenSequences.size(); i++)
-     showSequence(i);
+    {
+      Vector tmp = showSequence(i);
+      for(int t=0; t<tmp.size(); t++)
+        revealedSeqs.addElement(tmp.elementAt(t));
+    }
+    return revealedSeqs;
   }
 
-  public void showSequence(int alignmentIndex)
+  public Vector showSequence(int alignmentIndex)
   {
+    Vector revealedSeqs = new Vector();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
     if(repSequence!=null
        && repSequence.getHiddenSequences()==null
@@ -75,8 +95,10 @@ public class HiddenSequences
       SequenceI seq =  (SequenceI)hiddenSequences.remove(new Integer(
           index));
 
+
       if(seq!=null)
       {
+        revealedSeqs.addElement(seq);
         alignment.getSequences().insertElementAt(seq, alignmentIndex);
         if(repSequence!=null)
         {
@@ -84,6 +106,8 @@ public class HiddenSequences
         }
       }
     }
+
+    return revealedSeqs;
   }
 
   public Hashtable getHiddenSequences()
@@ -156,6 +180,6 @@ public class HiddenSequences
 
   public boolean isHidden(SequenceI seq)
   {
-    return hiddenSequences.containsValue(seq);
+    return hiddenSequences.contains(seq);
   }
 }