X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=d24f7948b4a312a5dcdc3460937903671acab058;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=ac71d4d508f0b9752f4271fe89678bccf4e47653;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index ac71d4d..d24f794 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,19 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * 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.
- *
+ *
* 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
@@ -140,14 +141,15 @@ public class HiddenSequences
alignment.deleteSequence(sequence);
}
- public Vector showAll(Hashtable hiddenReps)
+ public Vector showAll(
+ Map 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));
@@ -157,14 +159,15 @@ public class HiddenSequences
return revealedSeqs;
}
- public Vector showSequence(int alignmentIndex, Hashtable hiddenReps)
+ public Vector showSequence(int alignmentIndex,
+ Map 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);
}
@@ -175,25 +178,29 @@ public class HiddenSequences
end = hiddenSequences.length - 1;
}
- for (int index = end; index > start; index--)
+ List 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;