X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=2a6b601989f0891832c836401d8be1ca8c072bee;hb=aa213924876640ba82e866da5a750d9cdaa816d2;hp=7914d3db16cd83fdd8a16f15f0b213764f3bbb51;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 7914d3d..2a6b601 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,18 +1,18 @@
/*
* 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 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
+ * 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
+ *
+ * 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 .
*/
package jalview.datamodel;
@@ -140,7 +140,8 @@ public class HiddenSequences
alignment.deleteSequence(sequence);
}
- public Vector showAll(Map hiddenRepSequences)
+ public Vector showAll(
+ Map hiddenRepSequences)
{
Vector revealedSeqs = new Vector();
for (int i = 0; i < hiddenSequences.length; i++)
@@ -157,7 +158,8 @@ public class HiddenSequences
return revealedSeqs;
}
- public Vector showSequence(int alignmentIndex, Map hiddenRepSequences)
+ public Vector showSequence(int alignmentIndex,
+ Map hiddenRepSequences)
{
Vector revealedSeqs = new Vector();
SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
@@ -175,25 +177,29 @@ 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;