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Integration of David Corsars Phylip File support
[jalview.git]
/
src
/
jalview
/
datamodel
/
HiddenSequences.java
diff --git
a/src/jalview/datamodel/HiddenSequences.java
b/src/jalview/datamodel/HiddenSequences.java
index
7914d3d
..
aefb5cc
100755
(executable)
--- a/
src/jalview/datamodel/HiddenSequences.java
+++ b/
src/jalview/datamodel/HiddenSequences.java
@@
-1,19
+1,22
@@
/*
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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
*
* 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.
- *
+ * 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.
*
* 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
*/
package jalview.datamodel;
@@
-140,7
+143,8
@@
public class HiddenSequences
alignment.deleteSequence(sequence);
}
alignment.deleteSequence(sequence);
}
- public Vector showAll(Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public Vector showAll(
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
Vector revealedSeqs = new Vector();
for (int i = 0; i < hiddenSequences.length; i++)
{
Vector revealedSeqs = new Vector();
for (int i = 0; i < hiddenSequences.length; i++)
@@
-157,7
+161,8
@@
public class HiddenSequences
return revealedSeqs;
}
return revealedSeqs;
}
- public Vector showSequence(int alignmentIndex, Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public Vector showSequence(int alignmentIndex,
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
Vector revealedSeqs = new Vector();
SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
{
Vector revealedSeqs = new Vector();
SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
@@
-175,25
+180,29
@@
public class HiddenSequences
end = hiddenSequences.length - 1;
}
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;
}
return revealedSeqs;