/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
+ * 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 <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;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
public class HiddenSequences
{
alignment.deleteSequence(sequence);
}
- public Vector showAll(
+ public List<SequenceI> showAll(
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
for (int i = 0; i < hiddenSequences.length; i++)
{
if (hiddenSequences[i] != null)
{
- Vector tmp = showSequence(i, hiddenRepSequences);
- for (int t = 0; t < tmp.size(); t++)
+ List<SequenceI> tmp = showSequence(i, hiddenRepSequences);
+ for (SequenceI seq : tmp)
{
- revealedSeqs.addElement(tmp.elementAt(t));
+ revealedSeqs.add(seq);
}
}
}
return revealedSeqs;
}
- public Vector showSequence(int alignmentIndex,
+ public List<SequenceI> showSequence(int alignmentIndex,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List<SequenceI> revealedSeqs = new ArrayList<SequenceI>();
SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
if (repSequence != null && hiddenRepSequences != null
&& hiddenRepSequences.containsKey(repSequence))
{
hiddenRepSequences.remove(repSequence);
- revealedSeqs.addElement(repSequence);
+ revealedSeqs.add(repSequence);
}
int start = adjustForHiddenSeqs(alignmentIndex - 1);
{
if (seq.getLength() > 0)
{
- revealedSeqs.addElement(seq);
+ revealedSeqs.add(seq);
asequences.add(alignmentIndex, seq);
}
else
index++;
}
}
+ Alignment fAlignmt = new Alignment(seq);
+ fAlignmt.annotations = alignment.getAlignmentAnnotation();
+ fAlignmt.alignmentProperties = alignment.getProperties();
+ fAlignmt.groups = alignment.getGroups();
+ fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
- return new Alignment(seq);
+ return fAlignmt;
}
public boolean isHidden(SequenceI seq)
{
- for (int i = 0; i < hiddenSequences.length; i++)
+ if (hiddenSequences != null)
{
- if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+ for (int i = 0; i < hiddenSequences.length; i++)
{
- return true;
+ if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+ {
+ return true;
+ }
}
}