/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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
{
* holds a list of hidden sequences associated with an alignment.
*/
public SequenceI[] hiddenSequences;
+
AlignmentI alignment;
public HiddenSequences(AlignmentI al)
int width = 0;
for (int i = 0; i < hiddenSequences.length; i++)
{
- if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width)
+ if (hiddenSequences[i] != null
+ && hiddenSequences[i].getLength() > width)
{
width = hiddenSequences[i].getLength();
}
}
/**
- * Call this method if sequences are removed from the
- * main alignment
+ * Call this method if sequences are removed from the main alignment
*/
public void adjustHeightSequenceDeleted(int seqIndex)
{
}
/**
- * Call this method if sequences are added to or removed from the
- * main alignment
+ * Call this method if sequences are added to or removed from the main
+ * alignment
*/
public void adjustHeightSequenceAdded()
{
alignment.deleteSequence(sequence);
}
- public Vector showAll(Hashtable hiddenReps)
+ 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, hiddenReps);
- 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, Hashtable hiddenReps)
+ 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 &&
- hiddenReps != null
- && hiddenReps.containsKey(repSequence))
+ if (repSequence != null && hiddenRepSequences != null
+ && hiddenRepSequences.containsKey(repSequence))
{
- hiddenReps.remove(repSequence);
- revealedSeqs.addElement(repSequence);
+ hiddenRepSequences.remove(repSequence);
+ revealedSeqs.add(repSequence);
}
int start = adjustForHiddenSeqs(alignmentIndex - 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.add(seq);
+ asequences.add(alignmentIndex, seq);
+ }
+ else
+ {
+ System.out.println(seq.getName()
+ + " has been deleted whilst hidden");
+ }
}
- }
+ }
}
return revealedSeqs;
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;
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff