/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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
* 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.
- *
+ *
* 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
addSequenceFeature(new SequenceFeature(sf[i]));
}
}
- if (seq.getDBRef() != null)
+ setDatasetSequence(seq.getDatasetSequence());
+ if (datasetSequence == null && seq.getDBRef() != null)
{
+ // only copy DBRefs if we really are a dataset sequence
DBRefEntry[] dbr = seq.getDBRef();
for (int i = 0; i < dbr.length; i++)
{
addDBRef(new DBRefEntry(dbr[i]));
}
}
- setDatasetSequence(seq.getDatasetSequence());
if (seq.getAnnotation() != null)
{
AlignmentAnnotation[] sqann = seq.getAnnotation();
/*
* (non-Javadoc)
*
+ * @see jalview.datamodel.SequenceI#findPositionMap()
+ */
+ public int[] findPositionMap()
+ {
+ int map[] = new int[sequence.length];
+ int j = 0;
+ int pos = start;
+ int seqlen = sequence.length;
+ while ((j < seqlen))
+ {
+ map[j] = pos;
+ if (!jalview.util.Comparison.isGap(sequence[j]))
+ {
+ pos++;
+ }
+
+ j++;
+ }
+ return map;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.SequenceI#deleteChars(int, int)
*/
public void deleteChars(int i, int j)
{
createNewDs = true;
newend--; // decrease end position by one for the deleted residue
- // and search further
+ // and search further
}
}
}
public DBRefEntry[] getDBRef()
{
+ if (dbrefs == null && datasetSequence != null
+ && this != datasetSequence)
+ {
+ return datasetSequence.getDBRef();
+ }
return dbrefs;
}