/*
- * 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 2.8.2)
+ * 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
- * 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;
String vamsasId;
DBRefEntry[] dbrefs;
-
+
RNA rna;
/**
{
tmp = new char[i];
System.arraycopy(sequence, 0, tmp, 0, i);
- j=sequence.length;
+ j = sequence.length;
}
else
{
datasetSequence.setPDBId(getPDBId());
setPDBId(null);
datasetSequence.updatePDBIds();
+ if (annotation != null)
+ {
+ Vector<AlignmentAnnotation> _annot = annotation;
+ annotation = null;
+ for (AlignmentAnnotation aa : _annot)
+ {
+ aa.sequenceRef = datasetSequence;
+ aa.adjustForAlignment(); // uses annotation's own record of
+ // sequence-column mapping
+ datasetSequence.addAlignmentAnnotation(aa);
+ }
+ }
}
return datasetSequence;
}
{
index = value;
}
-
- public void setRNA(RNA r){rna=r;}
-
- public RNA getRNA() { return rna; }
-
+
+ public void setRNA(RNA r)
+ {
+ rna = r;
+ }
+
+ public RNA getRNA()
+ {
+ return rna;
+ }
+
}