/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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 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.
+ *
+ * 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.io;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
public class JnetAnnotationMaker
{
* adds the annotation parsed by prediction to al.
*
* @param prediction
- * JPredFile
+ * JPredFile
* @param al
- * AlignmentI
+ * AlignmentI
* @param firstSeq
- * int the index of the sequence to attach the annotation to
- * (usually zero)
+ * int the index of the sequence to attach the annotation to (usually
+ * zero)
* @param noMsa
- * boolean
+ * boolean
* @param delMap
- * mapping from columns in JPredFile prediction to residue
- * number in al.getSequence(firstSeq)
+ * mapping from columns in JPredFile prediction to residue number in
+ * al.getSequence(firstSeq)
*/
public static void add_annotation(JPredFile prediction, AlignmentI al,
int firstSeq, boolean noMsa, int[] delMap) throws Exception
if ((delMap != null && delMap.length > width)
|| (delMap == null && gapmap.length != width))
{
- throw (new Exception("Number of residues in "
- + (delMap == null ? "" : " mapped ")
- + "supposed query sequence ('"
- + al.getSequenceAt(firstSeq).getName() + "'\n"
- + al.getSequenceAt(firstSeq).getSequenceAsString()
- + ")\ndiffer from number of prediction sites in prediction ("
- + width + ")"));
+ throw (new Exception(MessageManager.formatMessage("exception.number_of_residues_in_query_sequence_differ_from_prediction", new String[]{
+ (delMap == null ? "" : MessageManager.getString("label.mapped")),
+ al.getSequenceAt(firstSeq).getName(),
+ al.getSequenceAt(firstSeq).getSequenceAsString(),
+ Integer.valueOf(width).toString()
+ })));
}
AlignmentAnnotation annot;
{
for (int j = 0; j < width; j++)
{
- annotations[gapmap[j]] = new Annotation("", "", preds[i]
- .getCharAt(j), 0);
+ annotations[gapmap[j]] = new Annotation("", "",
+ preds[i].getCharAt(j), 0);
}
}
else
{
float value = new Float(preds[i].getCharAt(j) + "")
.floatValue();
- annotations[gapmap[delMap[j]]] = new Annotation(preds[i]
- .getCharAt(j)
- + "", "", preds[i].getCharAt(j), value);
+ annotations[gapmap[delMap[j]]] = new Annotation(
+ preds[i].getCharAt(j) + "", "",
+ preds[i].getCharAt(j), value);
}
}
}
{
for (int j = 0; j < width; j++)
{
- annotations[gapmap[delMap[j]]] = new Annotation(preds[i]
- .getCharAt(j)
- + "", "", ' ', 0);
+ annotations[gapmap[delMap[j]]] = new Annotation(
+ preds[i].getCharAt(j) + "", "", ' ', 0);
}
}
}