/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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.io;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
public class JnetAnnotationMaker
{
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);
}
}
}