/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.ws.jws1;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.io.FileParse;
import jalview.io.FormatAdapter;
import jalview.io.InputStreamParser;
+import jalview.util.MessageManager;
import java.io.BufferedReader;
import java.io.FileReader;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLEncoder;
+import java.util.Iterator;
public class Annotate3D
{
sb.append(cbuff[i]);
}
}
-
- FileParse fp = new InputStreamParser(
- jalview.ext.paradise.Annotate3D.getRNAMLForPDBFileAsString(sb
- .toString()), source.getDataName());
- AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
- return nal;
+ Iterator<Reader> r = jalview.ext.paradise.Annotate3D
+ .getRNAMLForPDBFileAsString(sb.toString());
+ AlignmentI al = null;
+ while (r.hasNext())
+ {
+ FileParse fp = new InputStreamParser(r.next(), source.getDataName());
+ AlignmentI nal = new FormatAdapter().readFromFile(fp, "RNAML");
+ if (al == null)
+ {
+ al = nal;
+ }
+ else
+ {
+ al.append(nal);
+ }
+ }
+ return al;
} catch (Throwable x)
{
if (x instanceof IOException)
else
{
throw new IOException(
- "Unexpected exception when handling RNAML translation of PDB data",
+ MessageManager
+ .getString("exception.unexpected_handling_rnaml_translation_for_pdb"),
x);
}
}