/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel.xdb.embl;
+import jalview.datamodel.DBRefEntry;
+import jalview.ws.dbsources.Uniprot;
+
import java.io.File;
import java.io.FileReader;
+import java.io.PrintWriter;
import java.io.Reader;
import java.util.Vector;
import org.exolab.castor.mapping.Mapping;
import org.exolab.castor.xml.Unmarshaller;
+/**
+ * Data model for entries returned from an EMBL query, as marshalled by a Castor
+ * binding file
+ *
+ * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
+ *
+ * @see embl_mapping.xml
+ */
public class EmblFile
{
- Vector entries;
+ Vector<EmblEntry> entries;
+
+ Vector<EmblError> errors;
- Vector errors;
+ String text;
/**
* @return the entries
*/
- public Vector getEntries()
+ public Vector<EmblEntry> getEntries()
{
return entries;
}
/**
* @param entries
- * the entries to set
+ * the entries to set
*/
- public void setEntries(Vector entries)
+ public void setEntries(Vector<EmblEntry> entries)
{
this.entries = entries;
}
/**
* @return the errors
*/
- public Vector getErrors()
+ public Vector<EmblError> getErrors()
{
return errors;
}
/**
* @param errors
- * the errors to set
+ * the errors to set
*/
- public void setErrors(Vector errors)
+ public void setErrors(Vector<EmblError> errors)
{
this.errors = errors;
}
public static EmblFile getEmblFile(File file)
{
if (file == null)
+ {
return null;
+ }
try
{
return EmblFile.getEmblFile(new FileReader(file));
{
// 1. Load the mapping information from the file
Mapping map = new Mapping(record.getClass().getClassLoader());
+
java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
map.loadMapping(url);
try
{
// uncomment to DEBUG EMBLFile reading
- if (((String) jalview.bin.Cache.getDefault(
- jalview.bin.Cache.CASTORLOGLEVEL, "debug"))
+ if (jalview.bin.Cache
+ .getDefault(jalview.bin.Cache.CASTORLOGLEVEL, "debug")
.equalsIgnoreCase("DEBUG"))
+ {
unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
+ }
} catch (Exception e)
{
}
- ;
unmar.setIgnoreExtraElements(true);
+ unmar.setIgnoreExtraAttributes(true);
unmar.setMapping(map);
-
+ unmar.setLogWriter(new PrintWriter(System.out));
record = (EmblFile) unmar.unmarshal(file);
+
+ canonicaliseDbRefs(record);
} catch (Exception e)
{
e.printStackTrace(System.err);
return record;
}
- public static void main(String args[])
+ /**
+ * Change blank version to "0" in any DBRefEntry, to ensure consistent
+ * comparison with other DBRefEntry in Jalview
+ *
+ * @param record
+ * @see Uniprot#getDbVersion
+ */
+ static void canonicaliseDbRefs(EmblFile record)
{
- File mf = null;
- if (args.length == 1)
+ if (record.getEntries() == null)
{
- mf = new File(args[0]);
+ return;
}
- if (!mf.exists())
+ for (EmblEntry entry : record.getEntries())
{
- mf = new File(
- "C:\\Documents and Settings\\JimP\\workspace-3.2\\Jalview Release\\schemas\\embleRecordV1.1.xml");
+ if (entry.getDbRefs() != null)
+ {
+ for (DBRefEntry dbref : entry.getDbRefs())
+ {
+ if ("".equals(dbref.getVersion()))
+ {
+ dbref.setVersion("0");
+ }
+ }
+ }
+
+ if (entry.getFeatures() != null)
+ {
+ for (EmblFeature feature : entry.getFeatures())
+ {
+ if (feature.getDbRefs() != null)
+ {
+ for (DBRefEntry dbref : feature.getDbRefs())
+ {
+ if ("".equals(dbref.getVersion()))
+ {
+ dbref.setVersion("0");
+ }
+ }
+ }
+ }
+ }
}
- EmblFile myfile = EmblFile.getEmblFile(mf);
- if (myfile != null && myfile.entries != null
- && myfile.entries.size() > 0)
- System.out.println(myfile.entries.size() + " Records read. (" + mf
- + ")");
+ }
+
+ public String getText()
+ {
+ return text;
+ }
+
+ public void setText(String text)
+ {
+ this.text = text;
}
}
git://source.jalview.org / jalview.git / blobdiff