+/*
+ * 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
+ *
+ * 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.
+ *
+ * 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/>.
+ */
package jalview.datamodel.xdb.embl;
-
import java.io.File;
import java.io.FileReader;
import java.io.Reader;
import org.exolab.castor.mapping.Mapping;
import org.exolab.castor.xml.Unmarshaller;
-public class EmblFile {
- Vector entries;
- Vector errors;
- /**
- * @return the entries
- */
- public Vector getEntries() {
- return entries;
- }
- /**
- * @param entries the entries to set
- */
- public void setEntries(Vector entries) {
- this.entries = entries;
- }
- /**
- * @return the errors
- */
- public Vector getErrors() {
- return errors;
- }
- /**
- * @param errors the errors to set
- */
- public void setErrors(Vector errors) {
- this.errors = errors;
- }
- /**
- * Parse an EmblXML file into an EmblFile object
- * @param file
- * @return parsed EmblXML or null if exceptions were raised
- */
- public static EmblFile getEmblFile(File file)
+public class EmblFile
+{
+ Vector entries;
+
+ Vector errors;
+
+ /**
+ * @return the entries
+ */
+ public Vector getEntries()
+ {
+ return entries;
+ }
+
+ /**
+ * @param entries
+ * the entries to set
+ */
+ public void setEntries(Vector entries)
+ {
+ this.entries = entries;
+ }
+
+ /**
+ * @return the errors
+ */
+ public Vector getErrors()
+ {
+ return errors;
+ }
+
+ /**
+ * @param errors
+ * the errors to set
+ */
+ public void setErrors(Vector errors)
+ {
+ this.errors = errors;
+ }
+
+ /**
+ * Parse an EmblXML file into an EmblFile object
+ *
+ * @param file
+ * @return parsed EmblXML or null if exceptions were raised
+ */
+ public static EmblFile getEmblFile(File file)
+ {
+ if (file == null)
+ return null;
+ try
{
- if (file==null)
- return null;
- try {
- return EmblFile.getEmblFile(new FileReader(file));
- }
- catch (Exception e) {
- System.err.println("Exception whilst reading EMBLfile from "+file);
- e.printStackTrace(System.err);
- }
- return null;
+ return EmblFile.getEmblFile(new FileReader(file));
+ } catch (Exception e)
+ {
+ System.err.println("Exception whilst reading EMBLfile from " + file);
+ e.printStackTrace(System.err);
}
- public static EmblFile getEmblFile(Reader file) {
- EmblFile record = new EmblFile();
- try
- {
- // 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);
+ return null;
+ }
- // 2. Unmarshal the data
- Unmarshaller unmar = new Unmarshaller(record);
- try {
- // uncomment to DEBUG EMBLFile reading unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
- } catch (Exception e) {};
- unmar.setIgnoreExtraElements(true);
- unmar.setMapping(map);
+ public static EmblFile getEmblFile(Reader file)
+ {
+ EmblFile record = new EmblFile();
+ try
+ {
+ // 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);
- record = (EmblFile) unmar.unmarshal(file);
- }
- catch (Exception e)
- {
- e.printStackTrace(System.err);
- record=null;
- }
+ // 2. Unmarshal the data
+ Unmarshaller unmar = new Unmarshaller(record);
+ try
+ {
+ // uncomment to DEBUG EMBLFile reading
+ if (((String) 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.setMapping(map);
+ record = (EmblFile) unmar.unmarshal(file);
+ } catch (Exception e)
+ {
+ e.printStackTrace(System.err);
+ record = null;
+ }
- return record;
- }
- public static void main(String args[]) {
- EmblFile myfile = EmblFile.getEmblFile(new File("C:\\Documents and Settings\\JimP\\workspace-3.2\\Jalview Release\\schemas\\embleRecordV1.1.xml"));
- if (myfile!=null && myfile.entries!=null && myfile.entries.size()>0)
- System.out.println(myfile.entries.size()+" Records read.");
- }
+ return record;
+ }
+
+ public static void main(String args[])
+ {
+ File mf = null;
+ if (args.length == 1)
+ {
+ mf = new File(args[0]);
+ }
+ if (!mf.exists())
+ {
+ mf = new File(
+ "C:\\Documents and Settings\\JimP\\workspace-3.2\\Jalview Release\\schemas\\embleRecordV1.1.xml");
+ }
+ EmblFile myfile = EmblFile.getEmblFile(mf);
+ if (myfile != null && myfile.entries != null
+ && myfile.entries.size() > 0)
+ System.out.println(myfile.entries.size() + " Records read. (" + mf
+ + ")");
+ }
}
git://source.jalview.org / jalview.git / blobdiff