2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.datamodel.xdb.embl;
23 import jalview.bin.Cache;
26 import java.io.FileReader;
27 import java.io.PrintWriter;
28 import java.io.Reader;
29 import java.util.Vector;
31 import org.exolab.castor.mapping.Mapping;
32 import org.exolab.castor.xml.Unmarshaller;
35 * Data model for entries returned from an EMBL query, as marshalled by a Castor
38 * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
40 * @see embl_mapping.xml
44 Vector<EmblEntry> entries;
46 Vector<EmblError> errors;
51 public Vector<EmblEntry> getEntries()
60 public void setEntries(Vector<EmblEntry> entries)
62 this.entries = entries;
68 public Vector<EmblError> getErrors()
77 public void setErrors(Vector<EmblError> errors)
83 * Parse an EmblXML file into an EmblFile object
86 * @return parsed EmblXML or null if exceptions were raised
88 public static EmblFile getEmblFile(File file)
96 return EmblFile.getEmblFile(new FileReader(file));
99 System.err.println("Exception whilst reading EMBLfile from " + file);
100 e.printStackTrace(System.err);
105 public static EmblFile getEmblFile(Reader file)
107 EmblFile record = new EmblFile();
110 // 1. Load the mapping information from the file
111 Mapping map = new Mapping(record.getClass().getClassLoader());
113 java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
114 map.loadMapping(url);
116 // 2. Unmarshal the data
117 Unmarshaller unmar = new Unmarshaller(record);
120 // uncomment to DEBUG EMBLFile reading
121 if (Cache.getDefault(
122 Cache.CASTORLOGLEVEL, "debug")
123 .equalsIgnoreCase("DEBUG"))
125 unmar.setDebug(Cache.log.isDebugEnabled());
127 } catch (Exception e)
130 unmar.setIgnoreExtraElements(true);
131 unmar.setIgnoreExtraAttributes(true);
132 unmar.setMapping(map);
133 unmar.setLogWriter(new PrintWriter(System.out));
134 record = (EmblFile) unmar.unmarshal(file);
135 } catch (Exception e)
137 e.printStackTrace(System.err);