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.datamodel.DBRefEntry;
24 import jalview.ws.dbsources.Uniprot;
27 import java.io.FileReader;
28 import java.io.PrintWriter;
29 import java.io.Reader;
30 import java.util.Vector;
32 import org.exolab.castor.mapping.Mapping;
33 import org.exolab.castor.xml.Unmarshaller;
36 * Data model for entries returned from an EMBL query, as marshalled by a Castor
39 * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
41 * @see embl_mapping.xml
45 Vector<EmblEntry> entries;
47 Vector<EmblError> errors;
52 public Vector<EmblEntry> getEntries()
61 public void setEntries(Vector<EmblEntry> entries)
63 this.entries = entries;
69 public Vector<EmblError> getErrors()
78 public void setErrors(Vector<EmblError> errors)
84 * Parse an EmblXML file into an EmblFile object
87 * @return parsed EmblXML or null if exceptions were raised
89 public static EmblFile getEmblFile(File file)
97 return EmblFile.getEmblFile(new FileReader(file));
100 System.err.println("Exception whilst reading EMBLfile from " + file);
101 e.printStackTrace(System.err);
106 public static EmblFile getEmblFile(Reader file)
108 EmblFile record = new EmblFile();
111 // 1. Load the mapping information from the file
112 Mapping map = new Mapping(record.getClass().getClassLoader());
114 java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
115 map.loadMapping(url);
117 // 2. Unmarshal the data
118 Unmarshaller unmar = new Unmarshaller(record);
121 // uncomment to DEBUG EMBLFile reading
122 if (jalview.bin.Cache.getDefault(jalview.bin.Cache.CASTORLOGLEVEL,
123 "debug").equalsIgnoreCase("DEBUG"))
125 unmar.setDebug(jalview.bin.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);
136 canonicaliseDbRefs(record);
137 } catch (Exception e)
139 e.printStackTrace(System.err);
147 * Change blank version to "0" in any DBRefEntry, to ensure consistent
148 * comparison with other DBRefEntry in Jalview
151 * @see Uniprot#getDbVersion
153 static void canonicaliseDbRefs(EmblFile record)
155 if (record.getEntries() == null)
159 for (EmblEntry entry : record.getEntries())
161 if (entry.getDbRefs() != null)
163 for (DBRefEntry dbref : entry.getDbRefs())
165 if ("".equals(dbref.getVersion()))
167 dbref.setVersion("0");
172 if (entry.getFeatures() != null)
174 for (EmblFeature feature : entry.getFeatures())
176 if (feature.getDbRefs() != null)
178 for (DBRefEntry dbref : feature.getDbRefs())
180 if ("".equals(dbref.getVersion()))
182 dbref.setVersion("0");