/*
* 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.
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel.xdb.embl;
import jalview.bin.Cache;
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.net.URL;
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 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 Embl XML file into an EmblEntry object
*
* @param file
* @return parsed EmblXML or null if exceptions were raised
*/
public static EmblEntry getEmblEntry(File file)
{
if (file == null)
{
return null;
}
try
{
return EmblFile.getEntry(new FileReader(file));
} catch (Exception e)
{
System.err.println("Exception whilst reading EMBLfile from " + file);
e.printStackTrace(System.err);
}
return null;
}
/**
* Reads the XML response from file and unmarshals into a Java object
*
* @param fileReader
* @return
*/
public static EmblEntry getEntry(Reader fileReader)
{
EmblEntry record = new EmblEntry();
try
{
// 1. Load the mapping information from the file
Mapping map = new Mapping(record.getClass().getClassLoader());
URL url = record.getClass().getResource("/embl_mapping.xml");
map.loadMapping(url);
// 2. Unmarshal the data
Unmarshaller unmar = new Unmarshaller(record);
try
{
if (Cache.getDefault(Cache.CASTORLOGLEVEL,
"debug").equalsIgnoreCase("DEBUG"))
{
unmar.setDebug(Cache.log.isDebugEnabled());
// unmar.setDebug(true);// uncomment to debug unmarshalling
}
} catch (Exception e)
{
}
unmar.setIgnoreExtraElements(true);
unmar.setIgnoreExtraAttributes(true);
unmar.setMapping(map);
unmar.setLogWriter(new PrintWriter(System.out));
record = (EmblEntry) unmar.unmarshal(fileReader);
canonicaliseDbRefs(record);
} catch (Exception e)
{
e.printStackTrace(System.err);
record = null;
}
return record;
}
/**
* Change blank version to "0" in any DBRefEntry, to ensure consistent
* comparison with other DBRefEntry in Jalview
*
* @param entry
* @see Uniprot#getDbVersion
*/
static void canonicaliseDbRefs(EmblEntry entry)
{
if (entry == null)
{
return;
}
// for (EmblEntry entry : record.getEntries())
// {
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");
}
}
}
}
}
// }
}
}