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/* ReadAndWriteEntry.java
* This file is part of Artemis
*
* Copyright(C) 2008 Genome Research Limited
*
* 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 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.
*
* 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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
*/
package uk.ac.sanger.artemis.io;
import java.io.File;
import java.io.IOException;
import javax.swing.JFrame;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.util.DatabaseDocument;
import uk.ac.sanger.artemis.util.InputStreamProgressEvent;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.Options;
public class ReadAndWriteEntry
{
private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(ReadAndWriteEntry.class);
private static DatabaseEntrySource ENTRY_SOURCE;
/**
* Read from the database, given a srcFeature uniquename
* @param uniqueName
* @return
* @throws OutOfRangeException
* @throws NoSequenceException
* @throws IOException
*/
public static Entry readEntryFromDatabase(final String uniqueName,
DatabaseEntrySource entry_source)
throws OutOfRangeException, NoSequenceException, IOException
{
if(entry_source == null)
{
ReadAndWriteEntry.ENTRY_SOURCE = new DatabaseEntrySource();
entry_source = ENTRY_SOURCE;
boolean promptUser = true;
if(System.getProperty("read_only") != null)
promptUser = false;
if(!entry_source.setLocation(promptUser))
return null;
}
String url = (String)entry_source.getLocation();
int index = url.indexOf("?");
String userName = url.substring(index+1).trim();
if(userName.startsWith("user="))
userName = userName.substring(5);
final String srcFeatureId = getFeatureId(entry_source, uniqueName);
final InputStreamProgressListener stream_progress_listener =
new InputStreamProgressListener()
{
public void progressMade(final InputStreamProgressEvent event)
{
final int char_count = event.getCharCount();
if(char_count != -1)
logger4j.debug("chars read so far: " + char_count);
}
public void progressMade(String progress)
{
logger4j.debug(progress);
}
};
return entry_source.getEntry(srcFeatureId, userName,
stream_progress_listener);
}
/**
* Read from the database, given a srcFeature uniquename
* @param uniqueName
* @return
* @throws OutOfRangeException
* @throws NoSequenceException
* @throws IOException
*/
public static Entry readEntryFromDatabase(final String uniqueName)
throws OutOfRangeException, NoSequenceException, IOException
{
return readEntryFromDatabase(uniqueName, null);
}
/**
* Write entry to a file
* @param entry
* @param file
* @param flatten Flatten the gene model and combine the qualifiers if true.
* If false it will write all features and qualifiers out.
* @param force invalid qualifiers and any features with invalid keys will
* be quietly thrown away when saving.
* @param destination_type Should be one of EMBL_FORMAT, GENBANK_FORMAT,
* GFF_FORMAT or ANY_FORMAT. If ANY_FORMAT then the Entry will
* be saved in the same format it was created, otherwise it will be saved
* in the given format.
* @throws IOException
* @throws EntryInformationException
*/
public static void writeDatabaseEntryToFile(final Entry entry, final File file,
final boolean flatten,
final boolean ignoreObsolete,
final int destination_type,
final JFrame parent)
GeneUtils.lazyLoadAll(entry, parent);
EntryInformation artemis_entry_information = Options.getArtemisEntryInformation();
if(!flatten)
{
final FeatureVector features = entry.getAllFeatures();
for(int i=0; i<features.size(); i++)
addAllKeysQualifiers(artemis_entry_information, features.elementAt(i).getEmblFeature());
}
PublicDBDocumentEntry.IGNORE_OBSOLETE_FEATURES = ignoreObsolete;
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entry.save(file, destination_type, force, artemis_entry_information);
}
/**
* Add all keys and qualifiers for a given feature to the EntryInformation
* @param entry_information
* @param feature
*/
private static void addAllKeysQualifiers(final EntryInformation entry_information,
final Feature feature)
{
Key new_key = feature.getKey();
new_key = PublicDBDocumentEntry.mapKeys(new_key);
boolean keyAdded = false;
if(!entry_information.isValidKey(new_key))
{
entry_information.addKey(new_key);
keyAdded = true;
}
final QualifierVector feature_qualifiers = feature.getQualifiers();
// check the qualifiers
for(int i = 0 ; i < feature_qualifiers.size() ; ++i)
{
final Qualifier this_qualifier = (Qualifier)feature_qualifiers.elementAt(i);
final String this_qualifier_name = this_qualifier.getName();
if(!entry_information.isValidQualifier(this_qualifier_name) ||
!entry_information.isValidQualifier(new_key, this_qualifier_name) ||
keyAdded)
{
QualifierInfo qualifierInfo = entry_information.getQualifierInfo(this_qualifier_name);
if(qualifierInfo == null)
{
KeyVector keys = new KeyVector();
qualifierInfo = new QualifierInfo(this_qualifier_name, QualifierInfo.QUOTED_TEXT,
keys, null, false);
try
{
entry_information.addQualifierInfo(qualifierInfo);
}
catch(QualifierInfoException e)
{
e.printStackTrace();
}
}
if(qualifierInfo.getValidKeys() != null)
qualifierInfo.getValidKeys().add(new_key);
}
}
}
/**
* Get feature id
* @param entry_source
* @param srcUniqueName
* @return
*/
public static String getFeatureId(
final DatabaseEntrySource entry_source, final String srcUniqueName)
{
final DatabaseDocument doc = entry_source.getDatabaseDocument();
org.gmod.schema.sequence.Feature feature = doc.getFeatureByUniquename(srcUniqueName);
return Integer.toString(feature.getFeatureId());
}
public static void main(final String args[])
{
try
{
String names[];
boolean flatten = true;
boolean ignoreObsolete = true;
if(args != null && args.length == 1 && args[0].startsWith("-h"))
{
System.out.println("-h\tshow help");
System.out.println("-f\t[y|n] flatten the gene model, default is y");
System.out.println("-i\t[y|n] ignore obsolete features, default is y");
System.out.println("-s\tspace separated list of sequences to read and write out");
System.exit(0);
}
if(args == null || args.length < 1)
names = new String[]{
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for(int i=0; i<args.length; i++)
if(args[i].toLowerCase().equals("-f"))
{
if(i+1<args.length && args[i+1].toLowerCase().equals("n"))
flatten = false;
}
for(int i=0; i<args.length; i++)
if(args[i].toLowerCase().equals("-i"))
{
if(i+1<args.length && args[i+1].toLowerCase().equals("n"))
ignoreObsolete = false;
}
java.util.Vector files = null;
for(int i=0; i<args.length; i++)
{
if(args[i].toLowerCase().equals("-s"))
{
files = new java.util.Vector();
for(int j=i+1; j<args.length; j++)
{
if(args[j].startsWith("-"))
break;
files.add(args[j]);
}
}
}
if(files != null && files.size() > 0)
{
names = new String[files.size()];
files.toArray(names);
}
}
System.out.println(i+" read and write :: "+names[i]);
Entry entry = ReadAndWriteEntry.readEntryFromDatabase(names[i], ENTRY_SOURCE);
entry, new File(names[i]+".embl"), flatten, ignoreObsolete, false,
DocumentEntryFactory.EMBL_FORMAT, null);