/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.bio.seq.db.flat;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.NoSuchElementException;
import org.biojava.bio.Annotation;
import org.biojava.bio.BioException;
import org.biojava.bio.program.indexdb.BioStore;
import org.biojava.bio.program.indexdb.Record;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.SequenceIterator;
import org.biojava.bio.seq.db.IllegalIDException;
import org.biojava.bio.seq.db.SequenceDBLite;
import org.biojava.bio.seq.io.SeqIOTools;
import org.biojava.bio.seq.io.SequenceBuilderFactory;
import org.biojava.bio.seq.io.SequenceFormat;
import org.biojava.bio.seq.io.StreamReader;
import org.biojava.bio.seq.io.SymbolTokenization;
import org.biojava.bio.symbol.Alphabet;
import org.biojava.utils.ChangeVetoException;
import org.biojava.utils.Unchangeable;
import org.biojava.utils.io.RAF;
import org.biojava.utils.lsid.LifeScienceIdentifier;
import org.biojava.utils.lsid.LifeScienceIdentifierParseException;
/**
* FlatSequenceDB
is an OBDA flatfile sequence databank
* implementation. It is backed by an index created using the
* org.biojava.bio.program.indexdb
package.
*
* @author Keith James
*/
public class FlatSequenceDB extends Unchangeable implements SequenceDBLite
{
private BioStore index;
private String dbName;
private LifeScienceIdentifier format;
public FlatSequenceDB(String location, String dbName)
throws IOException, BioException
{
this.dbName = dbName;
index = new BioStore(new File(location), false);
try
{
Annotation config = index.getMetaData();
String lsid = (String) config.getProperty("format");
format = LifeScienceIdentifier.valueOf(lsid);
}
catch (NoSuchElementException nsee)
{
throw new BioException("Malformed OBDA index '"
+ location
+ "' does not indicate sequence format",nsee);
}
catch (LifeScienceIdentifierParseException lse)
{
throw new BioException("Malformed OBDA index '"
+ location
+ "' has a format identifier which is not a valid LSID",lse);
}
}
public String getName()
{
return dbName;
}
public Sequence getSequence(String id)
throws IllegalIDException, BioException
{
try
{
Record record = index.get(id);
RAF seqRAF = record.getFile();
int recLength = record.getLength();
seqRAF.seek(record.getOffset());
byte [] bytes = new byte [recLength];
seqRAF.readFully(bytes, 0, recLength);
InputStream is = new ByteArrayInputStream(bytes);
int formatId = SeqIOTools.identifyFormat(format.getNamespaceId(),
format.getObjectId());
SequenceFormat sf = SeqIOTools.getSequenceFormat(formatId);
Alphabet alpha = SeqIOTools.getAlphabet(formatId);
SymbolTokenization toke = alpha.getTokenization("token");
SequenceBuilderFactory sbf = SeqIOTools.getBuilderFactory(formatId);
SequenceIterator si = new StreamReader(is, sf, toke, sbf);
return si.nextSequence();
}
catch (NoSuchElementException nsee)
{
throw new IllegalIDException("Failed to find sequence with ID "
+ id
+ " in database "
+ getName());
}
catch (IOException ioe)
{
throw new BioException("Failed to retrieve sequence with ID "
+ id, ioe);
}
}
/**
* addSequence
always throws a
* ChangeVetoException
as this implementation is
* immutable.
*
* @param sequence a Sequence
.
*
* @exception ChangeVetoException
*/
public void addSequence(Sequence sequence) throws ChangeVetoException
{
throw new ChangeVetoException("Failed to add sequence."
+ " Sequences may not be added"
+ " to a flat database");
}
/**
* removeSequence
always throws a
* ChangeVetoException
as this implementation is
* immutable.
*
* @param id a String
.
*
* @exception ChangeVetoException
*/
public void removeSequence(String id) throws ChangeVetoException
{
throw new ChangeVetoException("Failed to add sequence."
+ " Sequences may not be removed"
+ " from a flat database");
}
}