/*
* 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.program.gff;
import org.biojava.bio.seq.StrandedFeature;
import org.biojava.utils.ParserException;
/**
* Interface which captures any errors which occur when parsing
* a GFF stream. Providing a custom implementation of this
* interface allows intelligent recovery from errors when
* parsing GFF.
*
*
* Each of these methods has three options:
*
*
* - Throw a ParserException. This need only contain a
* detail message, the parser will fill in other fields.
* parsing will be aborted.
* - Throw an IgnoreRecordException. This line of the GFF
* file will be ignored, but parsing will not be aborted
* - Return a value for the field.
*
*
*
* @author Thomas Down
* @author Matthew Pocock
*/
public interface GFFErrorHandler {
/**
* The `start' field of the GFF entry was not a valid value.
*
* @param token The start token found.
* @return A parsed value, if this is possible
* @throws ParserException If parsing should be aborted
* @throws IgnoreRecordException If this record should be silently skipped.
*/
public int invalidStart(String token)
throws ParserException, IgnoreRecordException;
/**
* The `end' field of the GFF entry was not a valid value.
*
* @param token The end token found.
* @return A parsed value, if this is possible
* @throws ParserException If parsing should be aborted
* @throws IgnoreRecordException If this record should be silently skipped.
*/
public int invalidEnd(String token)
throws ParserException, IgnoreRecordException;
/**
* The `score' field of the GFF entry was not a valid value.
*
* @param token The score token found.
* @return A parsed value, if this is possible
* @throws ParserException If parsing should be aborted
* @throws IgnoreRecordException If this record should be silently skipped.
*/
public double invalidScore(String token)
throws ParserException, IgnoreRecordException;
/**
* The `frame' field of the GFF entry was not a valid value.
*
* @param token The frame token found.
* @return A parsed value, if this is possible
* @throws ParserException If parsing should be aborted
* @throws IgnoreRecordException If this record should be silently skipped.
*/
public int invalidFrame(String token)
throws ParserException, IgnoreRecordException;
/**
* The `strand' field of the GFF entry was not a valid value.
*
* @param token The strand token found.
* @return A parsed value, if this is possible
* @throws ParserException If parsing should be aborted
* @throws IgnoreRecordException If this record should be silently skipped.
*/
public StrandedFeature.Strand invalidStrand(String token)
throws ParserException, IgnoreRecordException;
public static final GFFErrorHandler ABORT_PARSING = new AbortErrorHandler();
static class AbortErrorHandler implements GFFErrorHandler {
public int invalidStart(String token) throws ParserException {
throw new ParserException("Invalid start token");
}
public int invalidEnd(String token) throws ParserException {
throw new ParserException("Invalid end token");
}
public double invalidScore(String token) throws ParserException {
throw new ParserException("Invalid score token");
}
public int invalidFrame(String token) throws ParserException {
throw new ParserException("Invalid frame token");
}
public StrandedFeature.Strand invalidStrand(String token) throws ParserException {
throw new ParserException("Invalid strand token");
}
}
public static final GFFErrorHandler SKIP_RECORD = new SkipRecordErrorHandler();
static class SkipRecordErrorHandler implements GFFErrorHandler {
public int invalidStart(String token) throws IgnoreRecordException {
throw new IgnoreRecordException();
}
public int invalidEnd(String token) throws IgnoreRecordException {
throw new IgnoreRecordException();
}
public double invalidScore(String token) throws IgnoreRecordException {
throw new IgnoreRecordException();
}
public int invalidFrame(String token) throws IgnoreRecordException {
throw new IgnoreRecordException();
}
public StrandedFeature.Strand invalidStrand(String token) throws IgnoreRecordException {
throw new IgnoreRecordException();
}
}
}