/*
Copyright (C) 2003 EBI, GRL
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library 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
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package org.ensembl.mart.lib;
import java.io.IOException;
import java.io.OutputStream;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.ResultSetMetaData;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.ensembl.mart.util.FormattedSequencePrintStream;
import org.ensembl.util.SequenceUtil;
/**
* Writes out upstream or downstream sequences of transcripts in one of the supported formats.
*
* @author <a href="mailto:dlondon@ebi.ac.uk">Darin London</a>
* @author <a href="mailto:craig@ebi.ac.uk">Craig Melsopp</a>
* @see FormatSpec for supported formats
*/
public final class TranscriptFlankSeqQueryRunner extends BaseSeqQueryRunner {
private SequenceLocation calcLocation = null;
private Hashtable headerinfo = new Hashtable();
private Logger logger = Logger.getLogger(TranscriptFlankSeqQueryRunner.class.getName());
/**
* Constructs a TranscriptFlankSeqQueryRunner object to print
* transcript upstream or downstream flanking sequences
*
* @param query
* @param format
* @param os
*/
public TranscriptFlankSeqQueryRunner(Query query, FormatSpec format, OutputStream os) {
super(query);
this.format = format;
this.osr = new FormattedSequencePrintStream(maxColumnLen, os, true); //autoflush true
switch (format.getFormat()) {
case FormatSpec.TABULATED :
this.separator = format.getSeparator();
this.seqWriter = tabulatedWriter;
break;
case FormatSpec.FASTA :
this.separator = "|";
this.seqWriter = fastaWriter;
break;
}
}
protected void updateQuery() {
Attribute[] exportable = query.getSequenceDescription().getFinalLink();
queryID = exportable[0].getField();
qualifiedQueryID = exportable[0].getTableConstraint()+"."+queryID;
chrField = exportable[1].getField();
coordStart = exportable[2].getField();
coordEnd = exportable[3].getField();
strandField = exportable[4].getField();
}
protected void processResultSet(Connection conn, ResultSet rs) throws IOException, SQLException {
if (queryIDindex < 0) {
ResultSetMetaData rmeta = rs.getMetaData();
// process columnNames for required attribute indices
for (int i = 1, nColumns = rmeta.getColumnCount(); i <= nColumns; ++i) {
String column = rmeta.getColumnName(i);
if (column.equals(queryID) && queryIDindex < 0)
queryIDindex = i;
else if (column.equals(coordStart) && startIndex < 0)
startIndex = i;
else if (column.equals(coordEnd) && endIndex < 0)
endIndex = i;
else if (column.equals(chrField) && chromIndex < 0)
chromIndex = i;
else if (column.equals(strandField) && strandIndex < 0)
strandIndex = i;
else
otherIndices.add(new Integer(i));
}
}
while (rs.next()) {
Integer keyID = new Integer(rs.getInt(queryIDindex));
if ( keyID.intValue() != lastID ) {
if ( lastID > -1 ) {
//This is not the first ID in a batch, process the previous ID sequences
seqWriter.writeSequences(new Integer(lastID), conn);
}
//refresh the calcLocation
calcLocation = null;
headerinfo = new Hashtable();
lastIDRowsProcessed = 0; // refresh for the new ID
}
int start = rs.getInt(startIndex);
if (start > 0) {
// if start is not null, create a new SequenceLocation object from the chr, start, end, and strand
String chr = rs.getString(chromIndex);
int end = rs.getInt(endIndex);
int strand = rs.getInt(strandIndex);
if (calcLocation == null)
calcLocation = new SequenceLocation(chr, start, end, strand);
else {
if (start < calcLocation.getStart())
calcLocation = new SequenceLocation(chr, start, calcLocation.getEnd(), strand);
if (end > calcLocation.getEnd())
calcLocation = new SequenceLocation(chr, calcLocation.getStart(), end, strand);
}
}
if (headerinfo.isEmpty()) {
for (int i = 0, n = otherIndices.size(); i < n; i++) {
int currindex = ((Integer) otherIndices.get(i)).intValue();
if (rs.getString(currindex) != null) {
String field = attributes[currindex - 1].getField();
if (!fields.contains(field))
fields.add(field);
String value = rs.getString(currindex);
if (headerinfo.containsKey(field)) {
if (!((ArrayList) headerinfo.get(field)).contains(value))
((ArrayList) headerinfo.get(field)).add(value);
} else {
ArrayList values = new ArrayList();
values.add(value);
headerinfo.put(field, values);
}
}
}
}
totalRows++;
totalRowsThisExecute++;
resultSetRowsProcessed++;
lastID = keyID.intValue();
lastIDRowsProcessed++;
}
}
private final SeqWriter tabulatedWriter = new SeqWriter() {
void writeSequences(Integer geneID, Connection conn) throws SequenceException {
try {
for (int j = 0, n = fields.size(); j < n; j++) {
if (j > 0)
osr.print(separator);
String field = (String) fields.get(j);
if (headerinfo.containsKey(field)) {
ArrayList values = (ArrayList) headerinfo.get(field);
for (int vi = 0; vi < values.size(); vi++) {
if (vi > 0)
osr.print(",");
osr.print((String) values.get(vi));
}
}
}
osr.print(separator);
if (osr.checkError())
throw new IOException();
SequenceDescription seqd = query.getSequenceDescription();
int start = 0;
int end = 0;
// modify transcript location coordinates depending on flank requested
if (seqd.getLeftFlank() > 0) {
if (calcLocation.getStrand() < 0) {
start = calcLocation.getEnd() + 1;
end = calcLocation.getEnd() + seqd.getLeftFlank();
} else {
end = calcLocation.getStart() - 1;
start = calcLocation.getStart() - seqd.getLeftFlank();
}
} else if (seqd.getRightFlank() > 0) {
if (calcLocation.getStrand() < 0) {
end = calcLocation.getStart() - 1;
start = calcLocation.getStart() - seqd.getRightFlank();
} else {
start = calcLocation.getEnd() + 1;
end = calcLocation.getEnd() + seqd.getRightFlank();
}
} else
throw new SequenceException("Transcript Flank requests must have a flanking length\n");
calcLocation = new SequenceLocation(calcLocation.getChr(), start, end, calcLocation.getStrand());
if (calcLocation.getStrand() < 0)
osr.write(
SequenceUtil.reverseComplement(
dna.getSequence(calcLocation.getChr(), calcLocation.getStart(), calcLocation.getEnd())));
else
osr.write(dna.getSequence(calcLocation.getChr(), calcLocation.getStart(), calcLocation.getEnd()));
osr.print("\n");
if (osr.checkError())
throw new IOException();
} catch (SequenceException e) {
if (logger.isLoggable(Level.WARNING))
logger.warning(e.getMessage());
throw e;
} catch (IOException e) {
if (logger.isLoggable(Level.WARNING))
logger.warning("Couldnt write to OutputStream\n" + e.getMessage());
throw new SequenceException(e);
}
}
};
private final SeqWriter fastaWriter = new SeqWriter() {
void writeSequences(Integer geneID, Connection conn) throws SequenceException {
try {
osr.print(">");
for (int j = 0, n = fields.size(); j < n; j++) {
if (j > 0)
osr.print(separator);
String field = (String) fields.get(j);
if (headerinfo.containsKey(field)) {
ArrayList values = (ArrayList) headerinfo.get(field);
for (int vi = 0; vi < values.size(); vi++) {
if (vi > 0)
osr.print(",");
osr.print((String) values.get(vi));
}
}
}
osr.print("\n");
if (osr.checkError())
throw new IOException();
SequenceDescription seqd = query.getSequenceDescription();
int start = 0;
int end = 0;
// modify transcript location coordinates depending on flank requested
if (seqd.getLeftFlank() > 0) {
if (calcLocation.getStrand() < 0) {
start = calcLocation.getEnd() + 1;
end = calcLocation.getEnd() + seqd.getLeftFlank();
} else {
end = calcLocation.getStart() - 1;
start = calcLocation.getStart() - seqd.getLeftFlank();
}
} else if (seqd.getRightFlank() > 0) {
if (calcLocation.getStrand() < 0) {
end = calcLocation.getStart() - 1;
start = calcLocation.getStart() - seqd.getRightFlank();
} else {
start = calcLocation.getEnd() + 1;
end = calcLocation.getEnd() + seqd.getRightFlank();
}
} else
throw new SequenceException("Transcript Flank requests must have a flanking length\n");
calcLocation = new SequenceLocation(calcLocation.getChr(), start, end, calcLocation.getStrand());
if (calcLocation.getStrand() < 0)
osr.write(
SequenceUtil.reverseComplement(
dna.getSequence(calcLocation.getChr(), calcLocation.getStart(), calcLocation.getEnd())));
else
osr.write(dna.getSequence(calcLocation.getChr(), calcLocation.getStart(), calcLocation.getEnd()));
osr.print("\n");
if (osr.checkError())
throw new IOException();
} catch (SequenceException e) {
if (logger.isLoggable(Level.WARNING))
logger.warning(e.getMessage());
throw e;
} catch (IOException e) {
if (logger.isLoggable(Level.WARNING))
logger.warning("Couldnt write to OutputStream\n" + e.getMessage());
throw new SequenceException(e);
}
}
};
}