/*
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.TreeMap;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.ensembl.mart.util.FormattedSequencePrintStream;
import org.ensembl.util.SequenceUtil;
/**
* This object prints out Transcripts )Exons and Introns) 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 output formats
*/
public final class TranscriptEISeqQueryRunner extends BaseSeqQueryRunner {
private final String TRANSCRIPTS = "transcripts";
private final String LOCATION = "location";
private Logger logger = Logger.getLogger(TranscriptEISeqQueryRunner.class.getName());
/**
* Constructs a TranscriptEISeqQueryRunner object to print
* Transcripts (exons and introns), with optional flanking sequences
*
* @param query
* @param format
* @param os
*/
public TranscriptEISeqQueryRunner(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));
// want everything ordered by gene_id, transcript_id
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 iDs TreeMap
iDs = new TreeMap();
lastIDRowsProcessed = 0; // refresh for the new ID
Hashtable atts = new Hashtable();
iDs.put(keyID, atts);
}
Hashtable tranatts = (Hashtable) iDs.get(keyID);
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);
// keep track of the lowest start and highest end for the transcript
if (!(tranatts.containsKey(LOCATION)))
tranatts.put(LOCATION, new SequenceLocation(chr, start, end, strand));
else {
SequenceLocation tranloc = (SequenceLocation) tranatts.get(LOCATION);
if (start < tranloc.getStart())
tranatts.put(LOCATION, new SequenceLocation(chr, start, tranloc.getEnd(), strand));
if (end > tranloc.getEnd())
tranatts.put(LOCATION, new SequenceLocation(chr, tranloc.getStart(), end, strand));
}
}
// Rest can be duplicates, or novel values for a given field, collect lists of values for each field
// currindex is now the last index of the DisplayIDs. Increment it, and iterate over the rest of the ResultSet to print the description
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 (tranatts.containsKey(field)) {
if (!((ArrayList) tranatts.get(field)).contains(value))
((ArrayList) tranatts.get(field)).add(value);
} else {
ArrayList values = new ArrayList();
values.add(value);
tranatts.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 {
Hashtable tranatts = (Hashtable) iDs.get(geneID);
SequenceLocation tranloc = (SequenceLocation) tranatts.get(LOCATION);
for (int j = 0, n = fields.size(); j < n; j++) {
if (j > 0)
osr.print(separator);
String field = (String) fields.get(j);
if (tranatts.containsKey(field)) {
ArrayList values = (ArrayList) tranatts.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();
//extend flanks, if necessary, and write sequence
if (query.getSequenceDescription().getLeftFlank() > 0)
tranloc = tranloc.extendLeftFlank(query.getSequenceDescription().getLeftFlank());
if (query.getSequenceDescription().getRightFlank() > 0)
tranloc = tranloc.extendRightFlank(query.getSequenceDescription().getRightFlank());
if (tranloc.getStrand() < 0)
osr.write(
SequenceUtil.reverseComplement(
dna.getSequence(tranloc.getChr(), tranloc.getStart(), tranloc.getEnd())));
else
osr.write(dna.getSequence(tranloc.getChr(), tranloc.getStart(), tranloc.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 {
Hashtable tranatts = (Hashtable) iDs.get(geneID);
SequenceLocation tranloc = (SequenceLocation) tranatts.get(LOCATION);
osr.print(">");
if (osr.checkError())
throw new IOException();
for (int j = 0, n = fields.size(); j < n; j++) {
if (j > 0)
osr.print(separator);
String field = (String) fields.get(j);
if (tranatts.containsKey(field)) {
ArrayList values = (ArrayList) tranatts.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();
//extend flanks, if necessary, and write sequence
if (query.getSequenceDescription().getLeftFlank() > 0)
tranloc = tranloc.extendLeftFlank(query.getSequenceDescription().getLeftFlank());
if (query.getSequenceDescription().getRightFlank() > 0)
tranloc = tranloc.extendRightFlank(query.getSequenceDescription().getRightFlank());
if (tranloc.getStrand() < 0)
osr.writeSequence(
SequenceUtil.reverseComplement(
dna.getSequence(
tranloc.getChr(),
tranloc.getStart(),
tranloc.getEnd())));
else
osr.writeSequence(
dna.getSequence(
tranloc.getChr(),
tranloc.getStart(),
tranloc.getEnd()));
osr.print("\n");
osr.resetColumnCount();
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);
}
}
};
}