org.biojava.bio.program.sax.ClustalWAlignmentSAXParser Maven / Gradle / Ivy
/*
* 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.sax;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.StringTokenizer;
import org.xml.sax.Attributes;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.AttributesImpl;
/**
* A SAX2 parser for dealing with a multiple sequence
* alignment as produced by ClustalW outputing .aln format.
* For example,
*
K1C0_XENLA/125-441 DKVHALETANTELERKIKEWYEKQRPGSSSGDGAKDYSKYYT
K1C4_XENLA/81-396 EKVRALEAANADLELKIREWYEKQK-GSGIGAGSKDFSKYFE
K1C5_XENLA/73-384 DRVRSLEQANHELELKIREYLDKK-----AAVGSLDYSGYYN
keratin15 DKVRALEEANADLEVKIHDWYQKQTP----ASPECDYSQYFK
K1C0_XENLA/125-441 -----AKFLLQNDNARLAADDFKMKFEN--------------
K1C4_XENLA/81-396 -----SRVVLQIDNAKLAADDFRLKFEN--------------
K1C5_XENLA/73-384 -----TRLVLSIDNAKLAADDFKIKYES--------------
keratin15 -----SRVILEIDNARLAADDFRLKYEN--------------
*
*
* Please note, this parser reads the whole alignment in to
* core memory and thus does not scale to work with very large
* alignments on low-end hardware.
*
* Please also note that this class has not been tested with
* many version of CLUSTAL W.
*
* Copyright © 2000,2001 Cambridge Antibody Technology.
*
*
* Primary author -
* - Simon Brocklehurst (CAT)
*
* Other authors -
* - Neil Benn (CAT)
*
- Lawrence Bower (CAT)
*
- Derek Crockford (CAT)
*
- Tim Dilks (CAT)
*
- Colin Hardman (CAT)
*
- Stuart Johnston (CAT)
*
*
* @author Cambridge Antibody Technology (CAT)
* @author Greg Cox
* @version 1.0
*
*/
public class ClustalWAlignmentSAXParser extends AbstractNativeAppSAXParser {
private AttributesImpl oAtts = new AttributesImpl();
private QName oAttQName = new QName(this);
private char[] aoChars;
private String oSeqName;
private String oTmpSeq;
private StringBuffer oSeq = new StringBuffer();
private HashMap oAlignment = new HashMap();
private ArrayList oSeqNameList = new ArrayList();
private static final int STARTUP = 0;
private static final int IN_STREAM = 1;
/**
* Initialises internal state
* Sets namespace prefix to "biojava"
*/
public ClustalWAlignmentSAXParser() {
iState = STARTUP;
this.setNamespacePrefix("biojava");
}
/**
* Describe 'parse' method here.
*
* @param poSource -
*/
public void parse(InputSource poSource )
throws IOException,SAXException {
BufferedReader oContents;
String oLine = null;
//Use method form superclass
oContents = this.getContentStream(poSource);
// loop over file
try {
// loop over file
oLine = oContents.readLine();
while (oLine != null) {
//System.out.println(oLine);
this.interpret(oContents,oLine);
oLine = oContents.readLine();
} // end while
} catch (java.io.IOException x) {
System.out.println(x.getMessage());
System.out.println("Stream read interrupted");
} // end try/catch
//at end of stream...
//at this point, alignment is parsed, now cycle through
//and emit elements
for (int i = 0; i < oSeqNameList.size(); i++) {
oSeqName = (String) oSeqNameList.get(i);
this.emitSequence(oSeqName,
(String) oAlignment.get(oSeqName));
}
this.endElement(new QName(this,
this.prefix("SequenceCollection")));
oContents.close();
}
/**
* Describe interpret method here.
*
* @param poContents a BufferedReader value
* @param poLine a String value
* @exception SAXException if an error occurs
*/
private void interpret(BufferedReader poContents, String poLine)
throws SAXException {
if (iState == STARTUP) {
oAtts.clear();
this.startElement(
new QName(this,
this.prefix("SequenceCollection")),
(Attributes)oAtts);
this.changeState(IN_STREAM);
}
if (iState == IN_STREAM) {
if (this.lineIsRelevant(poLine)) {
//build aligment in memory
this.appendToAlignment(poLine);
}
}
}
/**
* Parse a relevant line, and add to alignment
*
* @param poLine a String value
*/
private void appendToAlignment(String poLine) {
//System.out.println(poLine);
StringTokenizer oSt = new StringTokenizer(poLine,"\n\t\r ");
//First token is sequence name
oSeqName = oSt.nextToken();
//System.out.println(oSeqName);
oSeq.setLength(0);
while (oSt.hasMoreTokens()) {
oSeq.append(oSt.nextToken());
}
//System.out.println(oSeq);
//At this point, have name of sequence, and a segment of the sequence
//Update object...
if (oAlignment.get(oSeqName) == null) {
//Here if on first occurence of this sequence
//Add to alignment
oAlignment.put(oSeqName,oSeq.substring(0));
//maintain ordered list of sequence names
oSeqNameList.add(oSeqName);
} else {
//Here if building up an existing sequence
oTmpSeq = (String) oAlignment.get(oSeqName);
oAlignment.put(oSeqName,oTmpSeq.concat(oSeq.substring(0)));
}
}
/**
* Only interested in lines that are part of the alignment.
* Returns true if line is in alignment, false if not.
*
* @param poLine a String value
* @return a boolean value
*/
private boolean lineIsRelevant(String poLine) {
//blank lines not relevant
//lines that starts with a space not relevant (consensus line)
//lines that start with "CLUSTAL W (" not relevant (title)
if ( (poLine.trim().equals("")) ||
(poLine.startsWith(" ")) ||
(poLine.startsWith("CLUSTAL W (")) ) {
//System.out.println("Irrelevant|"+poLine+"|");
return false;
}
//if here,line is part of alignment, so return true
return true;
}
/**
* Emit a sequence element
*
* @param poSequenceName a String value
* @param poSequence a String value
* @exception SAXException if an error occurs
*/
private void emitSequence(String poSequenceName, String poSequence) throws SAXException {
oAtts.clear();
oAttQName.setQName("sequenceName");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",poSequenceName);
this.startElement(
new QName(this,
this.prefix("Sequence")),
(Attributes)oAtts);
aoChars = poSequence.toCharArray();
this.characters(aoChars,0,aoChars.length);
this.endElement(new QName(this,this.prefix("Sequence")));
}
}
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