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org.biojava.bio.program.sax.HSPSummaryHelper 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.util.HashMap;
import java.util.StringTokenizer;
import org.xml.sax.SAXException;
/**
* A Helper class for parsing HSP summary sections...
* e.g. things like
*
* Score = 326 bits (826), Expect = 2e-89
*
* Should be passed in a comma separated list.
*
* Primary author -
* Simon Brocklehurst (CAT)
* Other authors -
* Tim Dilks (CAT)
* Colin Hardman (CAT)
* Stuart Johnston (CAT)
* Mathieu Wiepert (Mayo Foundation)
*
* Copyright 2000 Cambridge Antibody Technology Group plc.
*
*
* This code released to the biojava project, May 2000
* under the LGPL license.
*
* @author Cambridge Antibody Technology Group plc
* @author Greg Cox
* @version 0.1
*
*/
final class HSPSummaryHelper {
private HSPSummaryHelper() {
}
/**
* Takes a comma separated String of Blast-like HSP summary
* information e.g.
*
* Score = 210 bits (454), Expect = 6e-53, Frame = +2 / +2
*
* and sets the contents of the HashMap of key value pairs viz. e.g.
*
* key: bitScore - value: 210
* key: expectValue - value: 6e-53
*
* @param poLine A String representation of the HSP Summary.
* @param HashMap To put key/value info in.
* @param oVersion a BlastLikeVersionSupport value
* @exception SAXException if an error occurs
*/
public static void parse(String poLine, HashMap poMap,
BlastLikeVersionSupport poVersion)
throws SAXException {
int iProgram = poVersion.getProgram();
if ( (iProgram == BlastLikeVersionSupport.NCBI_BLASTN) ||
(iProgram == BlastLikeVersionSupport.NCBI_BLASTX) ||
(iProgram == BlastLikeVersionSupport.NCBI_BLASTP) ||
(iProgram == BlastLikeVersionSupport.NCBI_TBLASTN) ||
(iProgram == BlastLikeVersionSupport.NCBI_TBLASTX) ) {
parseNCBIBlast(poLine,poMap,poVersion);
return;
}
if ( (iProgram == BlastLikeVersionSupport.WU_BLASTN) ||
(iProgram == BlastLikeVersionSupport.WU_BLASTX) ||
(iProgram == BlastLikeVersionSupport.WU_BLASTP) ||
(iProgram == BlastLikeVersionSupport.WU_TBLASTN) ||
(iProgram == BlastLikeVersionSupport.WU_TBLASTX) ) {
parseWUBlast(poLine,poMap,poVersion);
return;
}
if ( (iProgram == BlastLikeVersionSupport.GCG_BLASTN)) {
//Similar enough to use NCBI parser for now
parseNCBIBlast(poLine,poMap,poVersion);
return;
}
//If get here, then program is not supported.
throw (new SAXException(
"Failed attempting to parse an HSP Summary because program ".
concat(poVersion.getProgramString()).
concat(" is not supported.")));
}
static void parseNCBIBlast(String poLine, HashMap poMap,
BlastLikeVersionSupport poVersion) {
String oToken;
String oToken2;
String oKey;
String oValue;
char[] aoTmpArray;
StringTokenizer oSt;
StringTokenizer oSt2;
StringTokenizer oTmp;
StringBuffer oTmpBuffer = new StringBuffer();
poMap.clear();
//System.out.println(">>>>" + poLine);
//Tokenize on commas, and make lower case...
oSt = new StringTokenizer(poLine.toLowerCase(),",");
while (oSt.hasMoreTokens()) {
oToken = oSt.nextToken().trim();
oSt2 = new StringTokenizer(oToken);
while (oSt2.hasMoreTokens()) {
oToken2 = oSt2.nextToken().trim();
//now grab info on a case-by-case basis
//and put into HashMap...
//NCBI-BLAST, WU-BLAST
if (oToken2.equals("score")) {
oKey = "score";
//assume "Token = value ..."
oSt2.nextToken(); //skip =
oValue = oSt2.nextToken(); //grab score
poMap.put(oKey,oValue);
break;
}
//NCBI Blast, WU-BLAST
if (oToken2.startsWith("expect")) {
//could be "expect" or "expect(2) etc."
oKey = "expectValue";
//assume " Token = value"
oSt2.nextToken(); //skip =
oValue = oSt2.nextToken();
poMap.put(oKey,oValue);
break;
}
//NCBI Blast, WU-BLAST
if (oToken2.equals("identities")) {
//assume " identities = 129/168 (76%)"
oSt2.nextToken(); //skip =
//this token is 129/157
oTmp = new StringTokenizer(oSt2.nextToken(),"/");
oKey = "numberOfIdentities";
oValue = oTmp.nextToken();
poMap.put(oKey,oValue);
oKey = "alignmentSize";
oValue = oTmp.nextToken();
poMap.put(oKey,oValue);
//here next token is (76%)
oTmp = new StringTokenizer(oSt2.nextToken(),"(%)");
oKey = "percentageIdentity";
oValue = oTmp.nextToken();
poMap.put(oKey,oValue);
break;
}
//NCBI Blast, WU-BLAST
if (oToken2.equals("positives")) {
//assume " positives = 129/168 (76%)"
oSt2.nextToken(); //skip =
//this token is 129/157
oTmp = new StringTokenizer(oSt2.nextToken(),"/");
oKey = "numberOfPositives";
oValue = oTmp.nextToken();
poMap.put(oKey,oValue);
//here next token is like (76%)
oTmp = new StringTokenizer(oSt2.nextToken(),"(%)");
oKey = "percentagePositives";
oValue = oTmp.nextToken();
poMap.put(oKey,oValue);
break;
}
//NCBI Blast, WU-BLAST
if (oToken2.equals("strand")) {
//assume " strand = plus / minus"
oSt2.nextToken(); //skip =
//this token is "plus"
oKey = "queryStrand";
oValue = oSt2.nextToken();
poMap.put(oKey,oValue);
oSt2.nextToken(); //skip "/"
oKey = "hitStrand";
oValue = oSt2.nextToken();
poMap.put(oKey,oValue);
break;
}
if (oToken2.equals("frame")) {
//assume " Frame = +3 " for blastx and tblastn
//assume " Frame = +3 / -1" for tblastx
oSt2.nextToken(); //skip =
if (poVersion.getProgram() ==
BlastLikeVersionSupport.NCBI_BLASTX) {
oKey = "queryFrame";
aoTmpArray = oSt2.nextToken().toCharArray();
oTmpBuffer.setLength(0);
if (aoTmpArray[0] == '+') {
oTmpBuffer.append("plus");
} else {
oTmpBuffer.append("minus");
}
oTmpBuffer.append(aoTmpArray[1]);
oValue = oTmpBuffer.substring(0);
poMap.put(oKey,oValue);
break;
}
if (poVersion.getProgram() ==
BlastLikeVersionSupport.NCBI_TBLASTN) {
oKey = "hitFrame";
aoTmpArray = oSt2.nextToken().toCharArray();
oTmpBuffer.setLength(0);
if (aoTmpArray[0] == '+') {
oTmpBuffer.append("plus");
} else {
oTmpBuffer.append("minus");
}
oTmpBuffer.append(aoTmpArray[1]);
oValue = oTmpBuffer.substring(0);
poMap.put(oKey,oValue);
break;
}
if (poVersion.getProgram() ==
BlastLikeVersionSupport.NCBI_TBLASTX) {
oKey = "queryFrame";
aoTmpArray = oSt2.nextToken().toCharArray();
oTmpBuffer.setLength(0);
if (aoTmpArray[0] == '+') {
oTmpBuffer.append("plus");
} else {
oTmpBuffer.append("minus");
}
oTmpBuffer.append(aoTmpArray[1]);
oValue = oTmpBuffer.substring(0);
poMap.put(oKey,oValue);
//skip "/"
oSt2.nextToken();
oKey = "hitFrame";
aoTmpArray = oSt2.nextToken().toCharArray();
oTmpBuffer.setLength(0);
if (aoTmpArray[0] == '+') {
oTmpBuffer.append("plus");
} else {
oTmpBuffer.append("minus");
}
oTmpBuffer.append(aoTmpArray[1]);
oValue = oTmpBuffer.substring(0);
poMap.put(oKey,oValue);
break;
}
}
} //end loop over
//System.out.println(oToken);
} //end loop over "score = 119 bits" type tokens
}
static void parseWUBlast(String poLine, HashMap poMap,
BlastLikeVersionSupport poVersion) {
String oToken;
String oToken2;
String oKey;
String oValue;
char[] aoTmpArray;
StringTokenizer oSt;
StringTokenizer oSt2;
StringTokenizer oTmp;
StringBuffer oTmpBuffer = new StringBuffer();
poMap.clear();
//System.out.println(">>>>" + poLine);
//Tokenize on commas, and make lower case...
oSt = new StringTokenizer(poLine.toLowerCase(),",");
while (oSt.hasMoreTokens()) {
oToken = oSt.nextToken().trim();
oSt2 = new StringTokenizer(oToken);
while (oSt2.hasMoreTokens()) {
oToken2 = oSt2.nextToken().trim();
//now grab info on a case-by-case basis
//and put into HashMap...
//NCBI-BLAST, WU-BLAST
if (oToken2.equals("score")) {
oKey = "score";
//assume "Token = value ..."
oSt2.nextToken(); //skip =
oValue = oSt2.nextToken(); //grab score
poMap.put(oKey,oValue);
break;
}
//NCBI Blast, WU-BLAST
if (oToken2.startsWith("expect")) {
//could be "expect" or "expect(2) etc."
oKey = "expectValue";
//assume " Token = value"
oSt2.nextToken(); //skip =
oValue = oSt2.nextToken();
poMap.put(oKey,oValue);
break;
}
//NCBI Blast, WU-BLAST
if (oToken2.equals("identities")) {
//assume " identities = 129/168 (76%)"
oSt2.nextToken(); //skip =
//this token is 129/157
oTmp = new StringTokenizer(oSt2.nextToken(),"/");
oKey = "numberOfIdentities";
oValue = oTmp.nextToken();
poMap.put(oKey,oValue);
oKey = "alignmentSize";
oValue = oTmp.nextToken();
poMap.put(oKey,oValue);
//here next token is (76%)
oTmp = new StringTokenizer(oSt2.nextToken(),"(%)");
oKey = "percentageIdentity";
oValue = oTmp.nextToken();
poMap.put(oKey,oValue);
break;
}
//NCBI Blast, WU-BLAST
if (oToken2.equals("positives")) {
//assume " positives = 129/168 (76%)"
oSt2.nextToken(); //skip =
//this token is 129/157
oTmp = new StringTokenizer(oSt2.nextToken(),"/");
oKey = "numberOfPositives";
oValue = oTmp.nextToken();
poMap.put(oKey,oValue);
//here next token is like (76%)
oTmp = new StringTokenizer(oSt2.nextToken(),"(%)");
oKey = "percentagePositives";
oValue = oTmp.nextToken();
poMap.put(oKey,oValue);
break;
}
//NCBI Blast, WU-BLAST
if (oToken2.equals("strand")) {
//assume " strand = plus / minus"
oSt2.nextToken(); //skip =
//this token is "plus"
oKey = "queryStrand";
oValue = oSt2.nextToken();
poMap.put(oKey,oValue);
oSt2.nextToken(); //skip "/"
oKey = "hitStrand";
oValue = oSt2.nextToken();
poMap.put(oKey,oValue);
break;
}
if (oToken2.equals("frame")) {
//assume " Frame = +3 " for blastx and tblastn
//assume " Frame = +3 / -1" for tblastx
oSt2.nextToken(); //skip =
if (poVersion.getProgram() ==
BlastLikeVersionSupport.WU_BLASTX) {
oKey = "queryFrame";
aoTmpArray = oSt2.nextToken().toCharArray();
oTmpBuffer.setLength(0);
if (aoTmpArray[0] == '+') {
oTmpBuffer.append("plus");
} else {
oTmpBuffer.append("minus");
}
oTmpBuffer.append(aoTmpArray[1]);
oValue = oTmpBuffer.substring(0);
poMap.put(oKey,oValue);
break;
}
if (poVersion.getProgram() ==
BlastLikeVersionSupport.WU_TBLASTN) {
oKey = "hitFrame";
aoTmpArray = oSt2.nextToken().toCharArray();
oTmpBuffer.setLength(0);
if (aoTmpArray[0] == '+') {
oTmpBuffer.append("plus");
} else {
oTmpBuffer.append("minus");
}
oTmpBuffer.append(aoTmpArray[1]);
oValue = oTmpBuffer.substring(0);
poMap.put(oKey,oValue);
break;
}
if (poVersion.getProgram() ==
BlastLikeVersionSupport.WU_TBLASTX) {
oKey = "queryFrame";
aoTmpArray = oSt2.nextToken().toCharArray();
oTmpBuffer.setLength(0);
if (aoTmpArray[0] == '+') {
oTmpBuffer.append("plus");
} else {
oTmpBuffer.append("minus");
}
oTmpBuffer.append(aoTmpArray[1]);
oValue = oTmpBuffer.substring(0);
poMap.put(oKey,oValue);
//skip "/"
oSt2.nextToken();
oKey = "hitFrame";
aoTmpArray = oSt2.nextToken().toCharArray();
oTmpBuffer.setLength(0);
if (aoTmpArray[0] == '+') {
oTmpBuffer.append("plus");
} else {
oTmpBuffer.append("minus");
}
oTmpBuffer.append(aoTmpArray[1]);
oValue = oTmpBuffer.substring(0);
poMap.put(oKey,oValue);
break;
}
}
} //end loop over
//System.out.println(oToken);
} //end loop over "score = 119 bits" type tokens
}
}
