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/*
* 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.util.ArrayList;
import java.util.HashMap;
import java.util.StringTokenizer;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.AttributesImpl;
/**
* A reusable class for parsing Detail
* sections of Blast-like programs:
* oNCBI Blast
*
* Primary author -
* Simon Brocklehurst (CAT)
* Other authors -
* Tim Dilks (CAT)
* Colin Hardman (CAT)
* Stuart Johnston (CAT)
* Mathieu Wiepert (Mayo Foundation)
* Travis Banks (AAFC)
*
* 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
* @author Travis Banks
* @version 0.1
*
*/
final class HitSectionSAXParser extends AbstractNativeAppSAXParser {
private BlastLikeAlignmentSAXParser oAlignmentParser;
private BlastLikeVersionSupport oVersion;
private BufferedReader oContents;
private AttributesImpl oAtts = new AttributesImpl();
private QName oAttQName = new QName(this);
private char[] aoChars;
private char[] aoLineSeparator;
private ArrayList oGlobalEndSignals;
private ArrayList oBuffer = new ArrayList();
private ArrayList oAlignmentBuffer = new ArrayList();
private StringBuffer oStringBuffer = new StringBuffer();
private StringBuffer oDescription = new StringBuffer();
private String oLine;
private HashMap oMap = new HashMap();
private String[] aoKeys;
private String[] aoArrayType = new String[1];
private boolean tClearOfWarning = true;
private static final int STARTUP = 0;
private static final int DONE = 1;
private static final int CAPTURING_HIT_SUMMARY = 2;
private static final int IN_HSP_COLLECTION = 3;
private static final int ON_FIRST_HSP = 4;
private static final int IN_HSP_SUMMARY = 5;
private static final int IN_ALIGNMENT = 6;
HitSectionSAXParser(BlastLikeVersionSupport poVersion,
String poNamespacePrefix) {
oVersion = poVersion;
this.setNamespacePrefix(poNamespacePrefix);
//For XSLT Parser Compliance
this.addPrefixMapping("biojava","http://www.biojava.org");
this.changeState(STARTUP);
aoLineSeparator = System.getProperty("line.separator").toCharArray();
}
public void parse(BufferedReader poContents, String poLine, ArrayList poEndSignals) throws SAXException {
oLine = null;
oContents = poContents;
setGlobalEndSignal(poEndSignals);
//return immediately if this is not the start
//of a hit...
if (!poLine.startsWith(">")) return;
try {
oLine = poLine;
while ((oLine != null) &&
(!this.matchesGlobalEndSignal(oLine)) &&
(!(iState == DONE)) )
{
//interpret line and send messages accordingly
this.interpret(oLine);
//check for End again cos stream read elsewhere
if (this.matchesGlobalEndSignal(oLine)) {
this.changeState(DONE);
oContents.reset();
break;
}
oContents.mark(10000000);
oLine = oContents.readLine();
} // end while
} catch (java.io.IOException x) {
System.out.println(x.getMessage());
System.out.println("File read interupted");
} // end try/catch
}
/**
* Typically parse a single line, and return
*
* @param poLine -
* @exception SAXException thrown if
* @exception thrown if
*/
private void interpret(String poLine) throws SAXException {
if (poLine.startsWith(">")) {
//start of hit, accumulate title into buffer.
//omit intial ">" character
oStringBuffer.setLength(0);
oStringBuffer.append(poLine.substring(1));
this.changeState(CAPTURING_HIT_SUMMARY);
return;
}
if (iState == CAPTURING_HIT_SUMMARY) {
if (poLine.trim().startsWith("Length =")) {
//here when HitSummary is complete
//get sequenceLength, and then startElement
StringTokenizer oSt = new StringTokenizer(poLine);
//zip through tokens up to last one
int iTmpTokenCount = oSt.countTokens() - 1;
for (int i = 0; i < iTmpTokenCount; i++) {
oSt.nextToken();
}
//last token is the length
String oLength = oSt.nextToken();
oAtts.clear();
oAttQName.setQName("sequenceLength");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oLength);
this.startElement(new QName(this,this.prefix("Hit")),
(Attributes)oAtts);
//Here, oStringBuffer contains ID + Description
oSt = new StringTokenizer(oStringBuffer.substring(0));
int iCount = oSt.countTokens();
String oId = oSt.nextToken(); //get Id
oAtts.clear();
oAttQName.setQName("id");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oId);
oAttQName.setQName("metaData");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA","none");
this.startElement(new QName(this,this.prefix("HitId")),
(Attributes)oAtts);
this.endElement(new QName(this,this.prefix("HitId")));
oDescription.setLength(0);
if (iCount > 0) {
//deal with hit description if one available
while (oSt.hasMoreTokens()) {
//construct description
oDescription.append(oSt.nextToken() + " ");
//System.out.println(oDescription);
}
oAtts.clear();
this.startElement(new QName(this,this.prefix("HitDescription")),
(Attributes)oAtts);
aoChars = oDescription.substring(0).trim().toCharArray();
this.characters(aoChars,0,aoChars.length);
this.endElement(new QName(this,this.prefix("HitDescription")));
} //end if there is a hit description
//Here when we have HitId and HitDescription
this.changeState(IN_HSP_COLLECTION);
return;
} else {
//here if collating multi-line hit descriptions
oStringBuffer.append(" " + poLine.trim());
return;
}
} //end capturingHitSummary
//parse HSPs
if (iState == IN_HSP_COLLECTION) {
//Look for start of a new HSP
if (poLine.trim().startsWith("Score")) {
//here if on a new HSP
oAtts.clear();
this.startElement(new QName(this,this.prefix("HSPCollection")),
(Attributes)oAtts);
//Note, this method will have changed
//the State when it returns
this.firstHSPEvent(poLine);
this.endElement(new QName(this,this.prefix("HSPCollection")));
this.endElement(new QName(this,this.prefix("Hit")));
this.changeState(CAPTURING_HIT_SUMMARY);
}
}
}
/**
* Deal with parsing of all HSPs in a Hit.
* Continue until a new Hit is reached...
*
* @param poLine The first line of the HSP
*
*/
private void firstHSPEvent(String poLine) throws SAXException {
this.changeState(ON_FIRST_HSP);
try {
oLine = poLine;
while ((oLine != null) &&
(!oLine.trim().startsWith(">")) &&
(!this.matchesGlobalEndSignal(oLine)) )
{
//interpret line and send messages accordingly
this.interpretHSP(oLine);
oLine = oContents.readLine();
} // end while
//output final HSP of collection
if (!(iState == ON_FIRST_HSP)) {
//output previous HSP-related data
this.outputHSPInfo();
this.endElement(new QName(this,this.prefix("HSP")));
}
} catch (java.io.IOException x) {
System.out.println(x.getMessage());
System.out.println("File read interupted");
} // end try/catch
//Here at the end of dealing with HSPCollection
//Could go on to next hit, or on to trailer...
if(oLine==null) {
return;
}
if (oLine.startsWith(">")) {
//here when a new Hit is starting...
//start of new hit, accumulate title into buffer.
//omit intial ">" character
oStringBuffer.setLength(0);
oStringBuffer.append(oLine.substring(1));
return;
}
if (this.matchesGlobalEndSignal(oLine)) {
//here when we've hit the trailer...
//this.endElement(this.prefix("HSP"));
this.changeState(DONE);
return;
}
}
/**
* Deal with a line of an HSP
*
* @param poLine A String representation of the line
*/
private void interpretHSP(String poLine) throws SAXException {
//System.out.println("HSPLine:>".concat(poLine));
//System.out.println("GlobalState:>".concat(iState));
if (!tClearOfWarning) {
//look for white space to indicate we're passed a multi-line
//warning (in WU-BLAST);
if (poLine.trim().equals("")) {
//here when clear
tClearOfWarning = true;
}
return;
}
//ignore Minus Strand HSP and Plus Strand HSP (WuBlast)
if (poLine.trim().toLowerCase().startsWith("minus strand")) return;
if (poLine.trim().toLowerCase().startsWith("plus strand")) return;
if (poLine.trim().toLowerCase().startsWith("warning")) {
tClearOfWarning = false;
return;
}
if (poLine.trim().startsWith("Score")) {
if (!(iState == ON_FIRST_HSP)) {
//output previous HSP-related data
this.outputHSPInfo();
this.endElement(new QName(this,this.prefix("HSP")));
}
oAtts.clear();
this.startElement(new QName(this,this.prefix("HSP")),
(Attributes)oAtts);
//Start accumulating all HSP summary information
//into buffer...
oStringBuffer.setLength(0);
oStringBuffer.append(poLine);
//and raw info
oBuffer.clear();
oBuffer.add(poLine);
this.changeState(IN_HSP_SUMMARY);
return;
}
//continue to accumulate summary info
//until an alignment is reached...
if (iState == IN_HSP_SUMMARY) {
//check for end of summary (Query: is end signal)
if (poLine.startsWith("Query:")) {
//System.out.println(oStringBuffer);
//at this point, all available summary info
//complete for current HSP (may need
//extra info derived from alignment, so
//so don't output HSPSummary element info yet
//Put available HSPSummary info into a Map
HSPSummaryHelper.parse(oStringBuffer.substring(0),oMap,
oVersion);
//really need to get alignment parsed before outputing
//suummary info - not all programs output
//alignment size (e.g. DBA).
//change state 'cos hit a Blast-like alignment
this.changeState(IN_ALIGNMENT);
//get information for first alignment line
oAlignmentBuffer.clear();
oAlignmentBuffer.add(poLine);
return;
} //end if found first line of alignment
//append summary
//ignore blank lines
if (poLine.trim().equals("")) return;
oBuffer.add(poLine); //keep raw info
oStringBuffer.append(", ");
oStringBuffer.append(poLine);
return;
} //end if state is inHSPSummary
//keep appending alignment info
if (iState == IN_ALIGNMENT) {
//ignore blank lines
if (poLine.trim().equals("")) return;
oAlignmentBuffer.add(poLine);
return;
}
}
/**
* Describe 'outputHSPInfo' method here.
*
* @param nil -
* @exception SAXException thrown if
* @exception thrown if
*/
private void outputHSPInfo() throws SAXException {
//Output HSP Summary info
//detailed info
aoKeys = (String[])(oMap.keySet().toArray(aoArrayType));
oAtts.clear();
for (int i = 0; i < aoKeys.length; i++) {
if ( (aoKeys[i].equals("queryFrame")) ||
(aoKeys[i].equals("hitFrame")) ||
(aoKeys[i].equals("queryStrand")) ||
(aoKeys[i].equals("hitStrand")) ) {
//nametoken if an enumeration
oAttQName.setQName(aoKeys[i]);
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"NMTOKEN",(String)oMap.get(aoKeys[i]));
} else {
//CDATA if regular attribute
oAttQName.setQName(aoKeys[i]);
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",(String)oMap.get(aoKeys[i]));
}
//System.out.print(aoKeys[i] + ": ");
//System.out.println(oMap.get(aoKeys[i]));
}
this.startElement(new QName(this,this.prefix("HSPSummary")),
(Attributes)oAtts);
//Raw HSPSummary Data
oAtts.clear();
oAttQName.setQName("xml:space");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"NMTOKEN","preserve");
this.startElement(new QName(this,this.prefix("RawOutput")),
(Attributes)oAtts);
int iTmpBufferSize = oBuffer.size();
for (int i = 0; i < iTmpBufferSize;i++) {
//aoChars = ((String)oBuffer.get(i)).trim().toCharArray();
aoChars = ((String)oBuffer.get(i)).toCharArray();
this.characters(aoChars,0,aoChars.length);
this.characters(aoLineSeparator,0,1);
}
this.endElement(new QName(this,this.prefix("RawOutput")));
this.endElement(new QName(this,this.prefix("HSPSummary")));
//Output Alignment info via delegation to
//a BlastLikeAlignmentSAXParser
oAlignmentParser =
new BlastLikeAlignmentSAXParser(this.getNamespacePrefix());
oAlignmentParser.setContentHandler(oHandler);
oAlignmentParser.parse(oAlignmentBuffer);
}
private void setGlobalEndSignal(ArrayList oGlobalEndSignal) {
this.oGlobalEndSignals = oGlobalEndSignal;
}
private boolean matchesGlobalEndSignal(String s) {
if(s==null) {
return true;
}
for(String signal: this.oGlobalEndSignals) {
if(s.trim().startsWith(signal)) {
return true;
}
}
return false;
}
}
