org.biojava.bio.program.BlastLikeToXMLConverter 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;
import java.io.BufferedReader;
import java.io.FileInputStream;
import java.io.InputStreamReader;
import org.biojava.bio.program.sax.BlastLikeSAXParser;
import org.biojava.bio.program.xml.SimpleXMLEmitter;
import org.xml.sax.ContentHandler;
import org.xml.sax.InputSource;
import org.xml.sax.XMLReader;
/**
*
* A class that converts the raw output from a variety of bioinformatics
* software and converts it to XML that will validate against the
* biojava:BlastLikeDataSetCollection DTD.
*
* For applications supported, please the documentation for the
* BlastLikeSAXParser.
*
* Examination of the source code of this application also serves as
* demonstration of the simplicity of using the biojava blast-like SAX2
* parsing framework. The main functionality of the application is
* simply built from the following code, viz.:
*
*
* !**
* * The following code creates a parser for native output
* * from BlastLike programs. That is,
* * Create a SAX2 Parser that takes the native output
* * from blast-like bioinformatics software.
* *!
*
* XMLReader oParser =
* (XMLReader) new BlastLikeSAXParser();
*
* !**
* * Namespace support controls the way in which
* * XML elements are reported. In XML, when an element
* * looks something like then,
* * the part before the colon, i.e. biojava is the namespace,
* * and the part after the colon i.e. Hit is the Local name.
* * The full "biojava:Hit" name is termed the Qualified Name (QNames).
* * By default SAX2 parsers report Local Names, in this
* * example, we decided we wanted to make the parser report QNames.
* *
* * If you don't want to change default namespace support, you
* * can ignore the next piece of code.
* *
* * Dynamically change configuration of the parser
* * in regard of Namespace support. Here,
* * the xml.org/features/namespaces feature is simply "reset"
* * to its default value for SAX2.
* * The xml.org/features/namespaces-prefixes feature is
* * also set to true. This is to ensure that xmlns attributes
* * are reported by the parser. These are required because we want
* * to configure the XMLEmitter to output qualified names (see below).
* *!
*
* try {
* oParser.setFeature("http://xml.org/sax/features/namespaces",true);
* oParser.setFeature(
* "http://xml.org/sax/features/namespace-prefixes",true);
*
* } catch (Exception e) {
* }
*
*
* !**
* * Having selected the parser, we now want to
* * choose an object to deal with the SAX2 events
* * that the parser produces. This is the class
* * that you would normally write yourself to deal
* * with particular events you are interested in.
* * This class implements the ContentHandler - usually,
* * you would inherit from a SAX2 helper class that
* * implements this interface for you.
* *
* * Create an XML ContentHandler. This
* * implementation of the DocumentHandler
* * interface simply outputs nicely formatted
* * XML. Passing a true value to the SimpleXMLEmitter
* * constructor instructs the ContentHandler
* * to take QNames from the SAXParser, rather
* * than LocalNames.
* *
*
* ContentHandler oHandler =
* (ContentHandler) new SimpleXMLEmitter(true);
*
*
* !**
* * Now, link the Parser and the ContentHandler.
* *
* * Give the parser a reference to the ContentHandler
* * so that it can send SAX2 mesagges.
* *!
*
* oParser.setContentHandler(oHandler);
*
* !**
* * Finally, parse your Blast-like output.
* *
* * Now make the Parser parse the output from the
* * blast-like software and emit XML as specificed
* * by the ContentHandler.
* *!
*
* oParser.parse(oInput);
*
*
*
*
* Copyright © 2000 Cambridge Antibody Technology.
*
*
* Primary author -
* - Simon Brocklehurst (CAT)
*
* Other authors -
* - Tim Dilks (CAT)
*
- Colin Hardman (CAT)
*
- Stuart Johnston (CAT)
*
- Mathieu Wiepert (Mayo Foundation)
*
*
*
* @author Cambridge Antibody Technology (CAT)
* @version 1.0
*
* @see BlastLikeSAXParser
* @see SimpleXMLEmitter
*/
public class BlastLikeToXMLConverter {
private String oInput;
private XMLReader oParser;
private boolean tStrict = true;
/**
* Creates a new BlastToXMLConverter instance.
*
*/
public BlastLikeToXMLConverter(String poInput) {
oInput = poInput;
}
public void convert() throws java.io.IOException,
org.xml.sax.SAXException {
//Access functionality of biojava classes through
//standard org.xml.sax interfaces...
/**
* Create a SAX Parser that takes the native output
* from blast-like bioinformatics software.
*/
oParser = (XMLReader) new BlastLikeSAXParser();
if (tStrict) {
((BlastLikeSAXParser) oParser).setModeStrict();
} else {
((BlastLikeSAXParser) oParser).setModeLazy();
}
/**
* Dynamically change configuration of the parser
* in regard of Namespace support. Here,
* the xml.org/sax/features/namespaces feature is simply "reset"
* to its default value for SAX2.
* The xml.org/sax/features/namespaces-prefixes feature is
* also set to true. This is to ensure that xmlns attributes
* are reported by the parser. These are required because we want
* to configure the XMLEmitter to output qualified names (see below).
*/
try {
oParser.setFeature("http://xml.org/sax/features/namespaces",true);
oParser.setFeature("http://xml.org/sax/features/namespace-prefixes",
true);
} catch (Exception e) {
//If an illegal conmbination of features is chosen,
//roll back to default settings. Output a warning,
//even though this might mess up the output...
System.out.println("WARNING: ignoring attempt to set illegal " +
"combination of parser features");
System.out.println(e);
}
/**
* Create an XML ContentHandler. This
* implementation of the DocumentHandler
* interface simple outputs nicely formatted
* XML. Passing a true value to the SimpleXMLEmitter
* constructor instructs the ContentHandler
* to take QNames from the SAXParser, rather
* than LocalNames.
*/
ContentHandler oHandler =
(ContentHandler) new SimpleXMLEmitter(true);
/**
* Give the parser a reference to the ContentHandler
* so that it can send SAX2 mesagges.
*/
oParser.setContentHandler(oHandler);
/**
* Now make the Parser parse the output from the
* blast-like software and emit XML as specificed
* by the DocumentHandler.
*/
//Test direct specification of URI
//oParser.parse(oInput);
//Test direct specification of URI via InputSource
//oParser.parse(new InputSource(oInput));
FileInputStream oInputFileStream;
BufferedReader oContents;
//Test parsing using ByteSteam as InputSource
// Open file and read all lines from file sequentially
// try{
// oInputFileStream = new FileInputStream(oInput);
// // create input stream
// oParser.parse(new InputSource(oInputFileStream));
// } catch (java.io.FileNotFoundException x) {
// System.out.println(x.getMessage());
// System.out.println("Couldn't open file");
// System.exit(0);
// }
//Test parsing using CharacterStream as InputSource
// Open file and read all lines from file sequentially
try{
oInputFileStream = new FileInputStream(oInput);
// create input stream
oContents = new
BufferedReader(new InputStreamReader(oInputFileStream));
oParser.parse(new InputSource(oContents));
} catch (java.io.FileNotFoundException x) {
System.out.println(x.getMessage());
System.out.println("Couldn't open file");
System.exit(0);
}
System.out.println();
}
public void setModeStrict() {
tStrict = true;
}
public void setModeLazy() {
tStrict = false;
}
}