AW: AW: [Biojava-l] BLAST Parser for extracting all BLAST data?

[Sébastien PETIT]

I try the code you sent me. I just change the path of the XML file.
But, in this file, there is this line :

<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN"
"NCBI_BlastOutput.dtd">

and I have exceptions and errors because of this line.

If you want, I send the XML file so that you test it...

But, I download the DTD and the MOD files necessary, I modified the DTD
file a little bit, and it works...
But, I would prefer to not have those files with my code...

Thank you...

Sebastien

--- "BIBIS, Garnier, Christophe" <cgarnier at ttz-Bremerhaven.de> a écrit
:

> Did you try just the code i sent you? Or did you integrate it inside
> your
> program?
> 
> As far as i know, jdom works without dtd files: it makes no control
> on the
> structure of the file
> It should word because I tested it without using the corresponding
> dtd file.
> 
> 
> christophe
> 
> 
> -----Ursprüngliche Nachricht-----
> Von: Sébastien PETIT [mailto:great_fred at yahoo.com]
> Gesendet: Dienstag, 28. Juni 2005 15:00
> An: biojava-l at biojava.org
> Betreff: RE: AW: [Biojava-l] BLAST Parser for extracting all BLAST
> data?
> 
> 
> Thank you for JDOM and the code...
> But, it generates a ton of exceptions and error because it doesn't
> find
> a DTD file (NCBI_BlastOutput.dtd) that I don't have...
> 
> So, I don't know how to do...
> 
> Sebastien
> 
> --- "BIBIS, Garnier, Christophe" <cgarnier at ttz-Bremerhaven.de> a
> écrit
> :
> 
> > 
> > if you don't find what you need through biojava, you can always
> write
> > a
> > small xml parser with for example jdom.
> > 
> > 1 - download jdom.jar
> > 2 - use the following code to find <Hsp_midline>:
> > 3 - replace the path of the xml file in the main method
> > 4 - it prints out every found Element
> > 
> > 
> > I hope it helps you
> > 
> > Best,
> > Christophe
> > 
> > +++++++++++++++++++++++++++++++++++++
> > 
> > import java.io.File;
> > import java.io.IOException;
> > import java.util.Iterator;
> > import java.util.List;
> > 
> > import org.jdom.Document;
> > import org.jdom.Element;
> > import org.jdom.JDOMException;
> > import org.jdom.input.SAXBuilder;
> > 
> > public class JDomParser
> > {
> > 
> > 	private static void parseResults(Element iterations)
> > 	{
> > 		System.out.println("*** parseResults ***") ;
> > 		
> > 		Element it = iterations.getChild("Iteration") ;
> > 		
> > 		List elts = it.getChildren();
> > 		
> > 		Iterator iterator = elts.iterator();
> > 		
> > 		while (iterator.hasNext())
> > 		{
> > 			Element child = (Element) iterator.next();
> > 
> > 			System.out.println(child + " - " + child.getText() +
> > " - "
> > 					+ child.getName());
> > 
> > 			if ( child.getName().equals("Iteration_hits"))
> > 			{
> > 				parseHits(child) ;
> > 			}
> > 			
> > 			if ( child.getName().equals("Iteration_stat"))
> > 			{
> > 				parseStatistics(child) ;
> > 			}
> > 			
> > 		
> > 		}
> > 	}
> > 
> > 	private static void parseHits(Element element)
> > 	{
> > 		List elts = element.getChildren();
> > 		
> > 		Iterator iterator = elts.iterator();
> > 		
> > 		while (iterator.hasNext())
> > 		{
> > 			Element child = (Element) iterator.next();
> > 
> > 			printElt(child) ;
> > 			
> > 			parseHit(child) ;
> > 			
> > 		}
> > 	}
> > 	
> > 	private static void parseHspHit(Element element)
> > 	{
> > 		Element hsp = element.getChild("Hsp") ;
> > 
> > 		List hsps = hsp.getChildren();
> > 		
> > 		Iterator iterator = hsps.iterator();
> > 		
> > 		while (iterator.hasNext())
> > 		{
> > 			Element child = (Element) iterator.next();
> > 
> > 			printElt(child) ;
> > 		}
> > 	}
> > 	
> > 	private static void printElt(Element elt)
> > 	{
> > 		System.out.println("Element: [" + elt.getName() + "] -
> > text:" + elt.getText() ) ;
> > 	}
> > 	
> > 	private static void parseHit(Element element)
> > 	{
> > 		List elts = element.getChildren();
> > 		
> > 		Iterator iterator = elts.iterator();
> > 		
> > 		while (iterator.hasNext())
> > 		{
> > 			Element child = (Element) iterator.next();
> > 
> > 			printElt(child) ;
> > 			
> > 			if (child.getName().equals("Hit_hsps"))
> > 					{
> > 					parseHspHit(child) ;
> > 					}
> > 			
> > 		}
> > 	}
> > 	
> > 	
> > 	private static void parseStatistics(Element element)
> > 	{
> > 		Element stat = element.getChild("Statistics") ;
> > 		
> > 		List elts = stat.getChildren();
> > 		
> > 		Iterator iterator = elts.iterator();
> > 		
> > 		while (iterator.hasNext())
> > 		{
> > 			Element child = (Element) iterator.next();
> > 
> > 			printElt(child) ;
> > 			
> > 		}
> > 		
> > 	}
> > 	
> > 	
> > 	public static void parseFile(File file) throws JDOMException,
> > IOException
> > 	{
> > 		SAXBuilder parser = new SAXBuilder();
> > 		Document doc = parser.build(file);
> > 
> > 		Element root = doc.getRootElement();
> > 
> > 		List elts = root.getChildren();
> > 		Iterator iterator = elts.iterator();
> > 
> > 		int index = 0;
> > 		while (iterator.hasNext())
> > 		{
> > 
> > 			Element child = (Element) iterator.next();
> > 
> > 			printElt(child) ;
> > 
> > 			if
> > (child.getName().equals("BlastOutput_iterations"))
> > 				parseResults(child);
> > 
> 
=== message truncated ===



	

	
		
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