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" <[EMAIL PROTECTED]> 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);
>
> }
>
> }
>
> /**
> * @param args
> */
> public static void main(String[] args)
> {
> File f = new File("E:/result.xml");
>
> try
> {
> parseFile(f);
> }
> catch (JDOMException e)
> {
> e.printStackTrace();
> }
> catch (IOException e)
> {
> e.printStackTrace();
> }
> }
>
> }
>
>
>
>
>
> +++++++++++++++++++++++++++++++++++++
>
>
>
>
>
=== message truncated ===
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