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" <[EMAIL PROTECTED]> 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:[EMAIL PROTECTED] > Gesendet: Dienstag, 28. Juni 2005 15:00 > An: biojava-l@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" <[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); > > > === message truncated === ___________________________________________________________________________ Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! 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