X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=runner%2Fcompbio%2Fpipeline%2F_jpred%2FBlastParser.java;fp=runner%2Fcompbio%2Fpipeline%2F_jpred%2FBlastParser.java;h=7039588f7a05fc33280472efcaec83267257b1a6;hb=3ce02f963043c66aedd16f12c789592e86149398;hp=73d9a99f63e3411e5919dcbf5c1333f796fc55ca;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/runner/compbio/pipeline/_jpred/BlastParser.java b/runner/compbio/pipeline/_jpred/BlastParser.java
index 73d9a99..7039588 100644
--- a/runner/compbio/pipeline/_jpred/BlastParser.java
+++ b/runner/compbio/pipeline/_jpred/BlastParser.java
@@ -16,59 +16,119 @@
  * must include this copyright and license notice.
  */
 package compbio.pipeline._jpred;
-import java.io.*;
-import java.util.*;
+
+import java.io.BufferedInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
 
 import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamException;
 import javax.xml.stream.XMLStreamReader;
 
-
 public class BlastParser {
-	
-	static class Psiseq {
-		String id;
-		String seq;
+
+    Map<Integer, Set<Hit>> iters;
+
+    public BlastParser(String file) throws FileNotFoundException,
+	    XMLStreamException {
+	XMLInputFactory f = XMLInputFactory.newInstance();
+	XMLStreamReader r = f.createXMLStreamReader(new BufferedInputStream(
+		new FileInputStream(new File(file))));
+	Set<Hit> pl = new HashSet<Hit>();
+	Hit psi = null;
+	this.iters = new HashMap<Integer, Set<Hit>>();
+	Integer iternum = null;
+	while (r.hasNext()) {
+	    int idx = r.next();
+	    if (r.isStartElement()) {
+		String name = r.getLocalName();
+		if (name.equals("Iteration_iter-num")) {
+		    iternum = Integer.parseInt(r.getElementText().trim());
+		    System.out.println("Iter " + iternum);
+		}
+		if (name.equals("Hit")) {
+		    psi = new Hit();
+		}
+		if (name.equals("Hit_num")) {
+		    psi.number = r.getElementText();
+		}
+		if (name.equals("Hit_accession")) {
+		    psi.accession = r.getElementText();
+		    // System.out.println(psi.id);
+		}
+		if (name.equals("Hit_def")) {
+		    // System.out.println(r.getElementText());
+		    psi.name = r.getElementText().split("\\s+")[0].trim();
+		    // System.out.println(psi.id);
+		}
+		if (name.equals("Hsp_hseq")) {
+		    psi.seq = r.getElementText();
+		    // System.out.println(psi.seq);
+		}
+		if (name.equals("Hsp_evalue")) {
+		    psi.evalue = r.getElementText();
+		    // System.out.println(psi.seq);
+		}
+
+	    }
+
+	    if (r.isEndElement()) {
+		String name = r.getLocalName();
+		if (name.equals("Hit")) {
+		    boolean replaced = pl.add(psi);
+		    assert replaced : "Expect unique elements only!";
+		    psi = null;
+		}
+		if (name.equals("Iteration")) {
+		    iters.put(iternum, pl);
+		    pl = new HashSet<Hit>();
+		}
+	    }
 	}
-	/**
-	 * args[0] is assumed to be the name of a Blast output file
-	 * @throws XMLStreamException 
-	 * @throws FileNotFoundException 
-	 */
-	public static void main(String[] args) throws FileNotFoundException, XMLStreamException {
-		XMLInputFactory f = XMLInputFactory.newInstance();
-		XMLStreamReader r = f.createXMLStreamReader( new BufferedInputStream(new FileInputStream(new File(args[0]))));
-		List<Psiseq> pl = new ArrayList<Psiseq>();
-		Psiseq psi = null;
-		while(r.hasNext()) {
-			int idx = r.next(); 
-			//System.out.println(idx);
 
-			if(r.isStartElement()) {
-				String name = r.getLocalName();
-				if(name.equals("Hit") ) {
-					psi = new Psiseq();
-				}
-				if(name.equals("Hit_id") ) {
-					//System.out.println(r.getElementText());
-					psi.id = r.getElementText();
-					System.out.println(psi.id);
-				} 
-				if(name.equals("Hsp_hseq")) {
-					psi.seq = r.getElementText();
-					System.out.println(psi.seq);
-				} 
-			}
-			
-			if(r.isEndElement()) {
-				String name = r.getLocalName();
-				if(name.equals("Hit") ) {
-					pl.add(psi);
-					psi = null;
-				}
-			}
+    }
 
-		} 
+    /**
+     * args[0] is assumed to be the name of a Blast output file
+     * 
+     * @throws XMLStreamException
+     * @throws FileNotFoundException
+     */
+    public static void main(String[] args) throws FileNotFoundException,
+	    XMLStreamException {
+	BlastParser parser = new BlastParser(args[0]);
+	printHits(parser.iters);
+    }
 
+    static final void printHits(Map<Integer, Set<Hit>> iterNumPsiSeqs) {
+	for (Integer iterNum : iterNumPsiSeqs.keySet()) {
+	    System.out.println("Iteration " + iterNum);
+	    printHits(iterNumPsiSeqs.get(iterNum));
 	}
+    }
+
+    static final void printHits(Collection<Hit> psiseqs) {
+	assert psiseqs != null;
+	System.out.println("Total hits: " + psiseqs.size());
+	for (Hit pseq : psiseqs) {
+	    System.out.println("Hit: " + pseq.number + " Accession: "
+		    + pseq.accession + " name " + pseq.name);
+	}
+    }
+
+    static final void printNames(Collection<Hit> psiseqs) {
+	assert psiseqs != null;
+	System.out.println("Total hits: " + psiseqs.size());
+	for (Hit pseq : psiseqs) {
+	    System.out.print(pseq.number + "     ");
+	    System.out.println(pseq.name);
+	}
+    }
+
 }