Thread: [DL-Learner SVN] SF.net SVN: dl-learner:[2598] trunk/scripts/src/main/java/org/dllearner/ examples/

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Revision: 2598
          http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2598&view=rev
Author:   kmpf
Date:     2011-01-11 23:04:45 +0000 (Tue, 11 Jan 2011)

Log Message:
-----------


Modified Paths:
--------------
    trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
    trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java

Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
===================================================================

--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java	2011-01-11 14:38:13 UTC (rev 2597)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java	2011-01-11 23:04:45 UTC (rev 2598)
@@ -1,11 +1,13 @@
 package org.dllearner.examples.pdb;
 
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
 import java.io.IOException;
-import java.io.OutputStream;
+import java.io.PrintStream;
 
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
@@ -13,9 +15,10 @@
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
 import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.ResIterator;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
 
 import com.dumontierlab.pdb2rdf.model.PdbRdfModel;
 import com.dumontierlab.pdb2rdf.parser.PdbXmlParser;
@@ -24,50 +27,57 @@
 
 
 public class HelixRDFCreator {
+	
+	private static ArrayList<Resource> positives;
+	private static ArrayList<Resource> negatives;
 
 	/**
 	 * @param args
+	 * TODO: remove beginsAt, endsAt from model
 	 */
 	public static void main(String[] args) {
 		
-		TrainAndTestSet sets = new TrainAndTestSet(2);
-		String[] trainIDs = sets.getTrainset();
+		
+		
+		TrainAndTestSet sets = new TrainAndTestSet(1);
 		PdbRdfModel trainmodel = new PdbRdfModel();
+		trainmodel.add(getRdfModelForIds(sets.getTrainset()));
+		/* 
+		 * String[] id = {"200L"};
+		 * trainmodel.add(getRdfModelForIds(id));
+		 */
 		
-		for(int i = 0; i < trainIDs.length; i++){
-			System.out.println(trainIDs[i]);
-			String[] ID = {trainIDs[i]};
-			trainmodel.add(getRdfModelForIds(ID));
-		}
-
-		getRdfModelForIds(sets.getTrainset());
 		// PdbRdfModel testmodel =  getRdfModelForIds(sets.getTestset());
 		
+		ResIterator niter = getFirstAA(trainmodel);
+		
+		/* take all amino acids which are in helices and put them into the
+		 * positives ArrayList, and all others in the negatives ArrayList
+		 */
+		createPositivesAndNegatives(niter, trainmodel);
+		
+		/*
+		 * writes the conf-File
+		 */
+		createConfFile();
+
+		
 		try
     	{
-    	String queryString = 
-    		"PREFIX pdb: <http://bio2rdf.org/pdb> " +
-    		"CONSTRUCT { ?x1 ?x2 ?x3 .} " +
-    		"WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> . ?x1 ?x2 ?x3 .}";
-    	Query query = QueryFactory.create(queryString);
+			SimpleDateFormat df = new SimpleDateFormat("_yyyy_MM_dd");
+			String filename = "Helixtrainer" + df.format(new Date()) + ".rdf";
+			PrintStream out = new PrintStream (new File(filename));
+			
+			// Output query results
+			trainmodel.write(out, "RDF/XML");
 
-    	// Execute the query and obtain results
-    	QueryExecution qe = QueryExecutionFactory.create(query, trainmodel);
-    	Model construct = qe.execConstruct();
-    	OutputStream out = new FileOutputStream (new File("qwertzu_iop.rdf"));
-    	// Output query results	
-    	construct.write(out, "RDF/XML");
-
-
-
-
-    	// Important - free up resources used running the query
+			// Important - free up resources used running the query
+			out.close();
     	}
-    	catch (FileNotFoundException e)
+    	catch (IOException e)
     	{
-    		System.err.println("Datei nicht gefunden!");
+    		System.err.println("OutputStream konnte nicht geschlossen werden!");
     	}
-
 	}
 
 	private static PdbRdfModel getRdfModelForIds(String[] pdbIDs) {
@@ -81,11 +91,10 @@
         	
         	while (i.hasNext()) {
         		final InputSource input = i.next();
-        		PdbRdfModel model = new PdbRdfModel();
-        		model = parser.parse(input, new PdbRdfModel());
+        		PdbRdfModel model = parser.parse(input, new PdbRdfModel());
         		// jedes Model muss gleich nach den relevanten Daten durchsucht werden, 
         		// da ansonsten Probleme mit der Speichergröße auftreten können.
-        		allmodels.add(getHelices(model));
+        		allmodels.add(getData(model));
         		
         		}
         } catch (IOException e) {
@@ -98,36 +107,156 @@
 	    return allmodels;
 	}
 	
-	private static PdbRdfModel collectData (PdbRdfModel inmodel) {
-		PdbRdfModel collectmodel = new PdbRdfModel();
-		collectmodel.add(getHelices(inmodel));
+	private static PdbRdfModel getData(PdbRdfModel model) {
+    	
+		// Beispiel einer SELECT Abfrage
+		/*	String selectQuery = 
+		 *		"SELECT { ?x1 ?x2 ?x3 .} " +
+		 *		"WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> .}";
+		 * 	Query query = QueryFactory.create(selectQuery);
+		 * 	QueryExecution qe = QueryExecutionFactory.create(query, model);
+		 * 	ResultSet select = qe.execSelect();
+		 * 	ResultSetFormatter.out (System.out, select, query); 
+		 * 
+		 */
 		
-		
-		return collectmodel;
-	}
-	
-	private static Model getHelices(PdbRdfModel model) {
-    	// Zweimal dasselbe Ergebnis einmal als SELECT und einmal als CONSTRUCT (für weitere Bearbeitung) Statement
-		// SELECT Abfrage
+		// CONSTRUCT Abfrage
+		 
+		PdbRdfModel construct = new PdbRdfModel();
 		String queryString = 
-    		" SELECT ?x1 ?x2 ?x3 WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> . ?x1 ?x2 ?x3 .}";
+			/* i do it kind of difficult, but i want to be certain that i only get the sequences of
+			 Polypeptides(L) which contain at least one Helix. Furthermore i collect the information
+			 about at which position helices begin and end.
+			 NOTE:	this information has to be removed before oututing the model. But i will use this
+			 		to check for positive and negative train amino acids
+			*/ 
+    		"PREFIX pdb: <http://bio2rdf.org/pdb:> " +
+    		"CONSTRUCT { ?x1 <http://bio2rdf.org/pdb:beginsAt> ?x2 ." +
+    		" ?x1 <http://bio2rdf.org/pdb:endsAt> ?x3 . " +
+    		" ?x5 <http://purl.org/dc/terms/isPartOf> ?x4 . " +
+    		" ?x5 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?x6 ." +
+    		" ?x5 <http://bio2rdf.org/pdb:isImmediatelyBefore> ?x7 . } " +
+    		"WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> ." +
+    		" ?x1 <http://bio2rdf.org/pdb:beginsAt> ?x2 ." +
+    		" ?x1 <http://bio2rdf.org/pdb:endsAt> ?x3 ." +
+    		" ?x3 <http://purl.org/dc/terms/isPartOf> ?x4 ." +
+    		" ?x4 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Polypeptide(L)> ." +
+    		" ?x5 <http://purl.org/dc/terms/isPartOf> ?x4 ." +
+    		" ?x5 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?x6 ." +
+    		// with the Optional clause i get the information by which amino acid
+    		// a amino acid is followed
+    		" OPTIONAL { ?x5 <http://bio2rdf.org/pdb:isImmediatelyBefore> ?x7 . } .}";
+
 		Query query = QueryFactory.create(queryString);
 		QueryExecution qe = QueryExecutionFactory.create(query, model);
-    	ResultSet select = qe.execSelect();
-    	ResultSetFormatter.out (System.out, select, query);
-		// CONSTRUCT Abfrage
-    	queryString = 
-    		"PREFIX pdb: <http://bio2rdf.org/pdb> " +
-    		"CONSTRUCT { ?x1 ?x2 ?x3 .} " +
-    		"WHERE { ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/pdb:Helix> . ?x1 ?x2 ?x3 .}";
-    	query = QueryFactory.create(queryString);
-
-    	// Execute the query and obtain results
-    	qe = QueryExecutionFactory.create(query, model);
-    	Model construct = qe.execConstruct();
+    	construct.add(qe.execConstruct()); 
     	qe.close();
     	return construct;
 	}
+
+	private static ResIterator getFirstAA( PdbRdfModel model) {
+		PdbRdfModel construct = new PdbRdfModel();
+		/* i search for all amino acids (AA) that have a successor
+		 * but do not have a predecessor -> it's the first AA of every
+		 * polypeptide chain
+		 */
+		
+		String queryString = 
+			"PREFIX pdb: <http://bio2rdf.org/pdb:> " +
+    		"CONSTRUCT { ?x1 pdb:isImmediatelyBefore ?x2 . } " +
+    		"WHERE { ?x1 pdb:isImmediatelyBefore ?x2 . " +
+    		// NOT EXISTS can be used with SPARQL 1.1
+    		//"NOT EXISTS { ?x3 pdb:isImmediatelyBefore ?x1 . } }";
+			" OPTIONAL { ?x3 pdb:isImmediatelyBefore ?x1 . } " +
+			" FILTER ( !BOUND(?x3) ) }";
+		Query query = QueryFactory.create(queryString);
+		QueryExecution qe = QueryExecutionFactory.create(query, model);
+    	construct.add(qe.execConstruct()); 
+    	qe.close();
+    	ResIterator niter = construct.listSubjects();
+    	return niter;
+	}
+
+	private static void createPositivesAndNegatives(ResIterator riter, PdbRdfModel model) {
+		
+		// Properties i have to use to check for while going through the AA-chain
+		Property iib = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "isImmediatelyBefore");
+		Property ba = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "beginsAt");
+		Property ea = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "endsAt");
+		ArrayList<Resource> pos = new ArrayList<Resource>();
+		ArrayList<Resource> neg = new ArrayList<Resource>();
+		
+		
+		// every first amino acid indicates a new AA-chain 
+		while (riter.hasNext()) {
+			// Initialization of variables needed
+			Resource aaOne = riter.nextResource();
+			Resource obj  = aaOne;
+			Resource nobj = aaOne;
+			boolean inHelix = false;
+						
+			// look if there is a next AA
+			do {
+				// looks weird, but is needed to enter loop even for the last AA which does not have a iib-Property
+				obj = nobj;
+				// die Guten ins Töpfchen ...
+				// if we get an non-empty iterator for pdb:beginsAt the next AAs are within a AA-chain
+				if(model.listResourcesWithProperty(ba, obj).hasNext() && !inHelix ){
+					inHelix = true;
+					System.out.println("Entering Helix!");
+				}
+				// die Schlechten ins Kröpfchen
+				// if we get an non-empty iterator for pdb:endsAt and are already within a AA-chain
+				// the AAs AFTER the current ones aren't within a helix
+				if (model.listResourcesWithProperty(ea, obj).hasNext() && inHelix){
+					inHelix = false;
+					System.out.println("Leaving Helix!");
+				}
+				// get next AA if there is one
+				if (model.listObjectsOfProperty(obj, iib).hasNext()){
+					nobj = model.getProperty(obj, iib).getResource();
+				}
+				
+				// do something different if we are in a helix
+				if (inHelix){
+					pos.add(obj);
+					System.out.println(obj.getURI() + " " + iib.getURI() + " " + nobj.getURI() + " we are in!");
+				} else {
+					neg.add(obj);
+					System.out.println(obj.getURI() + " " + iib.getURI() + " " + nobj.getURI());
+				}
+				
+			} while (obj.hasProperty(iib)) ;
+		}
+		positives = pos;
+		negatives = neg;
+	}
 	
+	private static void createConfFile(){
+		try
+    	{
+			SimpleDateFormat df = new SimpleDateFormat("_yyyy_MM_dd");
+			String filename = "pdb" + df.format(new Date()) + ".conf";
+			PrintStream out = new PrintStream (new File(filename));
+			
+			out.println("import(\"AA_properties.owl\");");
+			out.println("import(\"" + filename + "\");");
+			out.println();
+			
+			for (int i = 0 ; i < positives.size() ; i++ ) {
+				out.println("+\"" + positives.get(i).getURI() + "\"");
+			}
+			
+			for (int i = 0 ; i < negatives.size() ; i++ ) {
+				out.println("-\"" + negatives.get(i).getURI() + "\"");
+			}
 
+			// Important - free up resources used running the query
+			out.close();
+    	}
+    	catch (IOException e)
+    	{
+    		System.err.println("OutputStream konnte nicht geschlossen werden!");
+    	}
+	}
 }
\ No newline at end of file

Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java	2011-01-11 14:38:13 UTC (rev 2597)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java	2011-01-11 23:04:45 UTC (rev 2598)
@@ -1,8 +1,5 @@
 package org.dllearner.examples.pdb;
 
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.LineNumberReader;
@@ -81,14 +78,11 @@
 			this.pdbprotlines = arraylist;
 
 			return count;
-		} catch (FileNotFoundException e) {
+		}
+		catch (IOException e) {
 			// TODO Auto-generated catch block
 			e.printStackTrace();
 			return 0;
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-			return 0;
 		}
 	}
 	


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Thread: [DL-Learner SVN] SF.net SVN: dl-learner:[2598] trunk/scripts/src/main/java/org/dllearner/ examples/

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