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[DL-Learner SVN] SF.net SVN: dl-learner:[3320] trunk/scripts/src/main/java/org/dllearner/ examples/pdb
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From: <km...@us...> - 2011-10-26 07:52:41
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Revision: 3320
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3320&view=rev
Author: kmpf
Date: 2011-10-26 07:52:30 +0000 (Wed, 26 Oct 2011)
Log Message:
-----------
Added a few classes for hopefully nicer code. Especially the two classes for DL-Learner and Weka code. Even though the Weka thing does not work at the moment.
Modified Paths:
--------------
trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/examples/pdb/AminoAcids.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/ConfFileFilter.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBDLLearner.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBIdRdfModel.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBProtein.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/ProteinDataSet.java
Removed Paths:
-------------
trunk/scripts/src/main/java/org/dllearner/examples/pdb/PdbProtein.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/RdfFileFilter.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java
Added: trunk/scripts/src/main/java/org/dllearner/examples/pdb/AminoAcids.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/AminoAcids.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/AminoAcids.java 2011-10-26 07:52:30 UTC (rev 3320)
@@ -0,0 +1,121 @@
+package org.dllearner.examples.pdb;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintStream;
+import java.util.HashMap;
+
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
+
+public final class AminoAcids {
+ public static final Resource ALA = ResourceFactory.createResource("http://bio2rdf.org/pdb:Alanine");
+ public static final Resource CYS = ResourceFactory.createResource("http://bio2rdf.org/pdb:Cysteine");
+ public static final Resource ASP = ResourceFactory.createResource("http://bio2rdf.org/pdb:AsparticAcid");
+ public static final Resource GLU = ResourceFactory.createResource("http://bio2rdf.org/pdb:GlutamicAcid");
+ public static final Resource PHE = ResourceFactory.createResource("http://bio2rdf.org/pdb:Phenylalanine");
+ public static final Resource GLY = ResourceFactory.createResource("http://bio2rdf.org/pdb:Glycine");
+ public static final Resource HIS = ResourceFactory.createResource("http://bio2rdf.org/pdb:Histidine");
+ public static final Resource ILE = ResourceFactory.createResource("http://bio2rdf.org/pdb:Isoleucine");
+ public static final Resource LYS = ResourceFactory.createResource("http://bio2rdf.org/pdb:Lysine");
+ public static final Resource LEU = ResourceFactory.createResource("http://bio2rdf.org/pdb:Leucine");
+ public static final Resource MET = ResourceFactory.createResource("http://bio2rdf.org/pdb:Methionine");
+ public static final Resource ASN = ResourceFactory.createResource("http://bio2rdf.org/pdb:Asparagine");
+ public static final Resource PRO = ResourceFactory.createResource("http://bio2rdf.org/pdb:Proline");
+ public static final Resource GLN = ResourceFactory.createResource("http://bio2rdf.org/pdb:Glutamine");
+ public static final Resource ARG = ResourceFactory.createResource("http://bio2rdf.org/pdb:Arginine");
+ public static final Resource SER = ResourceFactory.createResource("http://bio2rdf.org/pdb:Serine");
+ public static final Resource THR = ResourceFactory.createResource("http://bio2rdf.org/pdb:Threonine");
+ public static final Resource VAL = ResourceFactory.createResource("http://bio2rdf.org/pdb:Valine");
+ public static final Resource TRP = ResourceFactory.createResource("http://bio2rdf.org/pdb:Tryptophan");
+ public static final Resource TYR = ResourceFactory.createResource("http://bio2rdf.org/pdb:Tyrosine");
+ public static final Resource SEL = ResourceFactory.createResource("http://bio2rdf.org/pdb:Selenomethionine");
+ public static final Resource HYT = ResourceFactory.createResource("http://bio2rdf.org/pdb:2-hydroxy-tryptophan");
+
+ public static HashMap<Resource, File> getAllConfFiles (String dir, String confFileName){
+ HashMap<Resource, File> aminoAcidsConfFiles = new HashMap<Resource, File>(30);
+ aminoAcidsConfFiles.put(ALA, new File(dir + confFileName.replace(".conf", "." + ALA.getLocalName()) + ".conf"));
+ aminoAcidsConfFiles.put(CYS, new File(dir + confFileName.replace(".conf", "." + CYS.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(ASP, new File(dir + confFileName.replace(".conf", "." + ASP.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(GLU, new File(dir + confFileName.replace(".conf", "." + GLU.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(PHE, new File(dir + confFileName.replace(".conf", "." + PHE.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(GLY, new File(dir + confFileName.replace(".conf", "." + GLY.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(HIS, new File(dir + confFileName.replace(".conf", "." + HIS.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(ILE, new File(dir + confFileName.replace(".conf", "." + ILE.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(LYS, new File(dir + confFileName.replace(".conf", "." + LYS.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(LEU, new File(dir + confFileName.replace(".conf", "." + LEU.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(MET, new File(dir + confFileName.replace(".conf", "." + MET.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(ASN, new File(dir + confFileName.replace(".conf", "." + ASN.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(PRO, new File(dir + confFileName.replace(".conf", "." + PRO.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(GLN, new File(dir + confFileName.replace(".conf", "." + GLN.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(ARG, new File(dir + confFileName.replace(".conf", "." + ARG.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(SER, new File(dir + confFileName.replace(".conf", "." + SER.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(THR, new File(dir + confFileName.replace(".conf", "." + THR.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(VAL, new File(dir + confFileName.replace(".conf", "." + VAL.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(TRP, new File(dir + confFileName.replace(".conf", "." + TRP.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(TYR, new File(dir + confFileName.replace(".conf", "." + TYR.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(SEL, new File(dir + confFileName.replace(".conf", "." + SEL.getLocalName() + ".conf")));
+ aminoAcidsConfFiles.put(HYT, new File(dir + confFileName.replace(".conf", "." + HYT.getLocalName() + ".conf")));
+ return aminoAcidsConfFiles;
+ }
+
+ public static HashMap<Resource, PrintStream> getAminoAcidPrintStreamMap(HashMap<Resource, File> allConfFiles){
+ // put all amino acid resources and the their conf-files together
+ HashMap<Resource, PrintStream> resprint = new HashMap<Resource, PrintStream>(30);
+ try{
+ resprint.put(ALA, new PrintStream(allConfFiles.get(ALA)));
+ resprint.put(CYS, new PrintStream(allConfFiles.get(CYS)));
+ resprint.put(ASP, new PrintStream(allConfFiles.get(ASP)));
+ resprint.put(GLU, new PrintStream(allConfFiles.get(GLU)));
+ resprint.put(PHE, new PrintStream(allConfFiles.get(PHE)));
+ resprint.put(GLY, new PrintStream(allConfFiles.get(GLY)));
+ resprint.put(HIS, new PrintStream(allConfFiles.get(HIS)));
+ resprint.put(ILE, new PrintStream(allConfFiles.get(ILE)));
+ resprint.put(LYS, new PrintStream(allConfFiles.get(LYS)));
+ resprint.put(LEU, new PrintStream(allConfFiles.get(LEU)));
+ resprint.put(MET, new PrintStream(allConfFiles.get(MET)));
+ resprint.put(ASN, new PrintStream(allConfFiles.get(ASN)));
+ resprint.put(PRO, new PrintStream(allConfFiles.get(PRO)));
+ resprint.put(GLN, new PrintStream(allConfFiles.get(GLN)));
+ resprint.put(ARG, new PrintStream(allConfFiles.get(ARG)));
+ resprint.put(SER, new PrintStream(allConfFiles.get(SER)));
+ resprint.put(THR, new PrintStream(allConfFiles.get(THR)));
+ resprint.put(VAL, new PrintStream(allConfFiles.get(VAL)));
+ resprint.put(TRP, new PrintStream(allConfFiles.get(TRP)));
+ resprint.put(TYR, new PrintStream(allConfFiles.get(TYR)));
+ resprint.put(SEL, new PrintStream(allConfFiles.get(SEL)));
+ } catch (FileNotFoundException e) {
+ e.printStackTrace();
+ }
+ return resprint;
+ }
+
+ public static HashMap<Resource, String> getAminoAcidArffAttributeMap(){
+ HashMap<Resource, String> resdata = new HashMap<Resource, String>(30);
+ resdata.put(ALA, new String("2,0,0.5,?,?"));
+ resdata.put(CYS, new String("1,0,1,?,0"));
+ resdata.put(ASP, new String("0,-1,1,?,-1"));
+ resdata.put(GLU, new String("0,-1,2,?,-1"));
+ resdata.put(PHE, new String("2,0,2,1,?"));
+ resdata.put(GLY, new String("2,0,0.5,?,?"));
+ resdata.put(HIS, new String("1,1,2,1,1"));
+ resdata.put(ILE, new String("2,0,2,0,?"));
+ resdata.put(LYS, new String("1,1,2,?,1"));
+ resdata.put(LEU, new String("2,0,2,0,?"));
+ resdata.put(MET, new String("2,0,2,?,?"));
+ resdata.put(ASN, new String("0,0,1,?,0"));
+ resdata.put(PRO, new String("?,0,1,?,?"));
+ resdata.put(GLN, new String("0,0,2,?,0"));
+ resdata.put(ARG, new String("0,1,2,?,1"));
+ resdata.put(SER, new String("0,0,0.5,?,0"));
+ resdata.put(THR, new String("1,0,1,?,0,"));
+ resdata.put(VAL, new String("2,0,1,0,?"));
+ resdata.put(TRP, new String("1,0,2,1,1"));
+ resdata.put(TYR, new String("1,0,2,1,0"));
+ resdata.put(SEL, new String("?,?,?,?,?"));
+
+ return resdata;
+ }
+
+
+}
Copied: trunk/scripts/src/main/java/org/dllearner/examples/pdb/ConfFileFilter.java (from rev 3298, trunk/scripts/src/main/java/org/dllearner/examples/pdb/RdfFileFilter.java)
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/ConfFileFilter.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/ConfFileFilter.java 2011-10-26 07:52:30 UTC (rev 3320)
@@ -0,0 +1,15 @@
+package org.dllearner.examples.pdb;
+
+import java.io.File;
+import java.io.FileFilter;
+
+public class ConfFileFilter implements FileFilter
+{
+ private final String extension = new String("conf");
+
+ public boolean accept(File file)
+ {
+ return file.getName().toLowerCase().endsWith(extension);
+ }
+}
+
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-10-25 07:49:07 UTC (rev 3319)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-10-26 07:52:30 UTC (rev 3320)
@@ -1,801 +1,389 @@
package org.dllearner.examples.pdb;
import java.io.File;
-import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.LineNumberReader;
import java.io.PrintStream;
-import java.text.SimpleDateFormat;
import java.util.ArrayList;
-import java.util.Date;
import java.util.HashMap;
import java.util.Iterator;
-import java.util.Set;
+import org.apache.log4j.ConsoleAppender;
+import org.apache.log4j.FileAppender;
+import org.apache.log4j.HTMLLayout;
+import org.apache.log4j.Layout;
+import org.apache.log4j.Level;
+import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
import org.dllearner.cli.Start;
import org.dllearner.core.ComponentInitException;
import org.dllearner.core.ComponentManager;
-import org.dllearner.core.AbstractKnowledgeSource;
-import org.dllearner.core.AbstractReasonerComponent;
+import org.dllearner.core.LearningProblemUnsupportedException;
+import org.dllearner.core.ReasonerComponent;
import org.dllearner.core.owl.Description;
-import org.dllearner.core.owl.Individual;
-import org.dllearner.kb.OWLFile;
import org.dllearner.reasoning.FastInstanceChecker;
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-import com.hp.hpl.jena.query.Query;
-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.QuerySolution;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.NodeIterator;
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.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.rdf.model.StmtIterator;
-import com.hp.hpl.jena.vocabulary.RDFS;
import com.dumontierlab.pdb2rdf.model.PdbRdfModel;
-import com.dumontierlab.pdb2rdf.parser.PdbXmlParser;
-import com.dumontierlab.pdb2rdf.util.Pdb2RdfInputIterator;
-import com.dumontierlab.pdb2rdf.util.PdbsIterator;
-import edu.stanford.nlp.io.EncodingPrintWriter.out;
-
-
public class HelixRDFCreator {
- private static Resource ala = ResourceFactory.createResource("http://bio2rdf.org/pdb:Alanine");
- private static Resource cys = ResourceFactory.createResource("http://bio2rdf.org/pdb:Cysteine");
- private static Resource asp = ResourceFactory.createResource("http://bio2rdf.org/pdb:AsparticAcid");
- private static Resource glu = ResourceFactory.createResource("http://bio2rdf.org/pdb:GlutamicAcid");
- private static Resource phe = ResourceFactory.createResource("http://bio2rdf.org/pdb:Phenylalanine");
- private static Resource gly = ResourceFactory.createResource("http://bio2rdf.org/pdb:Glycine");
- private static Resource his = ResourceFactory.createResource("http://bio2rdf.org/pdb:Histidine");
- private static Resource ile = ResourceFactory.createResource("http://bio2rdf.org/pdb:Isoleucine");
- private static Resource lys = ResourceFactory.createResource("http://bio2rdf.org/pdb:Lysine");
- private static Resource leu = ResourceFactory.createResource("http://bio2rdf.org/pdb:Leucine");
- private static Resource met = ResourceFactory.createResource("http://bio2rdf.org/pdb:Methionine");
- private static Resource asn = ResourceFactory.createResource("http://bio2rdf.org/pdb:Asparagine");
- private static Resource pro = ResourceFactory.createResource("http://bio2rdf.org/pdb:Proline");
- private static Resource gln = ResourceFactory.createResource("http://bio2rdf.org/pdb:Glutamine");
- private static Resource arg = ResourceFactory.createResource("http://bio2rdf.org/pdb:Arginine");
- private static Resource ser = ResourceFactory.createResource("http://bio2rdf.org/pdb:Serine");
- private static Resource thr = ResourceFactory.createResource("http://bio2rdf.org/pdb:Threonine");
- private static Resource val = ResourceFactory.createResource("http://bio2rdf.org/pdb:Valine");
- private static Resource trp = ResourceFactory.createResource("http://bio2rdf.org/pdb:Tryptophan");
- private static Resource tyr = ResourceFactory.createResource("http://bio2rdf.org/pdb:Tyrosine");
- private static Resource sel = ResourceFactory.createResource("http://bio2rdf.org/pdb:Selenomethionine");
- private static Resource hyt = ResourceFactory.createResource("http://bio2rdf.org/pdb:2-hydroxy-tryptophan");
+ private static Logger _logger = Logger.getLogger(HelixRDFCreator.class);
+ private static Logger _rootLogger = Logger.getRootLogger();
- private static ArrayList<Resource> positives;
- private static ArrayList<Resource> negatives;
-
- public void setNegatives(ArrayList<Resource> neg){
- negatives = neg;
- }
-
- public ArrayList<Resource> getPositives(){
- return positives;
- }
-
- public ArrayList<Resource> getNegatives(){
- return negatives;
- }
-
- private static String dataDir = "../test/pdb/";
- private static HashMap<Resource, File> confFilePerResidue;
- private static File confFileForAll;
-
- public void setPositives(ArrayList<Resource> pos){
- positives = pos;
- }
-
+ private static String _dataDir = "../test/pdb/";
+ private static File _dir = new File(_dataDir);
+
/**
* @param args
* TODO: remove beginsAt, endsAt from model
*/
public static void main(String[] args) {
+
+ // create loggers (a simple logger which outputs
+ // its messages to the console and a log file)
+
+ // logger 1 is the console, where we print only info messages;
+ // the logger is plain, i.e. does not output log level etc.
+ Layout layout = new PatternLayout();
+
+ ConsoleAppender consoleAppender = new ConsoleAppender(layout);
+ // setting a threshold suppresses log messages below this level;
+ // this means that if you want to e.g. see all trace messages on
+ // console, you have to set the threshold and log level to trace
+ // (but we recommend just setting the log level to trace and observe
+ // the log file)
+ consoleAppender.setThreshold(Level.DEBUG);
+
+ // logger 2 is writes to a file; it records all debug messages
+ // (you can choose HTML or TXT)
+ boolean htmlLog = false;
+ Layout layout2 = null;
+ FileAppender fileAppenderNormal = null;
+ String fileName;
+ if(htmlLog) {
+ layout2 = new HTMLLayout();
+ fileName = _dataDir + "log/log.html";
+ } else {
+ // simple variant: layout2 = new SimpleLayout();
+ layout2 = new PatternLayout("%r [%t] %-5p %c :\n%m%n\n");
+ fileName = _dataDir + "log/log.txt";
+ }
+ try {
+ fileAppenderNormal = new FileAppender(layout2, fileName, false);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ // add both loggers
+ _rootLogger.removeAllAppenders();
+ _rootLogger.addAppender(consoleAppender);
+ _rootLogger.addAppender(fileAppenderNormal);
+ _rootLogger.setLevel(Level.DEBUG);
+
+
+ Boolean fasta = true;
+
/*
- * test = true -> use test data
- * test = false -> use data set 1, 2, 3 or 4
- */
- Boolean test = true;
- /*
* rdfConf = true -> write out the .rdf and .conf-Files
* rdfConf = false -> does not generate those files
*/
Boolean rdfConf = true;
+
/*
* arff = true -> write out .arff-Files
* arff = false -> does not generate those files
*/
- Boolean arff = false;
+ Boolean arff = true;
/*
* load = true -> load alle .rdf, .conf and .arff Files that can be found within the directory dataDir
* load = false -> don't load anything
*/
- Boolean load = true;
- Boolean dlLearn = false;
- Boolean wekaLearn = false;
+ Boolean load = false;
+ Boolean dlLearn = true;
+ Boolean wekaLearn = true;
- int dataSet = 1;
+ int dataSet = 5;
+
/*
- * get data set files
- */
- // data set 1
- String bt426 = dataDir + "bt426.list";
- File bt426List = new File(bt426);
- // data set 2
- String plp273 = dataDir + "plp273.list";
- File plp273List = new File(plp273);
- // data set 3
- String plp364 = dataDir + "plp364.list";
- File plp364List = new File(plp364);
- // data set 4
- String plp399 = dataDir + "plp399.list";
- File plp399List = new File(plp399);
-
- /*
* data for test purpose
*/
- String pdbID = "1XFF";
- String chainID = "A";
- File dir = new File(dataDir);
+// PdbProtein testProtein = new PdbProtein("1XFF");
+ PDBProtein testProtein = new PDBProtein("1XFF", "A");
/*
- * generate trainset and fill trainmodel
+ * create a training data set
*/
- PdbRdfModel trainmodel = new PdbRdfModel();
- TrainAndTestSet trainSet = new TrainAndTestSet();
+ ProteinDataSet proteinSet;
- if ( !test )
- {
- switch (dataSet) {
- case 1:
- trainSet = new TrainAndTestSet(bt426List);
- break;
- case 2:
- trainSet = new TrainAndTestSet(plp273List);
- break;
- case 3:
- trainSet = new TrainAndTestSet(plp364List);
- break;
- case 4:
- trainSet = new TrainAndTestSet(plp399List);
- break;
- }
+ switch (dataSet) {
+ case 1:
+ proteinSet = ProteinDataSet.bt426();
+ break;
+ case 2:
+ proteinSet = ProteinDataSet.plp273();
+ break;
+ case 3:
+ proteinSet = ProteinDataSet.plp364();
+ break;
+ case 4:
+ proteinSet = ProteinDataSet.plp399();
+ break;
+ default:
+ proteinSet = new ProteinDataSet(testProtein);
+ break;
}
- else
- {
- trainSet = new TrainAndTestSet(pdbID, chainID);
- }
- HashMap<String,File> rdfFiles = new HashMap<String,File>();
- HashMap<String,File> arffFiles = new HashMap<String,File>();
-
- if (load)
- {
- System.out.println("Starting to load files in " + dataDir );
- File[] pdbDir = dir.listFiles(new DirectoryFileFilter());
- for (File actDir : pdbDir) {
- File[] rdfFilesInActDir = actDir.listFiles(new RdfFileFilter());
- try {
- System.out.println("Looking for Files in " + actDir.getCanonicalPath() );
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- for (File rdfFile : rdfFilesInActDir) {
- rdfFiles.put(rdfFile.getName().substring(0, 3), rdfFile);
- System.out.println("Found RDF File for PDB ID " + rdfFile.getName().substring(0, 3) );
- System.out.println("Found RDF File " + rdfFile.getName() );
- }
- File[] arffFilesInActDir = actDir.listFiles(new ArffFileFilter());
- for (File arffFile : arffFilesInActDir) {
- arffFiles.put(arffFile.getName().substring(0, 3), arffFile);
- System.out.println("Found RDF File for PDB ID " + arffFile.getName().substring(0, 3) );
- System.out.println("Found ARFF File " + arffFile.getName() );
- }
- }
- }
-
-
-
/*
* generate a PdbRdfModel for every pdbID
*/
+ PDBIdRdfModel trainmodel;
-
-
- for (int i = 0; i < trainSet.getTrainset().length; i++)
+ for (int i = 0; i < proteinSet.getProteinset().size(); i++)
{
- System.out.println("pdbId: " + trainSet.getTrainset()[i].getPdbID());
- System.out.println("chainID: " + trainSet.getTrainset()[i].getChainID());
- trainmodel.removeAll();
- trainmodel.add(getRdfModelForIds(trainSet.getTrainset()[i].getPdbID(), trainSet.getTrainset()[i].getChainID()));
-
- /*
- * extract the species the protein originates from
- */
- trainSet.getTrainset()[i].setSpecies(getSpecies(trainmodel, trainSet.getTrainset()[i].getPdbID()));
-
- /*
- * as we have sometimes to handle several amino acid chains we need the first
- * amino acid of every chain, they are returned within a ResIterator
- */
- ResIterator niter = getFirstAA(trainmodel);
-
- /*
- * we add the information of which amino acid is the fourth predecessor of which other amino acid
- */
- trainmodel = addDistanceInfo(trainmodel);
-
- /*
- * take all amino acids which are in helices and put them into the
- * global positives ArrayList, and all others in the global negatives ArrayList
- */
- createPositivesAndNegatives(niter, trainmodel);
- String rdfFile;
- String arffFile;
- if (trainSet.getTrainset()[i].getChainID().length() == 0)
- {
- rdfFile = trainSet.getTrainset()[i].getPdbID().toUpperCase() + ".rdf";
- arffFile = trainSet.getTrainset()[i].getPdbID().toUpperCase() + ".arff";
- }
- else
- {
- rdfFile = trainSet.getTrainset()[i].getPdbID().toUpperCase() + "."
- + trainSet.getTrainset()[i].getChainID().toUpperCase() + ".rdf";
- arffFile = trainSet.getTrainset()[i].getPdbID().toUpperCase() + "."
- + trainSet.getTrainset()[i].getChainID().toUpperCase() + ".arff";
- }
- String pdbDir = dataDir + trainSet.getTrainset()[i].getPdbID() + "/";
- File directory = new File(pdbDir);
- directory.mkdir();
- String rdfFilePath = pdbDir + rdfFile;
- String arffFilePath = pdbDir + arffFile;
-
- /*
- * if arff = true create pdbID.arff files
- */
- if (arff)
- {
- niter = getFirstAA(trainmodel);
- createArffFile(arffFilePath, trainmodel, trainSet, niter);
- }
-
- /*
- * if rdfConf = true create pdbID.rdf and *.conf files
- */
- if(rdfConf)
- {
- try
- {
- /*
- * creatConfFile()
- * writes the conf-Files and saves there File-objects in:
- * confFileForAll and confFilePerResidue
- */
- createConfFile(pdbDir, rdfFile, trainmodel);
- PrintStream out = new PrintStream (new File(rdfFilePath));
-
- // Output results
- trainmodel.write(out, "RDF/XML");
-
- // Important - free up resources used running the query
- out.close();
- }
- catch (IOException e)
- {
- System.err.println("OutputStream konnte nicht geschlossen werden!");
- }
- }
- /*
- * remove all triples that contain information about begin and end of helices
- */
-
- Property beginsAt = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "beginsAt");
- trainmodel = removeStatementsWithPoperty(trainmodel, beginsAt);
- Property endsAt = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "endsAt");
- trainmodel = removeStatementsWithPoperty(trainmodel, endsAt);
- Resource residue = ResourceFactory.createResource("http://bio2rdf.org/pdb:Residue");
- trainmodel = removeStatementsWithObject(trainmodel, residue);
- }
-
- /*
- * write out the files that contain information about which proteins originate from which species
- */
- HashMap<String, File> proteinsOfSpecies = new HashMap<String, File>();
- for (int i = 0; i < trainSet.getTrainset().length; i++){
- if (proteinsOfSpecies.get(trainSet.getTrainset()[i].getSpecies()) == null){
- File speciesProteins = new File(dataDir + trainSet.getTrainset()[i].getSpecies() + ".pos");
- proteinsOfSpecies.put(trainSet.getTrainset()[i].getSpecies(), speciesProteins);
- }
- if (proteinsOfSpecies.get(trainSet.getTrainset()[i].getSpecies()).canWrite()) {
+ if (rdfConf || arff) {
+
+ PDBProtein protein = proteinSet.getProteinset().get(i);
+ String pdbDir = _dataDir + protein.getPdbID() + "/";
+ File directory = new File(pdbDir);
+ if(! directory.exists()) directory.mkdir();
+ //
+ //String arffFilePath = pdbDir + protein.getArffFileName();
+
+ _logger.info("PDB ID: " + protein.getPdbID());
+ _logger.info("chain ID: " + protein.getChainID());
+ trainmodel = new PDBIdRdfModel(protein);
+
+ if (fasta){
+ trainmodel.createFastaFile(pdbDir);
+ }
+
+
+ /*
+ * if arff = true create pdbID.arff files
+ */
+
+ /*
+ * as we have sometimes to handle several amino acid chains we need the first
+ * amino acid of every chain, they are returned within a ResIterator
+ */
+
+ if (arff)
+ {
+ ResIterator niter = trainmodel.getFirstAA();
+ createArffFile(pdbDir, trainmodel, niter);
+ }
+
+ /*
+ * remove all triples that contain information about begin and end of helices
+ */
+ Property beginsAt = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "beginsAt");
+ trainmodel.removeStatementsWithPoperty(beginsAt);
+ Property endsAt = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "endsAt");
+ trainmodel.removeStatementsWithPoperty(endsAt);
+ Resource residue = ResourceFactory.createResource("http://bio2rdf.org/pdb:Residue");
+ trainmodel.removeStatementsWithObject(residue);
+
+ /*
+ * we add the information which amino acid is the fourth predecessor of which other amino acid
+ */
+ trainmodel.addDistanceInfo();
+
+ /*
+ * if rdfConf = true create pdbID.rdf and *.conf files
+ */
+
+
+
+ if(rdfConf)
+ {
+ String rdfFilePath = pdbDir + protein.getRdfFileName();
+ try
+ {
+ /*
+ * creatConfFile()
+ * writes the conf-Files and saves there File-objects in:
+ * confFileForAll and confFilePerResidue
+ */
+ createConfFile(pdbDir, trainmodel);
+
+ PrintStream out = new PrintStream (new File(rdfFilePath));
+
+ // Output results
+ trainmodel.getModel().write(out, "RDF/XML");
+
+ // Important - free up resources used running the query
+ out.close();
+ }
+ catch (FileNotFoundException e)
+ {
+ _logger.error("File " + rdfFilePath + " konnte nicht gefunden werden!");
+ e.printStackTrace();
+ }
+ }
+ /*
+ * For every protein source species create a file that contains a list of all
+ * proteins that originate from that particular species. If it already exists
+ * we will append to it.
+ */
+ File speciesProteins = new File(_dataDir + protein.getSpecies() + ".pos");
+
try {
- FileWriter out = new FileWriter(proteinsOfSpecies.get(trainSet.getTrainset()[i].getSpecies()), true);
- String line = trainSet.getTrainset()[i].getPdbID() + "."
- + trainSet.getTrainset()[i].getChainID() + ".\n";
+ String line = protein.getPdbID() + "." + protein.getChainID() + "." + protein.getSpecies() + "\n";
+ FileWriter out = new FileWriter(speciesProteins, true);
+ _logger.debug("Write " + line + "to file " + speciesProteins.getPath() + speciesProteins.getName());
out.write(line);
out.close();
} catch (FileNotFoundException e) {
- // TODO Auto-generated catch block
+ _logger.error("Could not find file " + speciesProteins.getPath() + speciesProteins.getName());
e.printStackTrace();
} catch (IOException e) {
- // TODO Auto-generated catch block
+ _logger.error("Something went wrong while trying to write to " + speciesProteins.getPath() + speciesProteins.getName());
e.printStackTrace();
}
-
}
}
if(dlLearn)
{
-
-
- /*
- * load RDF file and perform learn algorithm for every .conf-file
- */
- /*ComponentManager cm = ComponentManager.getInstance();
- KnowledgeSource ks = cm.knowledgeSource(OWLFile.class);
- cm.applyConfigEntry(ks, "url","file://" + filename );
- ReasonerComponent rc = cm.reasoner(FastInstanceChecker.class);
- try {
- rc.init();
- } catch (ComponentInitException e1) {
- e1.printStackTrace();
- }
- Start start = null;
- Iterator<Resource> aa = confFilePerResidue.keySet().iterator();
- while ( aa.hasNext() ){
- Resource nextRes = aa.next();
- System.out.println(confFilePerResidue.get(nextRes).getAbsolutePath());
- try{
- start = new Start(confFilePerResidue.get(nextRes));
- } catch (ComponentInitException e) {
- e.printStackTrace();
- } catch (FileNotFoundException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- } catch (org.dllearner.confparser.ParseException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- start.start(false);
- Description d = start.getLearningAlgorithm().getCurrentlyBestDescription();
- System.out.println(d.toKBSyntaxString());
- }
- */
+ startDlLearner();
}
if(wekaLearn)
{
+ startWekaLearner();
}
}
- private static PdbRdfModel getRdfModelForIds(String pdbID ,String chainID) {
-
- /*
- * i is an Iterator over an XML InputSource
- */
- String[] pdbIDs = {pdbID};
- Pdb2RdfInputIterator i = new PdbsIterator(pdbIDs);
- PdbXmlParser parser = new PdbXmlParser();
- PdbRdfModel allmodels = new PdbRdfModel();
- try {
- while (i.hasNext())
- {
- final InputSource input = i.next();
- 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(getData(model, pdbID, chainID));
- }
- }
- catch (IOException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
+ private static void startDlLearner(){
+ HashMap<String, File> pdbIDConfFile = loadConfFiles(_dir);
+ for (String pdbID : pdbIDConfFile.keySet()){
+ try {
+ new PDBDLLearner(pdbIDConfFile.get(pdbID));
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (ComponentInitException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (LearningProblemUnsupportedException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
}
- catch (SAXException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- return allmodels;
}
- private static PdbRdfModel getData(PdbRdfModel model, String pdbID, String chainID) {
-
- // 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);
- *
- */
-
- // CONSTRUCT Abfrage
-
- PdbRdfModel construct = new PdbRdfModel();
- /*
- * 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 outputing the model. But i will use this
- * to check for positive and negative train amino acids
- */
- /*
- * ich brauche noch die selektion der chain und die info über den genursprungsorganismus
- * rdf:resource="http://bio2rdf.org/pdb:3LQH/chain_A"
- * http://bio2rdf.org/pdb:3LQH/chain_A/position_1596
- */
-
- String queryString = "";
-
- if (chainID.length() != 1 || pdbID.length() != 4)
- {
- queryString =
- "PREFIX pdb: <http://bio2rdf.org/pdb:> " +
- "PREFIX dcterms: <http://purl.org/dc/terms/> " +
- "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
- "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> " +
- "PREFIX fn: <http://www.w3.org/2005/xpath-functions#> " +
- "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 ." +
- " ?xxx rdfs:label ?label .} " +
- "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 ." +
- " ?xxx rdfs:label ?label FILTER (str(?xxx) = fn:concat(str(?x4), '/extraction/source/gene/organism')) . " +
- // 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 . } .}";
+ private static void startWekaLearner() {
+ HashMap<String, File> pdbIDArffFile = loadArffFiles(_dir);
+ for (String pdbID: pdbIDArffFile.keySet()){
+ try {
+ new PDBWekaLearner(pdbIDArffFile.get(pdbID));
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
}
- else
- {
- queryString =
- "PREFIX pdb: <http://bio2rdf.org/pdb:> " +
- "PREFIX dcterms: <http://purl.org/dc/terms/> " +
- "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
- "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> " +
- "PREFIX fn: <http://www.w3.org/2005/xpath-functions#> " +
- "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 ." +
- " ?xxx rdfs:label ?label .} " +
- "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 ." +
- " ?x5 <http://bio2rdf.org/pdb:hasChainPosition> ?x8 ." +
- " ?x8 <http://purl.org/dc/terms/isPartOf> <http://bio2rdf.org/pdb:" + pdbID.toUpperCase() +
- "/chain_" + chainID.toUpperCase() + "> ." +
- " ?xxx rdfs:label ?label FILTER (str(?xxx) = fn:concat(str(?x4), '/extraction/source/gene/organism')) . " +
- // 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 . } .}";
- }
-
- //System.out.println(queryString);
- Query query = QueryFactory.create(queryString);
- QueryExecution qe = QueryExecutionFactory.create(query, model);
- construct.add(qe.execConstruct());
- qe.close();
- return construct;
- }
-
- private static String getSpecies( PdbRdfModel model, String pdbID) {
- String queryString ;
- queryString =
- "PREFIX pdb: <http://bio2rdf.org/pdb:> " +
- "PREFIX dcterms: <http://purl.org/dc/terms/> " +
- "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
- "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> " +
- "PREFIX fn: <http://www.w3.org/2005/xpath-functions#> " +
- "SELECT ?species " +
- "WHERE { ?x1 <http://purl.org/dc/terms/isPartOf> ?x4 ." +
- " ?x1 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?x2 ." +
- " ?x1 <http://bio2rdf.org/pdb:isImmediatelyBefore> ?x3 ." +
- " ?x5 rdfs:label ?species FILTER (str(?x5) = fn:concat(str(?x4), '/extraction/source/gene/organism')) . }";
-
- // System.out.println(queryString);
- Query query = QueryFactory.create(queryString);
- QueryExecution qe = QueryExecutionFactory.create(query, model);
- String species = "";
- try
- {
- ResultSet results = qe.execSelect() ;
- for ( ; results.hasNext() ; )
- {
- /*
- * every entry in the ResultSet has the same value
- */
- QuerySolution soln = results.nextSolution() ;
- Literal l = soln.getLiteral("species") ; // Get a result variable - must be a literal
- species = l.getString();
+ }
+ private static HashMap<String,File> loadConfFiles (File dir){
+ HashMap<String,File> confFiles = new HashMap<String,File>();
+ _logger.info("Starting to load files in " + dir );
+ File[] pdbDir = dir.listFiles(new DirectoryFileFilter());
+ for (File activeDirectory : pdbDir) {
+ File[] confFilesInActiveDirectory = activeDirectory.listFiles(new ConfFileFilter());
+ _logger.info("Looking for Files in " + activeDirectory.getPath() );
+ for (File confFile : confFilesInActiveDirectory) {
+ String confFileName = confFile.getName().substring(0, confFile.getName().indexOf(".conf"));
+ confFiles.put(confFileName, confFile);
+ _logger.info("Found .conf File " + confFile.getPath() );
}
}
- finally
- {
- qe.close() ;
- }
- return species;
+ return confFiles;
}
-
-
- private static ResIterator getFirstAA( PdbRdfModel model) {
- PdbRdfModel construct = new PdbRdfModel();
- /* i look 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 PdbRdfModel addDistanceInfo(PdbRdfModel model){
- String queryString =
- "PREFIX pdb: <http://bio2rdf.org/pdb:> " +
- "CONSTRUCT { ?x1 pdb:isFourAminoAcidsBefore ?x5 . } " +
- "WHERE { ?x1 pdb:isImmediatelyBefore ?x2 . " +
- " ?x2 pdb:isImmediatelyBefore ?x3 . " +
- " ?x3 pdb:isImmediatelyBefore ?x4 . " +
- " ?x4 pdb:isImmediatelyBefore ?x5 . }";
- Query query = QueryFactory.create(queryString);
- QueryExecution qe = QueryExecutionFactory.create(query, model);
- model.add(qe.execConstruct());
- qe.close();
- return model;
- }
-
- private static void createPositivesAndNegatives(ResIterator riter, PdbRdfModel model) {
+ private static HashMap<String,File> loadArffFiles (File dir){
+ HashMap<String,File> arffFiles = new HashMap<String,File>();
+ _logger.info("Starting to load files in " + dir );
- // Properties i have 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 element in riter stands for a AA-chain start
- // every first amino acid indicates a new AA-chain
- while (riter.hasNext()) {
- // Initialization of variables needed
- Resource aaOne = riter.nextResource();
- Resource currentaa = aaOne;
- Resource nextaa = 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
- currentaa = nextaa;
- // 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, currentaa).hasNext() && !inHelix ){
- inHelix = true;
- }
- // 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, currentaa).hasNext() && inHelix){
- inHelix = false;
- }
- // get next AA if there is one
- if (model.listObjectsOfProperty(currentaa, iib).hasNext()){
- nextaa = model.getProperty(currentaa, iib).getResource();
- }
-
- // add current amino acid to positives or negatives set
- if (inHelix){
- pos.add(currentaa);
- } else {
- neg.add(currentaa);
- }
-
- } while (currentaa.hasProperty(iib)) ;
+ File[] pdbDir = dir.listFiles(new DirectoryFileFilter());
+ for (File activeDirectory : pdbDir) {
+ File[] arffFilesInActDir = activeDirectory.listFiles(new ArffFileFilter());
+ _logger.info("Looking for .arff Files in " + activeDirectory.getPath());
+ for (File arffFile : arffFilesInActDir) {
+ String arffFileName = arffFile.getName().substring(0, arffFile.getName().indexOf(".arff"));
+ arffFiles.put(arffFileName, arffFile);
+ _logger.info("Found .arff File " + arffFile.getPath());
+ }
}
- positives = pos;
- negatives = neg;
+ return arffFiles;
}
-
-
-
- private static PdbRdfModel removeStatementsWithPoperty(PdbRdfModel model, Property prop){
-
- String queryString =
- "PREFIX x:<" + prop.getNameSpace() + "> " +
- "CONSTRUCT { ?x1 x:" + prop.getLocalName()+ " ?x2 . } " +
- "WHERE { ?x1 x:" + prop.getLocalName() + " ?x2 . }";
- //System.out.println(queryString);
- Query query = QueryFactory.create(queryString);
- QueryExecution qe = QueryExecutionFactory.create(query, model);
- StmtIterator stmtiter = qe.execConstruct().listStatements();
- qe.close();
- while(stmtiter.hasNext()){
- model.remove(stmtiter.next());
- }
-
- return model;
- }
-
- private static PdbRdfModel removeStatementsWithObject(PdbRdfModel model, Resource res){
-
- String queryString =
- "PREFIX x:<" + res.getNameSpace() + "> " +
- "CONSTRUCT { ?x1 ?x2 x:" + res.getLocalName() + " . } " +
- "WHERE { ?x1 ?x2 x:" + res.getLocalName() + " . }";
- // System.out.println(queryString);
- Query query = QueryFactory.create(queryString);
- QueryExecution qe = QueryExecutionFactory.create(query, model);
- StmtIterator stmtiter = qe.execConstruct().listStatements();
- qe.close();
- while(stmtiter.hasNext()){
- model.remove(stmtiter.next());
- }
-
- return model;
- }
-
-
- private static void createConfFile(String dir, String rdffile, PdbRdfModel model){
+ private static void createConfFile(String pdbDir, PDBIdRdfModel model){
try
{
+ PDBProtein protein = model.getProtein();
// the file with all amino acids
- String pdbname = dir + "pdb" + ".conf";
- confFileForAll = new File(pdbname);
- PrintStream out = new PrintStream (confFileForAll);
- // add import statements
- out.println("import(\"AA_properties.owl\");");
- out.println("import(\"" + rdffile + "\");");
- out.println();
+ String confFilePath = pdbDir + protein.getConfFileName();
+ PrintStream confFile = new PrintStream (new File(confFilePath));
+ // add import statements to confFile
+ String importStmt = new String("import(\"../AA_properties.owl\");\n" +
+ "import(\"" + protein.getRdfFileName() + "\");\n");
+ confFile.println(importStmt);
- HashMap<Resource, File> resConfFiles = new HashMap<Resource, File>(30);
- resConfFiles.put(ala, new File(dir + ala.getLocalName() + ".conf"));
- resConfFiles.put(cys, new File(dir + cys.getLocalName() + ".conf"));
- resConfFiles.put(asp, new File(dir + asp.getLocalName() + ".conf"));
- resConfFiles.put(glu, new File(dir + glu.getLocalName() + ".conf"));
- resConfFiles.put(phe, new File(dir + phe.getLocalName() + ".conf"));
- resConfFiles.put(gly, new File(dir + gly.getLocalName() + ".conf"));
- resConfFiles.put(his, new File(dir + his.getLocalName() + ".conf"));
- resConfFiles.put(ile, new File(dir + ile.getLocalName() + ".conf"));
- resConfFiles.put(lys, new File(dir + lys.getLocalName() + ".conf"));
- resConfFiles.put(leu, new File(dir + leu.getLocalName() + ".conf"));
- resConfFiles.put(met, new File(dir + met.getLocalName() + ".conf"));
- resConfFiles.put(asn, new File(dir + asn.getLocalName() + ".conf"));
- resConfFiles.put(pro, new File(dir + pro.getLocalName() + ".conf"));
- resConfFiles.put(gln, new File(dir + gln.getLocalName() + ".conf"));
- resConfFiles.put(arg, new File(dir + arg.getLocalName() + ".conf"));
- resConfFiles.put(ser, new File(dir + ser.getLocalName() + ".conf"));
- resConfFiles.put(thr, new File(dir + thr.getLocalName() + ".conf"));
- resConfFiles.put(val, new File(dir + val.getLocalName() + ".conf"));
- resConfFiles.put(trp, new File(dir + trp.getLocalName() + ".conf"));
- resConfFiles.put(tyr, new File(dir + tyr.getLocalName() + ".conf"));
- resConfFiles.put(sel, new File(dir + sel.getLocalName() + ".conf"));
- resConfFiles.put(hyt, new File(dir + hyt.getLocalName() + ".conf"));
- confFilePerResidue = resConfFiles;
+ HashMap<Resource, File> confFilePerResidue = AminoAcids.getAllConfFiles(pdbDir, protein.getConfFileName());
+
+ HashMap<Resource, PrintStream> resprint = AminoAcids.getAminoAcidPrintStreamMap(confFilePerResidue);
-
-
- // put all amino acid resources and the their conf-files together
- HashMap<Resource, PrintStream> resprint = new HashMap<Resource, PrintStream>(30);
- resprint.put(ala, new PrintStream(resConfFiles.get(ala)));
- resprint.put(cys, new PrintStream(resConfFiles.get(cys)));
- resprint.put(asp, new PrintStream(resConfFiles.get(asp)));
- resprint.put(glu, new PrintStream(resConfFiles.get(glu)));
- resprint.put(phe, new PrintStream(resConfFiles.get(phe)));
- resprint.put(gly, new PrintStream(resConfFiles.get(gly)));
- resprint.put(his, new PrintStream(resConfFiles.get(his)));
- resprint.put(ile, new PrintStream(resConfFiles.get(ile)));
- resprint.put(lys, new PrintStream(resConfFiles.get(lys)));
- resprint.put(leu, new PrintStream(resConfFiles.get(leu)));
- resprint.put(met, new PrintStream(resConfFiles.get(met)));
- resprint.put(asn, new PrintStream(resConfFiles.get(asn)));
- resprint.put(pro, new PrintStream(resConfFiles.get(pro)));
- resprint.put(gln, new PrintStream(resConfFiles.get(gln)));
- resprint.put(arg, new PrintStream(resConfFiles.get(arg)));
- resprint.put(ser, new PrintStream(resConfFiles.get(ser)));
- resprint.put(thr, new PrintStream(resConfFiles.get(thr)));
- resprint.put(val, new PrintStream(resConfFiles.get(val)));
- resprint.put(trp, new PrintStream(resConfFiles.get(trp)));
- resprint.put(tyr, new PrintStream(resConfFiles.get(tyr)));
- resprint.put(sel, new PrintStream(resConfFiles.get(sel)));
-
Property type = ResourceFactory.createProperty("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "type");
- // add import statements to .conf files for amino acids
+ // add import statements to <PDB ID>_<Amino Acid>.conf files
Iterator<Resource> keys = resprint.keySet().iterator();
-
while (keys.hasNext()){
- Resource k = keys.next();
- resprint.get(k).println("import(\"AA_properties.owl\");");
- resprint.get(k).println("import(\"" + rdffile + "\");");
- resprint.get(k).println();
+ resprint.get(keys.next()).println(importStmt);
}
-
- /*
- * the for-loops beneath may cause trouble, if there exists an amino acid within a structure that
- * doesn't exists in our HashMap
- */
+
+ // add every amino acid in positive list to <PDB ID>.conf and its corresponding <PDB ID>_<Amino Acid>.conf
+ ArrayList<Resource> positives = model.getPositives();
for (int i = 0 ; i < positives.size() ; i++ ) {
- out.println("+\"" + positives.get(i).getURI() + "\"");
+ confFile.println("+\"" + positives.get(i).getURI() + "\"");
try{
- Statement spo = model.getProperty(positives.get(i), type);
+ Statement spo = model.getModel().getProperty(positives.get(i), type);
resprint.get(spo.getResource()).println("+\"" + positives.get(i).getURI() + "\"");
} catch (NullPointerException e) {
// What was the Object that probably caused the pain?
- System.err.println("Object probably not in our HashMap: " +
- model.getProperty(positives.get(i), type).getResource());
- e.getStackTrace();
+ _logger.error("Object probably not in our HashMap: " +
+ model.getModel().getProperty(positives.get(i), type).getResource());
+ e.printStackTrace();
}
- // System.out.println("Couldn't find AA: " + positives.get(i).getURI());
-
}
+ // add every amino acid in negative list to <PDB ID>.conf and its corresponding <PDB ID>_<Amino Acid>.conf
+ ArrayList<Resource> negatives = model.getNegatives();
for (int i = 0 ; i < negatives.size() ; i++ ) {
- out.println("-\"" + negatives.get(i).getURI() + "\"");
+ confFile.println("-\"" + negatives.get(i).getURI() + "\"");
try{
- Statement spo = model.getProperty(negatives.get(i), type);
+ Statement spo = model.getModel().getProperty(negatives.get(i), type);
resprint.get(spo.getResource()).println("-\"" + negatives.get(i).getURI() + "\"");
} catch (NullPointerException e) {
// What was the Object that probably caused the pain?
- System.err.println("Object probably not in our HashMap: " +
- model.getProperty(negatives.get(i), type).getResource());
- e.getStackTrace();
+ _logger.error("Object probably not in our HashMap: " +
+ model.getModel().getProperty(negatives.get(i), type).getResource());
+ e.printStackTrace();
}
-
- // System.out.println("Couldn't find AA: " + positives.get(i).getURI());
-
}
// Important - free up resources used running the query
- out.close();
+ confFile.close();
Iterator<Resource> newkeys = resprint.keySet().iterator();
while ( newkeys.hasNext() ){
@@ -805,143 +393,103 @@
}
catch (IOException e)
{
- System.err.println("OutputStream konnte nicht geschlossen werden!");
+ _logger.error("OutputStream konnte nicht geschlossen werden!");
}
}
- private static void createArffFile(String arffFilePath, PdbRdfModel model, TrainAndTestSet sets, ResIterator riter){
-
- String relation = "@RELATION ";
- for (int i = 0; i < sets.getTrainset().length ; i++){
- System.out.println("Element " + i + " = " + sets.getTrainset()[i].getPdbID());
- relation += sets.getTrainset()[i];
- }
-
- /*
- * ATTRIBUTES
- */
-
- // Integer declaring Position in chain
- String attrPosInChain = "@ATTRIBUTE position_in_chain NUMERIC\n";
- // Helix = 1 Other = 0
- String attrHelix = "@ATTRIBUTE in_helix NUMERIC\n";
- // Hydrophilic = 0 Hydrophobic = 1 Very_hydrophobic = 2
- String attrHydrophob = "@ATTRIBUTE hydrophob NUMERIC\n";
- // Negative = -1 Neutral = 0 Positive = 1
- String attrCharge = "@ATTRIBUTE charge NUMERIC\n";
- // Large = 2 Small = 1 Tiny = 0.5
- String attrSize = "@ATTRIBUTE size NUMERIC\n";
- // Aliphatic = 0 Aromatic = 1
- String attrAromaticity = "@ATTRIBUTE aromaticity NUMERIC\n";
- // Donor = 1 Donor/Acceptor = 0 Acceptor = -1
- String attrHydrogenbonding = "@ATTRIBUTE hydrogen_bonding NUMERIC\n";
-
- String attribute = attrPosInChain + attrHelix + attrHydrophob +
- attrCharge + attrSize + attrAromaticity + attrHydrogenbonding + "\n";
-
- String data = "@DATA\n";
-
- HashMap<Resource, String> resdata = new HashMap<Resource, String>(30);
- resdata.put(ala, new String("2,0,0.5,?,?\n"));
- resdata.put(cys, new String("1,0,1,?,0\n"));
- resdata.put(asp, new String("0,-1,1,?,-1\n"));
- resdata.put(glu, new String("0,-1,2,?,-1\n"));
- resdata.put(phe, new String("2,0,2,1,?\n"));
- resdata.put(gly, new String("2,0,0.5,?,?\n"));
- resdata.put(his, new String("1,1,2,1,1\n"));
- resdata.put(ile, new String("2,0,2,0,?\n"));
- resdata.put(lys, new String("1,1,2,?,1\n"));
- resdata.put(leu, new String("2,0,2,0,?\n"));
- resdata.put(met, new String("2,0,2,?,?\n"));
- resdata.put(asn, new String("0,0,1,?,0\n"));
- resdata.put(pro, new String("?,0,1,?,?\n"));
- resdata.put(gln, new String("0,0,2,?,0\n"));
- resdata.put(arg, new String("0,1,2,?,1\n"));
- resdata.put(ser, new String("0,0,0.5,?,0\n"));
- resdata.put(thr, new String("1,0,1,?,0,\n"));
- resdata.put(val, new String("2,0,1,0,?\n"));
- resdata.put(trp, new String("1,0,2,1,1\n"));
- resdata.put(tyr, new String("1,0,2,1,0\n"));
- resdata.put(sel, new String("?,?,?,?,\n"));
-
-
- // Properties i have 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");
-
- Property type = ResourceFactory.createProperty("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "type");
-
- // every element in riter stands for a AA-chain start
- // every first amino acid indicates a new AA-chain
- while (riter.hasNext())
- {
- // Initialization of variables needed
- int i = 0;
- Resource aaOne = riter.nextResource();
- Resource currentaa = aaOne;
- Resource nextaa = aaOne;
- boolean inHelix = false;
- System.out.println(currentaa.getURI());
- // look if there is a next AA
- do {
- ++i;
- System.out.print(i + " ");
- //looks weird, but is needed to enter loop even for the last AA which does not have a iib-Property
- currentaa = nextaa;
- NodeIterator resType = model.listObjectsOfProperty(currentaa,type);
+ private static void createArffFile(String pdbDir, PDBIdRdfModel model, ResIterator firstAAs){
+
+ try {
+ PDBProtein protein = model.getProtein();
+ String arffFilePath = pdbDir + protein.getArffFileName();
+ PrintStream out = new PrintStream (arffFilePath);
+ _logger.debug("Creating ARFF file: " + arffFilePath);
+
+ /*
+ * RELATION
+ */
+ String relation = "@RELATION " + protein.getPdbID();
+ out.println(relation);
+ _logger.debug(relation);
+
+ /*
+ * ATTRIBUTES
+ */
+ // Integer declaring Position in chain
+ String attributes = "@ATTRIBUTE hydrophob NUMERIC\n" + // Hydrophilic = 0; Hydrophobic = 1; Very_hydrophobic = 2
+ "@ATTRIBUTE charge NUMERIC\n" + // Negative = -1; Neutral = 0; Positive = 1
+ "@ATTRIBUTE size NUMERIC\n" + // Large = 2; Small = 1; Tiny = 0.5
+ "@ATTRIBUTE aromaticity NUMERIC\n" + // Aliphatic = 0; Aromatic = 1
+ "@ATTRIBUTE hydrogen_bonding NUMERIC\n"; // Donor = 1; Donor/Acceptor = 0; Acceptor = -1
+
+ for (int i = -8; i < 8; i++) {
+ attributes += "@ATTRIBUTE aa_position_" + i + " CLASS\n"; // amino acid at position $i from current amino acid
+ }
+ attributes += "@ATTRIBUTE in_helix NUMERIC\n"; // Helix = 1 Other = 0
+
+ _logger.debug(attributes);
+ out.println(attributes);
+
+ /*
+ * @DATA
+ */
+ String data = "@DATA\n";
+ _logger.debug(data);
+ out.println(data);
+
+ // HashMap containing information about the properties of every amino acid
+ HashMap<Resource, String> resdata = AminoAcids.getAminoAcidArffAttributeMap();
+ ArrayList<Resource> positives = model.getPositives();
+ ArrayList<Resource> negatives = model.getNegatives();
+ Property type = ResourceFactory.createProperty("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "type");
+ Property iib = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "isImmediatelyBefore");
+
+
+ while (firstAAs.hasNext()){
+ Resource firstAA = firstAAs.next();
+ Resource currentAA = firstAA;
+ Resource nextAA = firstAA;
- // die Guten ins Töpfchen ...
- // if we get an non-empty iterator for pdb:beginsAt the next AAs are within a AA-helix
- if(model.listResourcesWithProperty(ba, currentaa).hasNext() && !inHelix )
- {
- inHelix = true;
- }
- // die Schlechten ins Kröpfchen
- // if we get an non-empty iterator for pdb:endsAt and are already within a AA-helix
- // the AAs AFTER the current ones aren't within a helix
- if (model.listResourcesWithProperty(ea, currentaa).hasNext() && inHelix)
- {
- inHelix = false;
- }
- // get next AA if there is one
- if (model.listObjectsOfProperty(currentaa, iib).hasNext())
- {
- nextaa = model.getProperty(currentaa, iib).getResource();
- }
-
- // add current amino acid to positives or negatives set
- while(resType.hasNext())
- {
- Resource aaType = resType.next().asResource();
- System.out.println(aaType.getURI());
- if (resdata.get(aaType) != null)
- {
- if (inHelix)
- {
- data += i + "," + 1 + "," + resdata.get(aaType);
+ int i = 0;
+ String dataLine;
+ do {
+ dataLine = "";
+ currentAA = nextAA;
+
+ NodeIterator niter = model.getModel().listObjectsOfProperty(currentAA, type);
+ while (niter.hasNext()){
+ Resource key = niter.next().asResource();
+ if (resdata.containsKey(key)){
+ dataLine += resdata.get(key) +",";
}
- else
- {
- data += i + "," + 0 + "," + resdata.get(aaType);
+ }
+
+ for (int j = (i - 8...
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