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[DL-Learner SVN] SF.net SVN: dl-learner:[2927] trunk/scripts/src/main/java/org/dllearner/ examples/pdb
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From: <km...@us...> - 2011-06-23 08:48:25
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Revision: 2927
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2927&view=rev
Author: kmpf
Date: 2011-06-23 08:48:18 +0000 (Thu, 23 Jun 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
Added Paths:
-----------
trunk/scripts/src/main/java/org/dllearner/examples/pdb/ArffFileFilter.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/DirectoryFileFilter.java
trunk/scripts/src/main/java/org/dllearner/examples/pdb/RdfFileFilter.java
Added: trunk/scripts/src/main/java/org/dllearner/examples/pdb/ArffFileFilter.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/ArffFileFilter.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/ArffFileFilter.java 2011-06-23 08:48:18 UTC (rev 2927)
@@ -0,0 +1,14 @@
+package org.dllearner.examples.pdb;
+
+import java.io.File;
+import java.io.FileFilter;
+
+public class ArffFileFilter implements FileFilter
+{
+ private final String extension = new String("arff");
+
+ public boolean accept(File file)
+ {
+ return file.getName().toLowerCase().endsWith(extension);
+ }
+}
\ No newline at end of file
Added: trunk/scripts/src/main/java/org/dllearner/examples/pdb/DirectoryFileFilter.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/DirectoryFileFilter.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/DirectoryFileFilter.java 2011-06-23 08:48:18 UTC (rev 2927)
@@ -0,0 +1,17 @@
+package org.dllearner.examples.pdb;
+
+import java.io.File;
+import java.io.FileFilter;
+
+public class DirectoryFileFilter implements FileFilter
+{
+ public boolean accept(File file)
+ {
+ if (file.isDirectory() && file.getName().length() == 4 && !file.getName().startsWith(".")) {
+ return true;
+ }
+ else {
+ return false;
+ }
+ }
+}
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-06-23 08:17:44 UTC (rev 2926)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-06-23 08:48:18 UTC (rev 2927)
@@ -3,6 +3,7 @@
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;
@@ -75,6 +76,7 @@
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 ArrayList<Resource> positives;
private static ArrayList<Resource> negatives;
@@ -104,16 +106,26 @@
* TODO: remove beginsAt, endsAt from model
*/
public static void main(String[] args) {
- Boolean test = false;
+ /*
+ * 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;
/*
- * save: saves the whole trainset into the memory file
- * load: loads the whole memory file into the trainset
+ * load = true -> load alle .rdf, .conf and .arff Files that can be found within the directory dataDir
+ * load = false -> don't load anything
*/
- Boolean save = true;
- Boolean load = false;
- String savePdbInfos = ".info";
+ Boolean load = true;
Boolean dlLearn = false;
Boolean wekaLearn = false;
@@ -137,57 +149,65 @@
/*
* data for test purpose
*/
- String pdbID = "3LQH";
+ String pdbID = "1XFF";
String chainID = "A";
+ File dir = new File(dataDir);
/*
* generate trainset and fill trainmodel
*/
PdbRdfModel trainmodel = new PdbRdfModel();
TrainAndTestSet trainSet = new TrainAndTestSet();
- String pdbIdInfo = "";
- String bt426Info = "";
- String plp273Info = "";
- String plp364Info = "";
- String plp399Info = "";
-
- if (test && !load )
- {
- trainSet = new TrainAndTestSet(pdbID, chainID);
- pdbIdInfo = dataDir + pdbID + savePdbInfos;
- }
- if ( !test && !load )
+ if ( !test )
{
switch (dataSet) {
case 1:
trainSet = new TrainAndTestSet(bt426List);
- bt426Info = dataDir + bt426 + savePdbInfos;
break;
case 2:
trainSet = new TrainAndTestSet(plp273List);
- plp273Info = dataDir + plp273 + savePdbInfos;
break;
case 3:
trainSet = new TrainAndTestSet(plp364List);
- plp364Info = dataDir + plp364 + savePdbInfos;
break;
case 4:
trainSet = new TrainAndTestSet(plp399List);
- plp399Info = dataDir + plp399 + savePdbInfos;
break;
}
}
- File memory = new File(savePdbInfos);
- File bt426InfoFile = new File(bt426Info);
- File plp273InfoFile = new File(plp273Info);
- File plp364InfoFile = new File(plp364Info);
- File plp399InfoFile = new File(plp399Info);
+ else
+ {
+ trainSet = new TrainAndTestSet(pdbID, chainID);
+ }
+
+ HashMap<String,File> rdfFiles = new HashMap<String,File>();
+ HashMap<String,File> arffFiles = new HashMap<String,File>();
- if(load && memory.canRead())
+ if (load)
{
- System.out.println("Hier!");
- trainSet = new TrainAndTestSet(memory);
+ 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() );
+ }
+ }
}
@@ -197,17 +217,19 @@
*/
+
+
for (int i = 0; i < trainSet.getTrainset().length; i++)
{
- String[] pdbIDs = {trainSet.getTrainset()[i].getPdbID()};
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
@@ -215,9 +237,8 @@
*/
ResIterator niter = getFirstAA(trainmodel);
-
/*
- * we add some distance Information to our model
+ * we add the information of which amino acid is the fourth predecessor of which other amino acid
*/
trainmodel = addDistanceInfo(trainmodel);
@@ -240,11 +261,11 @@
arffFile = trainSet.getTrainset()[i].getPdbID().toUpperCase() + "."
+ trainSet.getTrainset()[i].getChainID().toUpperCase() + ".arff";
}
- String dir = dataDir + trainSet.getTrainset()[i].getPdbID() + "/";
- File directory = new File(dir);
+ String pdbDir = dataDir + trainSet.getTrainset()[i].getPdbID() + "/";
+ File directory = new File(pdbDir);
directory.mkdir();
- String rdfFilePath = dir + rdfFile;
- String arffFilePath = dir + arffFile;
+ String rdfFilePath = pdbDir + rdfFile;
+ String arffFilePath = pdbDir + arffFile;
/*
* if arff = true create pdbID.arff files
@@ -256,18 +277,6 @@
}
/*
- * remove all triples that contain information about begin and end of helices
- */
-
- Property ba = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "beginsAt");
- trainmodel = removeStatementsWithPoperty(trainmodel, ba);
- Property ea = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "endsAt");
- trainmodel = removeStatementsWithPoperty(trainmodel, ea);
- Resource residue = ResourceFactory.createResource("http://bio2rdf.org/pdb:Residue");
- trainmodel = removeStatementsWithObject(trainmodel, residue);
-
-
- /*
* if rdfConf = true create pdbID.rdf and *.conf files
*/
if(rdfConf)
@@ -279,7 +288,7 @@
* writes the conf-Files and saves there File-objects in:
* confFileForAll and confFilePerResidue
*/
- createConfFile(dir, rdfFile, trainmodel);
+ createConfFile(pdbDir, rdfFile, trainmodel);
PrintStream out = new PrintStream (new File(rdfFilePath));
// Output results
@@ -293,77 +302,86 @@
System.err.println("OutputStream konnte nicht geschlossen werden!");
}
}
+ /*
+ * remove all triples that contain information about begin and end of helices
+ */
- if(dlLearn)
- {
- File filename = confFileForAll;
-
- /*
- * 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);
+ 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()) {
try {
- rc.init();
- } catch (ComponentInitException e1) {
- e1.printStackTrace();
+ FileWriter out = new FileWriter(proteinsOfSpecies.get(trainSet.getTrainset()[i].getSpecies()), true);
+ String line = trainSet.getTrainset()[i].getPdbID() + "."
+ + trainSet.getTrainset()[i].getChainID() + ".\n";
+ out.write(line);
+ out.close();
+ } catch (FileNotFoundException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.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());
- }
- */
- }
-
- if(wekaLearn)
- {
}
}
- if(save)
+ if(dlLearn)
{
- String infos = "";
- for(int i=0; i < trainSet.getTrainset().length; i++)
- {
- infos = trainSet.getTrainset()[i].getPdbID() + "." +
- trainSet.getTrainset()[i].getChainID() + "." +
- trainSet.getTrainset()[i].getSpecies();
- if(i != trainSet.getTrainset().length - 1)
- {
- infos += "\n";
- }
- }
+
- try
- {
- PrintStream out = new PrintStream (memory);
- out.println(infos);
- out.close();
+ /*
+ * 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();
}
- catch(FileNotFoundException e)
- {
- e.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());
}
+ */
+ }
+ if(wekaLearn)
+ {
}
}
@@ -700,6 +718,7 @@
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;
Added: trunk/scripts/src/main/java/org/dllearner/examples/pdb/RdfFileFilter.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/RdfFileFilter.java (rev 0)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/RdfFileFilter.java 2011-06-23 08:48:18 UTC (rev 2927)
@@ -0,0 +1,15 @@
+package org.dllearner.examples.pdb;
+
+import java.io.File;
+import java.io.FileFilter;
+
+public class RdfFileFilter implements FileFilter
+{
+ private final String extension = new String("rdf");
+
+ public boolean accept(File file)
+ {
+ return file.getName().toLowerCase().endsWith(extension);
+ }
+}
+
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java 2011-06-23 08:17:44 UTC (rev 2926)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java 2011-06-23 08:48:18 UTC (rev 2927)
@@ -148,6 +148,10 @@
return set;
}
+ private String[] pdbEntry(int linenr, ArrayList<String> lines){
+ String line =(String) lines.get(linenr);
+ return line.split("\t");
+ }
private String getPdbID (int lineNumber, ArrayList<String> lines ) {
// Initialize a LineNumberReader
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