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[DL-Learner SVN] SF.net SVN: dl-learner:[2799] trunk/scripts/src/main/java/org/dllearner/ examples/pdb
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From: <km...@us...> - 2011-05-12 15:41:52
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Revision: 2799
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=2799&view=rev
Author: kmpf
Date: 2011-05-12 15:41:41 +0000 (Thu, 12 May 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/PdbProtein.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 2011-05-12 14:17:45 UTC (rev 2798)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java 2011-05-12 15:41:41 UTC (rev 2799)
@@ -1,8 +1,11 @@
package org.dllearner.examples.pdb;
import java.io.File;
+import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.LineNumberReader;
import java.io.PrintStream;
import java.text.SimpleDateFormat;
@@ -71,10 +74,6 @@
private static ArrayList<Resource> positives;
private static ArrayList<Resource> negatives;
- public void setPositives(ArrayList<Resource> pos){
- positives = pos;
- }
-
public void setNegatives(ArrayList<Resource> neg){
negatives = neg;
}
@@ -91,22 +90,43 @@
private static HashMap<Resource, File> confFilePerResidue;
private static File confFileForAll;
+ public void setPositives(ArrayList<Resource> pos){
+ positives = pos;
+ }
+
/**
* @param args
* TODO: remove beginsAt, endsAt from model
*/
public static void main(String[] args) {
- Boolean test = true;
+ Boolean test = false;
+ Boolean rdfConf = true;
+ Boolean arff = false;
+ /*
+ * save: saves the whole trainset into the memory file
+ * load: loads the whole memory file into the trainset
+ */
+ Boolean save = true;
+ Boolean load = false;
+ File memory = new File(dataDir + "memory.txt");
+ Boolean dlLearn = false;
+ Boolean wekaLearn = false;
+
+
int dataSet = 1;
/*
- * get dataset files
+ * 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);
@@ -114,7 +134,7 @@
* data for test purpose
*/
String pdbID = "3LQH";
- String chainID = "";
+ String chainID = "A";
/*
* generate trainset and fill trainmodel
@@ -122,21 +142,29 @@
PdbRdfModel trainmodel = new PdbRdfModel();
TrainAndTestSet trainSet = new TrainAndTestSet();
- if (test)
+ if (test && !load )
{
trainSet = new TrainAndTestSet(pdbID, chainID);
}
- else
+
+ if ( !test && !load )
{
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;
- }
+ }
}
-
+ if(load && memory.canRead())
+ {
+ System.out.println("Hier!");
+ trainSet = new TrainAndTestSet(memory);
+ }
+
+
+
/*
* generate a PdbRdfModel for every pdbID
*/
@@ -145,6 +173,8 @@
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()));
@@ -153,7 +183,7 @@
* amino acid of every chain, they are returned within a ResIterator
*/
ResIterator niter = getFirstAA(trainmodel);
- ResIterator riter = niter;
+
/*
* we add some distance Information to our model
@@ -165,22 +195,19 @@
* global positives ArrayList, and all others in the global negatives ArrayList
*/
createPositivesAndNegatives(niter, trainmodel);
-
- SimpleDateFormat df = new SimpleDateFormat("_yyyy_MM_dd_HH_mm");
- String date = df.format(new Date());
String rdfFile;
String arffFile;
if (trainSet.getTrainset()[i].getChainID().length() == 0)
{
- rdfFile = trainSet.getTrainset()[i].getPdbID().toUpperCase() + date + ".rdf";
- arffFile = trainSet.getTrainset()[i].getPdbID().toUpperCase() + date + ".arff";
+ 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() + date + ".rdf";
+ + trainSet.getTrainset()[i].getChainID().toUpperCase() + ".rdf";
arffFile = trainSet.getTrainset()[i].getPdbID().toUpperCase() + "."
- + trainSet.getTrainset()[i].getChainID().toUpperCase() + date + ".arff";
+ + trainSet.getTrainset()[i].getChainID().toUpperCase() + ".arff";
}
String dir = dataDir + trainSet.getTrainset()[i].getPdbID() + "/";
File directory = new File(dir);
@@ -188,8 +215,16 @@
String rdfFilePath = dir + rdfFile;
String arffFilePath = dir + arffFile;
- createArffFile(arffFilePath, trainmodel, trainSet, riter);
/*
+ * if arff = true create pdbID.arff files
+ */
+ if (arff)
+ {
+ niter = getFirstAA(trainmodel);
+ createArffFile(arffFilePath, trainmodel, trainSet, niter);
+ }
+
+ /*
* remove all triples that contain information about begin and end of helices
*/
Property ba = ResourceFactory.createProperty("http://bio2rdf.org/pdb:", "beginsAt");
@@ -199,64 +234,104 @@
Resource residue = ResourceFactory.createResource("http://bio2rdf.org/pdb:Residue");
trainmodel = removeStatementsWithObject(trainmodel, residue);
+
+ /*
+ * 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(dir, rdfFile, trainmodel);
+ PrintStream out = new PrintStream (new File(rdfFilePath));
+
+ // Output results
+ trainmodel.write(out, "RDF/XML");
- try
- {
+ // Important - free up resources used running the query
+ out.close();
+ }
+ catch (IOException e)
+ {
+ System.err.println("OutputStream konnte nicht geschlossen werden!");
+ }
+ }
+
+ if(dlLearn)
+ {
+ File filename = confFileForAll;
+
/*
- * creatConfFile()
- * writes the conf-Files and saves there File-objects in:
- * confFileForAll and confFilePerResidue
- */
- createConfFile(dir, date, rdfFile, trainmodel);
- PrintStream out = new PrintStream (new File(rdfFilePath));
+ * 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());
+ }
+ }
+
+ if(wekaLearn)
+ {
- // 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!");
- }
-
+ }
}
- /*
- * 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);
- rc.init();
- */
- /*
- 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) {
+ if(save)
+ {
+ 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();
+ }
+ catch(FileNotFoundException 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());
+
}
- */
}
private static PdbRdfModel getRdfModelForIds(String pdbID ,String chainID) {
@@ -509,11 +584,11 @@
}
- private static void createConfFile(String dir, String date, String rdffile, PdbRdfModel model){
+ private static void createConfFile(String dir, String rdffile, PdbRdfModel model){
try
{
// the file with all amino acids
- String pdbname = dir + "pdb" + date + ".conf";
+ String pdbname = dir + "pdb" + ".conf";
confFileForAll = new File(pdbname);
PrintStream out = new PrintStream (confFileForAll);
// add import statements
@@ -522,27 +597,27 @@
out.println();
HashMap<Resource, File> resConfFiles = new HashMap<Resource, File>(30);
- resConfFiles.put(ala, new File(dir + ala.getLocalName() + date + ".conf"));
- resConfFiles.put(cys, new File(dir + cys.getLocalName() + date + ".conf"));
- resConfFiles.put(asp, new File(dir + asp.getLocalName() + date + ".conf"));
- resConfFiles.put(glu, new File(dir + glu.getLocalName() + date + ".conf"));
- resConfFiles.put(phe, new File(dir + phe.getLocalName() + date + ".conf"));
- resConfFiles.put(gly, new File(dir + gly.getLocalName() + date + ".conf"));
- resConfFiles.put(his, new File(dir + his.getLocalName() + date + ".conf"));
- resConfFiles.put(ile, new File(dir + ile.getLocalName() + date + ".conf"));
- resConfFiles.put(lys, new File(dir + lys.getLocalName() + date + ".conf"));
- resConfFiles.put(leu, new File(dir + leu.getLocalName() + date + ".conf"));
- resConfFiles.put(met, new File(dir + met.getLocalName() + date + ".conf"));
- resConfFiles.put(asn, new File(dir + asn.getLocalName() + date + ".conf"));
- resConfFiles.put(pro, new File(dir + pro.getLocalName() + date + ".conf"));
- resConfFiles.put(gln, new File(dir + gln.getLocalName() + date + ".conf"));
- resConfFiles.put(arg, new File(dir + arg.getLocalName() + date + ".conf"));
- resConfFiles.put(ser, new File(dir + ser.getLocalName() + date + ".conf"));
- resConfFiles.put(thr, new File(dir + thr.getLocalName() + date + ".conf"));
- resConfFiles.put(val, new File(dir + val.getLocalName() + date + ".conf"));
- resConfFiles.put(trp, new File(dir + trp.getLocalName() + date + ".conf"));
- resConfFiles.put(tyr, new File(dir + tyr.getLocalName() + date + ".conf"));
- resConfFiles.put(sel, new File(dir + sel.getLocalName() + date + ".conf"));
+ 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"));
confFilePerResidue = resConfFiles;
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/PdbProtein.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/PdbProtein.java 2011-05-12 14:17:45 UTC (rev 2798)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/PdbProtein.java 2011-05-12 15:41:41 UTC (rev 2799)
@@ -6,19 +6,25 @@
private String chainID;
private String species;
+ public PdbProtein() {
+ this("", "", "");
+ }
+
public PdbProtein(String pdbID) {
- this.pdbID = pdbID;
+ this(pdbID, "", "");
}
public PdbProtein(String pdbID, String chainID) {
+ this(pdbID, chainID, "");
+ }
+
+ public PdbProtein(String pdbID, String chainID, String species) {
this.pdbID = pdbID;
this.chainID = chainID;
+ this.species = species;
}
- public PdbProtein() {
- this.pdbID = "";
- this.chainID = "";
- }
+
public String getPdbID() {
return pdbID;
}
@@ -37,7 +43,4 @@
public void setSpecies(String species) {
this.species = species;
}
-
-
-
}
Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java 2011-05-12 14:17:45 UTC (rev 2798)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/TrainAndTestSet.java 2011-05-12 15:41:41 UTC (rev 2799)
@@ -22,7 +22,9 @@
public TrainAndTestSet () {
String pdbID = "";
- PdbProtein[] pdbProteins = {new PdbProtein(pdbID)};
+ String chainID = "";
+ String species = "";
+ PdbProtein[] pdbProteins = {new PdbProtein(pdbID, chainID, species)};
this.trainset = pdbProteins;
}
@@ -36,6 +38,11 @@
this.trainset = pdbProteins;
}
+ public TrainAndTestSet (String pdbID, String chainID, String species) {
+ PdbProtein[] pdbProteins = {new PdbProtein(pdbID, chainID, species)};
+ this.trainset = pdbProteins;
+ }
+
public TrainAndTestSet (String[] pdbIDs) {
PdbProtein pdbProt;
PdbProtein[] pdbProteins = new PdbProtein[pdbIDs.length];
@@ -85,20 +92,22 @@
try
{
LineNumberReader pdbproteins = new LineNumberReader(new FileReader(pdbIDlist));
- ArrayList<String> lines = this.readInFile(pdbproteins);
+ ArrayList<String> lines = this.readInFile(pdbproteins);
pdbproteins.close();
// get number of lines
int linenr = lines.size();
+ System.out.println("File "+ pdbIDlist.getCanonicalPath() + " has " + linenr + " lines.");
PdbProtein[] proteins = new PdbProtein[linenr];
for (int i = 0; i < linenr; i++)
{
- proteins[i].setPdbID(getpdbid(i, lines));
- proteins[i].setChainID(getChainID(i, lines));
+ System.out.println("LINES element " + i + " contains " + lines.get(i));
+ proteins[i] = new PdbProtein(getPdbID(i, lines), getChainID(i, lines), getSpecies(i, lines));
}
this.trainset = proteins;
}
catch (IOException e)
{
+ System.err.println("File " + pdbIDlist.getAbsolutePath() + " could not be read in!");
// TODO Auto-generated catch block
e.printStackTrace();
}
@@ -133,26 +142,34 @@
while (setmap.containsKey(Integer.valueOf(lnr))) {
lnr = gen.nextInt(linenr);
}
- set[i].setPdbID(this.getpdbid(lnr, lines));
+ set[i].setPdbID(this.getPdbID(lnr, lines));
setmap.put(Integer.valueOf(lnr), set[i].getPdbID());
}
return set;
}
- private String getpdbid (int lineNumber, ArrayList<String> lines ) {
+ private String getPdbID (int lineNumber, ArrayList<String> lines ) {
// Initialize a LineNumberReader
String line =(String) lines.get(lineNumber);
- String pdb_id = line.substring(0, 4);
- return pdb_id;
+ String pdbID;
+ if ( line.length() >= 4 )
+ {
+ pdbID = line.substring(0, line.indexOf("."));
+ }
+ else
+ {
+ pdbID = "";
+ }
+ return pdbID;
}
private String getChainID (int lineNumber, ArrayList<String> lines) {
String line =(String) lines.get(lineNumber);
String chainID;
- if (line.length() > 4)
+ if (line.contains(".") )
{
- chainID = line.substring(5, 7);
+ chainID = line.substring(line.indexOf(".") + 1, line.lastIndexOf("."));
}
else
{
@@ -160,4 +177,18 @@
}
return chainID;
}
+
+ private String getSpecies (int lineNumber, ArrayList<String> lines) {
+ String line =(String) lines.get(lineNumber);
+ String species;
+ if (line.length() > 6)
+ {
+ species = line.substring(line.lastIndexOf("."));
+ }
+ else
+ {
+ species = "";
+ }
+ return species;
+ }
}
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