[DL-Learner SVN] SF.net SVN: dl-learner:[3327] trunk/scripts/src/main/java/org/dllearner/ examples/pdb

[<km...@us...>]

Revision: 3327
          http://dl-learner.svn.sourceforge.net/dl-learner/?rev=3327&view=rev
Author:   kmpf
Date:     2011-10-26 14:34:10 +0000 (Wed, 26 Oct 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/PDBWekaLearner.java

Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java	2011-10-26 13:48:52 UTC (rev 3326)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/HelixRDFCreator.java	2011-10-26 14:34:10 UTC (rev 3327)
@@ -415,8 +415,8 @@
 					"@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
+			for (int i = -8; i <= 8; i++) {
+				attributes += "@ATTRIBUTE aa_position_" + i + " {A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y}\n"; // amino acid at position $i from current amino acid
 			}
 			attributes += "@ATTRIBUTE in_helix NUMERIC\n"; // Helix = 1 Other = 0
 					

Modified: trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java
===================================================================
--- trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java	2011-10-26 13:48:52 UTC (rev 3326)
+++ trunk/scripts/src/main/java/org/dllearner/examples/pdb/PDBWekaLearner.java	2011-10-26 14:34:10 UTC (rev 3327)
@@ -3,7 +3,6 @@
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
-import java.util.List;
 import java.util.Random;
 
 import org.apache.log4j.ConsoleAppender;
@@ -11,18 +10,19 @@
 import org.apache.log4j.Level;
 import org.apache.log4j.Logger;
 import org.apache.log4j.SimpleLayout;
-
+/*
 import weka.classifiers.Evaluation;
-import weka.classifiers.trees.J48;
+import weka.classifiers.bayes.NaiveBayes;
 import weka.core.Instances;
 import weka.core.converters.ConverterUtils.DataSource;
+*/
 
 public class PDBWekaLearner {
 	
 	private static Logger logger = Logger.getRootLogger();
 	
 	public PDBWekaLearner (File arffFile) throws IOException{
-		
+		/*
 		// create logger (configure this to your needs)
 		SimpleLayout layout = new SimpleLayout();
 		FileAppender fileAppender = new FileAppender(layout, "log/sample_log.txt", false);
@@ -42,13 +42,13 @@
 			 if (data.classIndex() == -1)
 			   data.setClassIndex(data.numAttributes() - 1);
 			 
-			 String[] options = new String[1];
-			 options[0] = "-U";            // unpruned tree
-			 J48 tree = new J48();         // new instance of tree
-			 tree.setOptions(options);     // set the options
-			 //tree.buildClassifier(data);   // build classifier
+			 // String[] options = new String[0];
+			 
+			 NaiveBayes classifier = new NaiveBayes();         // new instance of tree
+			 // classifier.setOptions(options);     // set the options
+			 classifier.buildClassifier(data);   // build classifier
 			 Evaluation eval = new Evaluation(data);
-			 eval.crossValidateModel(tree, data, 10, new Random(1));
+			 eval.crossValidateModel(classifier, data, 10, new Random(1));
 			 
 			 // gather the results of the evaluation process
 	        String resultsFileName = arffFile.getPath().replace(".arff", ".weka.res");
@@ -70,5 +70,6 @@
 		} catch (Exception e){
 			e.printStackTrace();
 		}
+		*/
 	}
 }

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