new package for weka libio. And tests

git-svn-id: https://cdk.svn.sourceforge.net/svnroot/cdk/trunk/cdk@6317 eb4e18e3-b210-0410-a6ab-dec725e4b171

build.xml

@@ -593,6 +593,7 @@
             <antcall target="compile-module"><param name="module" value="extra"/></antcall>
             <antcall target="compile-module"><param name="module" value="smiles"/></antcall>
             <antcall target="compile-module"><param name="module" value="libio-cml"/></antcall>
+        	<antcall target="compile-module"><param name="module" value="libio-weka"/></antcall>
             <antcall target="compile-module"><param name="module" value="pdb-cml"/></antcall>
             <antcall target="compile-module"><param name="module" value="reaction"/></antcall>
     	    <antcall target="compile-module"><param name="module" value="charges"/></antcall>
@@ -616,6 +617,7 @@
         <antcall target="compile-module"><param name="module" value="test-io"/></antcall>
         <antcall target="compile-module"><param name="module" value="test-extra"/></antcall>
         <antcall target="compile-module"><param name="module" value="test-smiles"/></antcall>
+        <antcall target="compile-module"><param name="module" value="test-libio-weka"/></antcall>
         <antcall target="compile-module"><param name="module" value="test-reaction"/></antcall>
         <antcall target="compile-module"><param name="module" value="test-forcefield"/></antcall>
         <antcall target="compile-module"><param name="module" value="test-valencycheck"/></antcall>
@@ -644,6 +646,7 @@
                     <includesfile name="${metainf}/io-jmol.libdepends"/>
                     <includesfile name="${metainf}/io.libdepends"/>
                     <includesfile name="${metainf}/libio-cml.libdepends"/>
+                    <includesfile name="${metainf}/libio-weka.libdepends"/>
                     <includesfile name="${metainf}/nonotify.libdepends"/>
                     <includesfile name="${metainf}/pdb-cml.libdepends"/>
                     <includesfile name="${metainf}/pdb.libdepends"/>
@@ -675,6 +678,7 @@
                     <include name="cdk-qsar.jar"/>
                     <include name="cdk-qsar-cml.jar"/>
                     <include name="cdk-qsar-pdb.jar"/>
+                    <include name="cdk-libio-weka.jar"/>
                     <include name="cdk-reaction.jar"/>
                     <include name="cdk-render.jar"/>
                     <include name="cdk-standard.jar"/>
@@ -854,7 +858,8 @@
             <antcall target="test-module"><param name="module" value="forcefield"/></antcall> 
 	        <antcall target="test-module"><param name="module" value="extra"/></antcall>
         	<antcall target="test-module"><param name="module" value="valencycheck"/></antcall> 
-        	<antcall target="test-module"><param name="module" value="reaction"/></antcall> 
+        	<antcall target="test-module"><param name="module" value="reaction"/></antcall>  
+        	<antcall target="test-module"><param name="module" value="libio-weka"/></antcall>
             <antcall target="test-module"><param name="module" value="smiles"/></antcall> 
         	<antcall target="test-module"><param name="module" value="experimental"/></antcall> 
         	<antcall target="test-module"><param name="module" value="qsar"/></antcall> 

src/META-INF/libio-weka.cdkdepends

@@ -0,0 +1,2 @@
+
+

src/META-INF/libio-weka.datafiles

@@ -0,0 +1 @@
+data/arff/**

src/META-INF/libio-weka.libdepends

@@ -0,0 +1,2 @@
+weka.jar
+

src/META-INF/test-libio-weka.cdkdepends

@@ -0,0 +1,4 @@
+cdk-core.jar
+cdk-data.jar
+cdk-libio-weka.jar
+cdk-test-core.jar

src/META-INF/test-libio-weka.datafiles

@@ -0,0 +1 @@
+data/arff/**

src/META-INF/test-libio-weka.devellibdepends

@@ -0,0 +1,2 @@
+junit.jar
+

src/META-INF/test-libio-weka.libdepends

@@ -0,0 +1,2 @@
+weka.jar
+

src/data/arff/Table1.arff

@@ -0,0 +1,27 @@
+@relation 'table1' 
+@attribute 'EffectivePolarizabilityDescriptor' real 
+@attribute 'SigmaElectronegativityDescriptor' real 
+@attribute 'ProtonTotalPartialChargeDescriptor' real
+@attribute 'predicted valency' real  
+@data 
+0.39 ,   9.62 ,  -0.15 ,12.74,   
+1.64 ,   9.77 ,  -0.13 ,11.3 ,   
+1.06 ,  12.56 ,  -0.16 ,13.0 ,   
+1.26 ,  10.51 ,  -0.05 ,12.6 ,   
+1.45 ,  10.15 ,  -0.09 ,11.9 ,   
+2.27 ,   9.8  ,  -0.13 ,11.01,   
+1.89 ,  10.54 ,  -0.05 ,12.5 ,   
+1.06 ,  10.15 ,   0.01 ,12.9 ,   
+2.59 ,   9.81 ,  -0.13 ,10.88,   
+2.74 ,   9.81 ,  -0.13 ,10.84,   
+2.79 ,   9.85 ,  -0.12 ,11.21,   
+0.39 ,   9.14 ,  -0.11 ,11.67,   
+1.64 ,   9.28 ,  -0.1  ,10.53,   
+1.06 ,  10.34 ,   0.03 ,12.0 ,   
+1.06 ,  10.15 ,   0.01 ,11.83,   
+2.27 ,   9.31 ,  -0.09 ,10.28,   
+2.59 ,   9.31 ,  -0.09 ,10.18,   
+2.74 ,   9.31 ,  -0.09 ,10.15,   
+2.79 ,   9.35 ,  -0.09 ,10.43,   
+0.39 ,   9.06 ,  -0.11 ,10.38,   
+1.64 ,   9.2  ,  -0.09 ,9.5 ,   

src/data/arff/Table2.arff

@@ -0,0 +1,7 @@
+@relation 'table1' 
+@attribute 'EffectivePolarizabilityDescriptor' real 
+@attribute 'SigmaElectronegativityDescriptor' real 
+@attribute 'ProtonTotalPartialChargeDescriptor' real  
+@attribute 'ProtonTotalPa' real
+@data 
+0.39 ,   9.06 ,  -0.11,0.0

src/org/openscience/cdk/libio/weka/Weka.java

@@ -0,0 +1,226 @@
+/* $RCSfile$
+ * $Author: egonw $ 
+ * $Date: 2006-05-01 10:43:42 +0200 (Mo, 01 Mai 2006) $
+ * $Revision: 6095 $
+ * 
+ * Copyright (C) 2003-2006  The Chemistry Development Kit (CDK) project
+ * 
+ * Contact: cdk-devel@lists.sourceforge.net
+ *
+ *  This library is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU Lesser General Public
+ *  License as published by the Free Software Foundation; either
+ *  version 2.1 of the License, or (at your option) any later version.
+ *
+ *  This library is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *  Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public
+ *  License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.libio.weka;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.StringReader;
+
+import weka.classifiers.Classifier;
+import weka.core.Instance;
+import weka.core.Instances;
+
+
+/**
+ * <p>Weka class is a library which use the program WEKA: a Machine Learning Project.</p>
+ * To inizalizate weka class is typically done like: <pre>
+ *  Classifier lr = new LinearRegression(); 
+ *  weka.setDataset("/some/where/dataTraining.arff", lr);
+ *  String testARFF = "/some/where/dataTest.arff";
+ *  double[] result = weka.getPrediction(testARFF);
+ *  </pre>
+ *  You have also the possibility to introduce directly values, done like:
+ *  <pre>
+ *  Classifier lr = new LinearRegression();
+ *   String[] attrib = {"aX","bX","cX","PY" };
+ *   int[] typAttrib = {Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC, };
+ *   double[][] x = {{0.39,9.62 ,-0.15 },
+ *                   {1.64,9.77 ,-0.13},
+ *                   {1.06,12.56,-0.16},
+ *   double[] y = {12.74,11.3 ,13.0};
+ *  weka.setDataset(attrib, typAttrib, y, x, lr);
+ *  double[] testX = {0.39,9.06,-0.11};
+ *  double resultY = weka.getPrediction(testX);
+ *  </pre>
+ * @author      Miguel Rojas
+ * @cdk.created 2006-05-23
+ * @cdk.module  libio-weka
+ * @cdk.keyword   weka,Machine Learning
+ * @cdk.depends   weka.jar
+ */
+public class Weka {
+
+	public static final int NUMERIC = 0;
+	public static final int NOMINAL = 1;
+
+	/** type of classifier*/
+	private Classifier classifier;
+
+	private Instances labeled;
+	/**
+     * Constructor of the Weka
+     */
+    public Weka() {
+    }
+    /**
+     * Set the file format arff to analize which contains the dataset and the type of classifier
+     *  
+     * @param setDataset  Path of the dataset file format arff to train
+     * @param classifier  Type of Classifier
+     * @return            The Instances value
+     * @throws Exception 
+     */
+    public Instances setDataset(String pathTable, Classifier classifier) throws Exception{
+    	this.classifier = classifier;
+    	InputStream ins = this.getClass().getClassLoader().getResourceAsStream(pathTable);
+    	Reader insr = new InputStreamReader(ins);
+        Instances instances = new Instances(new BufferedReader(insr));
+		instances.setClassIndex(instances.numAttributes() - 1);
+
+		labeled = new Instances(instances);
+		classifier.buildClassifier(labeled);
+
+		for (int i = 0; i < instances.numInstances(); i++) {
+		  double clsLabel = classifier.classifyInstance(instances.instance(i));
+		  labeled.instance(i).setClassValue(clsLabel);
+		}
+		return labeled;
+    }
+    /**
+     * 
+     * Set the array which contains the dataset and the type of classifier. This method
+     * will be used for classifier which work with numerical values.
+     *  
+     * @param attrib      String with the attribut names
+     * @param typAttrib   Attribute type: NUMERICAL or NOMINAL. 
+     * @param x           An array of independent variables. The observations should be in the rows
+     *                    and the variables should be in the columns
+     * @param y           An array containing the dependent variable. It is possible numeric or string.
+     * @param classifier  Type of Classifier
+     * @return            The Instances value
+     * @throws Exception
+     */
+    public Instances setDataset(String[] attrib, int[] typAttrib, Object[]y, double[][] x, Classifier classifier) throws Exception{
+    	return setDataset(attrib, typAttrib ,null,y,x,classifier);
+    }
+    /**
+     * 
+     * Set the array which contains the dataset and the type of classifier.This method
+     * will be used for classifier which work with String values.
+     *  
+     * @param attrib      String with the attribut names.
+     * @param typAttrib   Attribute type: NUMERICAL or NOMINAL.
+     * @param classAttrib String with the attribut class.
+     * @param x           An array of independent variables. The observations should be in the rows
+     *                    and the variables should be in the columns
+     * @param y           An array containing the dependent variable. It is possible numeric or string.
+     * @param classifier  Type of classifier
+     * @return            The Instances value
+     * @throws Exception
+     */
+    public Instances setDataset(String[] attrib, int[] typAttrib, String[] classAttrib, Object[]y, double[][] x, Classifier classifier) throws Exception{
+    	this.classifier = classifier;
+    	Reader reader = createAttributes(attrib,typAttrib,classAttrib,y,x);
+    	Instances instances = new Instances(reader);
+    	instances.setClassIndex(instances.numAttributes() - 1);
+		labeled = new Instances(instances);
+		classifier.buildClassifier(labeled);
+
+		for (int i = 0; i < instances.numInstances(); i++) {
+		  double clsLabel = classifier.classifyInstance(instances.instance(i));
+		  labeled.instance(i).setClassValue(clsLabel);
+		}
+    		return labeled;
+    }
+    /**
+     * Return of the predicted value
+     *  
+     * @param value   An array of independent variables which contians the values with whose to test
+     * @return	      Result of the prediction
+     * @throws Exception 
+     */
+    public double getPrediction(double[] value) throws Exception{
+    	Instance instance = new Instance(labeled.numAttributes());
+    	instance.setDataset(labeled);
+    	for(int i = 0 ; i < value.length ; i++)
+        	instance.setValue(i, value[i]);
+//    	instance.setValue(value.length, 0.0);
+		return classifier.classifyInstance(instance);
+    }
+    /**
+     * Return of the predicted value
+     *  
+     * @param pathARRF  path of the file format arff which contians the values with whose to test.
+     * @return	        Result of the prediction.
+     * @throws Exception 
+     */
+    public double[] getPrediction(String pathARFF) throws Exception{
+    	InputStream ins = this.getClass().getClassLoader().getResourceAsStream(pathARFF);
+    	Reader insr = new InputStreamReader(ins);
+        Instances test = new Instances(new BufferedReader(insr));
+    	double[] result = new double[test.numInstances()];
+    	for(int i = 0 ; i < test.numInstances(); i++){
+    		result[i] = classifier.classifyInstance(test.instance(i));
+    	}
+		return result;
+    }
+    /**
+     * create a Reader with necessary attributes to iniziate a Instances for weka.
+     * 
+     * @param attrib      String with the attribut class
+     * @param typAttrib   Attribute type: NOMINAL or NUMERIC.
+     * @param y           An array containing the independent variable. 
+     * @param x           An array of dependent variables.
+     * @return            The Reader containing the attributes
+     * @throws IOException
+     */
+    private Reader createAttributes(String[] attrib, int[] typAttrib, String[] classAttrib, Object[]y, double[][] x) throws IOException{
+    	String string ="@relation table1 \n";
+    	for(int i = 0; i < attrib.length ; i++){
+    		string += ("@attribute "+attrib[i]);
+    		if(typAttrib[i] == NUMERIC)
+    			string += " numeric \n";
+    		else if(typAttrib[i] == NOMINAL)
+    			string += " string \n";
+    	}
+
+    	if(classAttrib != null){
+	    	string += "@attribute class ";
+	    	string += "{";
+	    	for(int i = 0; i < classAttrib.length ; i++){
+	    		string += (classAttrib[i]);
+	    		if(i != classAttrib.length -1)
+	    			string += ",";
+	    	}
+	    	string += "}\n";
+	    	}
+
+    	string += ("@data ");
+    	if(x != null && y != null){
+    		for(int j = 0 ; j < x.length; j++){
+    	    	for(int i = 0 ; i < x[0].length ; i++){
+    	    		string += x[j][i]+",";
+    	    	}
+   	    		string += y[j]+", \n";
+    		}
+    	}
+
+
+    	Reader reader = new StringReader(string);
+    	return reader;
+    }
+}