entities.WekaNGGFeatureVector.java Source code

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Here is the source code for entities.WekaNGGFeatureVector.java

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package entities;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import weka.core.Attribute;
import weka.core.DenseInstance;
import weka.core.Instance;
import weka.core.Instances;
import weka.core.converters.ArffSaver;

/**
 *
 * @author nikos
 */
public class WekaNGGFeatureVector implements WekaFeatureVector {

    @Override
    public ArrayList<Attribute> initializeWekaFeatureVector() {
        //Declaration of the numeric value dMaxProb
        Attribute Attribute1 = new Attribute("containmentSimilarity1");
        Attribute Attribute2 = new Attribute("sizeSimilarity1");
        Attribute Attribute3 = new Attribute("valueSimilarity1");
        Attribute Attribute4 = new Attribute("nvsSimilarity1");
        Attribute Attribute5 = new Attribute("containmentSimilarity2");
        Attribute Attribute6 = new Attribute("sizeSimilarity2");
        Attribute Attribute7 = new Attribute("valueSimilarity2");
        Attribute Attribute8 = new Attribute("nvsSimilarity2");
        //Declare the class attribute along with its values
        ArrayList<String> fvClassVal = new ArrayList<>();
        fvClassVal.add("Nucleosome Free Region");
        fvClassVal.add("Nucleosome Binding Site");
        Attribute ClassAttribute = new Attribute("theClass", fvClassVal);

        //Declare the feature vector
        ArrayList<Attribute> fvWekaAttributesNgg;
        fvWekaAttributesNgg = new ArrayList<>();
        fvWekaAttributesNgg.add(Attribute1);
        fvWekaAttributesNgg.add(Attribute2);
        fvWekaAttributesNgg.add(Attribute3);
        fvWekaAttributesNgg.add(Attribute4);
        fvWekaAttributesNgg.add(Attribute5);
        fvWekaAttributesNgg.add(Attribute6);
        fvWekaAttributesNgg.add(Attribute7);
        fvWekaAttributesNgg.add(Attribute8);
        fvWekaAttributesNgg.add(ClassAttribute);

        return fvWekaAttributesNgg;
    }

    public Instance fillFeatureVector(NGGFeatureVector vSource, Instances data) {

        double[] values = new double[data.numAttributes()];

        values[0] = vSource.getContainmentSimilarityArrayAtIndex(0);
        values[1] = vSource.getSizeSimilarityArrayAtIndex(0);
        values[2] = vSource.getValueSimilarityArrayAtIndex(0);
        values[3] = vSource.getNVSArrayAtIndex(0);
        values[4] = vSource.getContainmentSimilarityArrayAtIndex(1);
        values[5] = vSource.getSizeSimilarityArrayAtIndex(1);
        values[6] = vSource.getValueSimilarityArrayAtIndex(1);
        values[7] = vSource.getNVSArrayAtIndex(1);
        values[8] = data.attribute(8).indexOfValue(vSource.getLabel());

        Instance inst = new DenseInstance(1.0, values);

        return inst;
    }

    public Instances fillInstanceSet(ArrayList<NGGFeatureVector> vList, ArrayList<NGGFeatureVector> vList2,
            String datasetType) throws IOException {
        ArrayList<Attribute> attributes = initializeWekaFeatureVector();
        Instances isSet = new Instances(vList.get(0).getLabel(), attributes, vList.size());

        isSet.setClassIndex(isSet.numAttributes() - 1);

        for (NGGFeatureVector NGGv : vList) {

            Instance i = fillFeatureVector(NGGv, isSet);

            isSet.add(i);
        }

        for (NGGFeatureVector NGGv : vList2) {

            Instance i = fillFeatureVector(NGGv, isSet);

            isSet.add(i);
        }

        ArffSaver saver = new ArffSaver();
        saver.setInstances(isSet);
        saver.setFile(new File("./data/" + datasetType + ".arff"));
        saver.writeBatch();

        return isSet;
    }

}