sirius.nnsearcher.main.Constraints.java Source code

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Here is the source code for sirius.nnsearcher.main.Constraints.java

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/*==========================================================================
 SiriusPSB - A Generic System for Analysis of Biological Sequences
       http://compbio.ddns.comp.nus.edu.sg/~sirius/index.php
============================================================================
 Copyright (C) 2007 by Chuan Hock Koh
       
 This program is free software; you can redistribute it and/or
 modify it under the terms of the GNU General Public
 License as published by the Free Software Foundation; either
 version 3 of the License, or (at your option) any later version.
       
 This program 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
 General Public License for more details.
        
 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>.
==========================================================================*/
package sirius.nnsearcher.main;

import java.io.Serializable;
import java.util.Enumeration;

import sirius.main.ApplicationData;
import sirius.trainer.features.Feature;
import sirius.trainer.features.GenerateFeatures;
import sirius.utils.FastaFormat;
import weka.core.Attribute;

public class Constraints implements Serializable {
    static final long serialVersionUID = sirius.Sirius.version;

    private Feature featureData;
    /*
     * 0) >= 
     * 1) >
     * 2) ==
     * 3) !=
     * 4) <=
     * 5) <      
     */
    private int operator;
    private double value;
    private Attribute attributeName;
    private int index;

    public Constraints(Feature featureData, int operator, double value) {
        this.featureData = featureData;
        this.operator = operator;
        this.value = value;
        this.attributeName = new Attribute(featureData.getName());
        this.index = -1;
    }

    public Feature getStep2FeatureData() {
        return this.featureData;
    }

    public double getValue() {
        return this.value;
    }

    public int getOperator() {
        return this.operator;
    }

    public String getOperatorString() {
        switch (this.operator) {
        case 0:
            return ">=";
        case 1:
            return ">";
        case 2:
            return "==";
        case 3:
            return "!=";
        case 4:
            return "<=";
        case 5:
            return "<";
        default:
            return "Unknown Operator";
        }
    }

    public String display() {
        return this.featureData.getDetails() + " " + getOperatorString() + " " + getValue();
    }

    @SuppressWarnings("unchecked")
    private void findIndex(weka.core.Instance instance) {
        for (Enumeration<Attribute> e = instance.enumerateAttributes(); e.hasMoreElements();) {
            Attribute attr = e.nextElement();
            if (attr.name().compareTo(this.attributeName.name()) == 0) {
                this.index = attr.index();
                break;
            }
        }
    }

    public boolean isViolated(FastaFormat fastaFormat, weka.core.Instance instance,
            ApplicationData applicationData) {
        double attributeValue;
        if (instance == null) {
            //attribute not found in Instance
            //generate it
            attributeValue = GenerateFeatures.getValue(fastaFormat, this.featureData, applicationData);
        } else {
            if (this.index == -1)
                //find the index of attribute in instance
                findIndex(instance);
            else if (instance.attribute(this.index).name().compareTo(this.attributeName.name()) != 0)
                findIndex(instance);
            if (this.index == -1)
                //attribute not found in Instance
                //generate it
                attributeValue = GenerateFeatures.getValue(fastaFormat, this.featureData, applicationData);
            else
                attributeValue = instance.value(this.index);
        }

        //Then check if it violate the constraint
        /*
         * 0) >= 
         * 1) >
         * 2) ==
         * 3) !=
         * 4) <=
         * 5) <      
         */
        boolean violated = true;
        switch (operator) {
        case 0:
            if (attributeValue >= this.value)
                violated = false;
            break;
        case 1:
            if (attributeValue > this.value)
                violated = false;
            break;
        case 2:
            if (attributeValue == this.value)
                violated = false;
            break;
        case 3:
            if (attributeValue != this.value)
                violated = false;
            break;
        case 4:
            if (attributeValue <= this.value)
                violated = false;
            break;
        case 5:
            if (attributeValue < this.value)
                violated = false;
            break;
        default:
            throw new Error("Unknown Operator");
        }
        return violated;
    }
}