StringToGCCounts.java

/*
 * Created on Apr 18, 2007
 */
package org.seqcode.genome.sequence;

import java.util.Map;

import org.seqcode.gsebricks.types.*;
import org.seqcode.gsebricks.verbs.Mapper;
import org.seqcode.gseutils.Pair;


public class StringToGCCounts
    implements Mapper<String,Pair<Integer,Integer>>, SelfDescribingVerb {

    public Pair<Integer, Integer> execute(String a) {
        int length = a.length();
        int count = 0;
        for(int i = 0; i < a.length(); i++) { 
            char c = Character.toUpperCase(a.charAt(i));
            if(c == 'G' || c == 'C') { 
                count += 1;
            }
        }
        return new Pair<Integer,Integer>(count, length);
    }
    
    private static final String[] inputNames = { "Strings" };
    private static final EchoType[] inputTypes = { new ClassType(String.class) };
    private static final EchoType outputType = 
        new PairType(new ClassType(Integer.class), new ClassType(Integer.class));
    

    public EchoType[] getInputClasses() {
        return inputTypes;
    }

    public String[] getInputNames() {
        return inputNames;
    }

    public EchoType getOutputClass() {
        return outputType;
    }

    public EchoType[] getParameterClasses() {
        return null;
    }

    public String[] getParameterNames() {
        return null;
    }

    public void init(Map<String, Object> params) {
    }

}