SampleData.java

package evoker;

import java.util.Vector;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;

/**
 * Holds the SampleIDs of a given fam file in a Vector
 */

public class SampleData {
    Vector<String> inds;
    
    SampleData(String famFilename, boolean isOx) throws IOException{

        this.inds = new Vector<String>();

        BufferedReader famReader = new BufferedReader(new FileReader(famFilename));
        String currentLine;
        String[] bits;
        if (isOx){
            //strip headers
            famReader.readLine();
            famReader.readLine();
        }
        while ((currentLine = famReader.readLine()) != null){
            bits = currentLine.split("\\s");
            String sample = bits[1];
            inds.add(sample);
        }
        famReader.close();


    }
    
    /**
     * Returns the index of a given ind
     * @param ind
     * @return 
     */
    public int getIndex(String ind){
        for(int i = 0; i < inds.size(); i++){
            String s = inds.get(i);
            if(s.equals(ind)){
               return i;
            }
        }
        return -1;
    }

    public String getInd(int i){
        return inds.get(i);
    }

    public int getNumInds(){
        return inds.size();
    }

}