server-scripts/qhtcp-workflow/apps/java/weka-clustering/src/Matrix.java

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import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Iterator;

/**
 *
 * @author DTian
 */
public class Matrix {

    private HashMap matrix; // store data
    private int rowSize; // row size of matrix
    private int colSize; // column size of value array
    private final int lookupTableSize = 9000; //size of look up table

    public int getColSize() {
        return colSize;
    }

    public void setColSize(int colSize) {
        this.colSize = colSize;
    }

    public HashMap getMatrix() {
        return matrix;
    }

    public void setMatrix(HashMap matrix) {
        this.matrix = matrix;
    }

    public int getRowSize() {
        return rowSize;
    }

    public void setRowSize(int rowSize) {
        this.rowSize = rowSize;
    }

    public Matrix() {
        rowSize = 0;
        colSize = 0;
        matrix = new HashMap();
    }

    /**
     * constructor with 1 String parameter
     *
     * @param filename : the name of the input file
     *
     * @result: create a matrix from a input file
     *
     */
    public Matrix(String filename) {

        // Initialize variables
        this.setRowSize(0);
        this.setColSize(0);
        matrix = new HashMap(lookupTableSize);

        try {

            FileReader fr = new FileReader(filename);
            BufferedReader br = new BufferedReader(fr);

            // strRow is used to read line from file(skip first row)
            String strRow = br.readLine();

            // The while loop read the data from data file to vvf
            while ((strRow = br.readLine()) != null) {

                // strArray was used to store the float value from data file in
                // string format
                String delimiter = "";
                if (strRow.indexOf(",") >= 0) { //for CSV file
                    delimiter = "\\,";
                } else { // for whitespace delimited file
                    delimiter = "\\s";
                }

                String[] strArray = strRow.trim().split(delimiter);
                String[] strArrValue = Arrays.copyOfRange(strArray, 1, strArray.length);
                // strArray[0] is the orf name, others are value
                matrix.put(strArray[0].trim().toLowerCase(), strArrValue);
                rowSize++;
                colSize = strArrValue.length;
            }

            br.close();
            fr.close();
        } catch (IOException e) {
            // catch possible io errors from readLine()
            System.out.println("IOException error in  'class Matrix, constructor'");
        }
    }

    /**
     *
     * @param index, the specifed key
     * @return:  the string array of the value
     */
    public String[] getSpecifiedValue(Object key) {
        return (String[]) matrix.get(key);
    }

    /**
     * @return the list of orf names
     */
    public ArrayList getOrfNames() {
        ArrayList result = new ArrayList(this.getRowSize());
        Iterator it = matrix.keySet().iterator();
        while (it.hasNext()) {
            result.add(it.next());
        }
        return result;
    }

    public void addValue(Object key, Object value) {
        matrix.put(key, value);
    }
}