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

/*
 * the input: 3 files, 1 is cluster file, 2 is Go matrix file (lookup table)
 *   3 is back ground file(pool)
 *
 *
 */

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Random;

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

    private ArrayList clusterGeneList;  // for the input cluster file
    private Matrix poolTable;  //for the filtered gene pool list
    private Matrix lookupTable; // for the lookup attribute table
    private int oriClusterSize; //for the original cluster size
    private ArrayList oriPoolOrfsName;//for the complete list of pool table
    // private String randomFilename;

    public Matrix getLookupTable() {
        return lookupTable;
    }

    public void setLookupTable(Matrix lookupTable) {
        this.lookupTable = lookupTable;
    }

    public Matrix getPoolTable() {
        return poolTable;
    }

    public void setPoolTable(Matrix poolTable) {
        this.poolTable = poolTable;
    }

    public ArrayList getClusterGeneList() {
        return clusterGeneList;
    }

    public void setClusterGeneList(ArrayList clusterGeneList) {
        this.clusterGeneList = clusterGeneList;
    }

    public RawGoID() {
        clusterGeneList = new ArrayList();
        poolTable = new Matrix();
        lookupTable = new Matrix();
        // randomFilename ="";
    }
    
    public void setOriClusterSize(int oriClusterSize) {
    	this.oriClusterSize = oriClusterSize;
    }

    public int getOriClusterSize () {
    	return oriClusterSize;
    }
    
    public void setOriPoolOrfsName(ArrayList oriPoolOrfsName) {
    	this.oriPoolOrfsName = oriPoolOrfsName;
    }

    public ArrayList getOriPoolOrfsName() {
    	return oriPoolOrfsName;
    }
    	
    /**
     * 
     * @param clusterFilename : cluster Filename
     * @param GoMatrixFilename : GoMatrix Filename
     * @param backGroundFilename : backGround Filename
     */
    public RawGoID(String clusterFilename, String GoMatrixFilename, String backGroundFilename) {
        try {
            clusterGeneList = new ArrayList(200);
            ArrayList refClusterGeneList = new ArrayList (200);

            // Get the smallGeneList (a cluster )
            BufferedReader br = new BufferedReader(new FileReader(clusterFilename));

            // strRow is used to read line from file
            String strRow = "";
            while ((strRow = br.readLine()) != null) {
                clusterGeneList.add(strRow.trim().toLowerCase());
            }
            // System.out.println(clusterGeneList.size());    
            setOriClusterSize(clusterGeneList.size());
            // System.out.println("original cluster size =" + clusterGeneList.size());
            
            // Get the mtrix (lookup table)
            lookupTable = new Matrix(GoMatrixFilename);

            // Get the bigGeneList (pool or back ground file)
            br = new BufferedReader(new FileReader(backGroundFilename));

            ArrayList poolOrfsName = new ArrayList(5000);
            while ((strRow = br.readLine()) != null) {
                poolOrfsName.add(strRow.trim().toLowerCase());
            }
            this.setOriPoolOrfsName(poolOrfsName);
            poolTable = new Matrix();
            for (int i = 0; i < poolOrfsName.size(); i++) {
                Object tempKey = poolOrfsName.get(i);
                if (lookupTable.getMatrix().containsKey(tempKey)) {
                    poolTable.addValue(tempKey, lookupTable.getMatrix().get(tempKey));
                }
            }
            poolTable.setRowSize(poolTable.getMatrix().size());
            poolTable.setColSize(lookupTable.getColSize());
            br.close();
            
            // This loop is to take out any ORF from the cluster gene list if not exist in pool table
            // not necessary if all cluster ORFs are from pool table
            for (int i=0;i<refClusterGeneList.size();i++){
            	Object tempKey = clusterGeneList.get(i);
            	if (!poolTable.getMatrix().containsKey(tempKey)){
            		clusterGeneList.remove(i);
            	}
            }

            // System.out.println("length of real cluster gene List after filtering = " + clusterGeneList.size());
            // Check point
            // System.out.println(clusterGeneList);
        } catch (IOException e) {
            // Catch possible io errors from readLine()
            System.out.println("IOException error in  'class GetGoID, constructor'");
        }

        // Checkpoint
        // System.out.println("Column size of pooltable is:"+ poolTable.getColSize() +'\t'+ "Row size of pooltable is :"+ poolTable.getRowSize());
        // randomFilename = "randomOrfName.txt";
    }

    /**
     *
     * @param clusterFilename : cluster Filename
     * @param GoMatrixFilename : GoMatrix Filename
     * @param backGroundFilename : backGround Filename
     */
    public RawGoID(String[] clusterName, String GoMatrixFilename, String backGroundFilename) {
        try {
            clusterGeneList = new ArrayList(clusterName.length);
            ArrayList refClusterGeneList = new ArrayList (200);

            // Get the smallGeneList (a cluster )
            for(String name: clusterName){
                clusterGeneList.add(name.trim().toLowerCase());
            }

            // System.out.println(clusterGeneList.size());
            setOriClusterSize(clusterGeneList.size());
            // System.out.println("original cluster size =" + clusterGeneList.size());

            // Get the mtrix (lookup table)
            lookupTable = new Matrix(GoMatrixFilename);

            // Get the bigGeneList (pool or back ground file)
            BufferedReader br = new BufferedReader(new FileReader(backGroundFilename));
            ArrayList poolOrfsName = new ArrayList(5000);
            String strRow = "";
            while ((strRow = br.readLine()) != null) {
                poolOrfsName.add(strRow.trim().toLowerCase());
            }
            this.setOriPoolOrfsName(poolOrfsName);
            poolTable = new Matrix();
            for (int i = 0; i < poolOrfsName.size(); i++) {
                Object tempKey = poolOrfsName.get(i);
                if(lookupTable.getMatrix().containsKey(tempKey)){
                    poolTable.addValue(tempKey, lookupTable.getMatrix().get(tempKey));
                }
            }
            poolTable.setRowSize(poolTable.getMatrix().size());
            poolTable.setColSize(lookupTable.getColSize());
            br.close();

            // This loop is to take out any ORF from the cluster gene list if not exist in pool table
            // not necessary if all cluster ORFs are from pool table
            for (int i=0;i<refClusterGeneList.size();i++){
            	Object tempKey = clusterGeneList.get(i);
            	if (!poolTable.getMatrix().containsKey(tempKey)){
            		clusterGeneList.remove(i);
            	}
            }

            // System.out.println("length of real cluster gene List after filtering = " + clusterGeneList.size());
            // Checkpoint
            // System.out.println(clusterGeneList);
        } catch (IOException e) {
            // Catch possible io errors from readLine()
            System.out.println("IOException error in  'class GetGoID, constructor'");
        }

        // Checkpoint
        // System.out.println("Column size of pooltable is:"+ poolTable.getColSize() +'\t'+ "Row size of pooltable is :"+ poolTable.getRowSize());
        // randomFilename = "randomOrfName.txt";
    }

    public double getRawGoID() {
        double result = 0.0;
        ArrayList fullMatrix = new ArrayList(this.getPoolTable().getRowSize());
        ArrayList subMatrix = new ArrayList(this.getClusterGeneList().size());
        
        // Fill the fullMatrix with pool table data
        Iterator it = this.getPoolTable().getMatrix().keySet().iterator();
        while (it.hasNext()) {
            Object key = it.next();
            fullMatrix.add(this.getPoolTable().getMatrix().get(key.toString().toLowerCase()));
        }
        // System.out.println("size of fullMatrix is:"+ fullMatrix.size());

        // Fill the subMatrix with lookup table data and cluster information
        for (Object element : this.getClusterGeneList()) {
            if (this.getLookupTable().getMatrix().containsKey(element)) {
                subMatrix.add(this.getLookupTable().getMatrix().get(element.toString().toLowerCase()));
            }
        }
        // System.out.println("size of subMatrix is:"+ subMatrix.size());
        
        // Transpose the 2 matrix
        ArrayList attrByOrfFullMatrix = this.transpose(fullMatrix);
        ArrayList attrByOrfSubMatrix = this.transpose(subMatrix);
        
        // System.out.println("size of transposed fullMatrix is:"+ attrByOrfFullMatrix.size());
        // System.out.println("size of transposed subMatrix is:"+ attrByOrfSubMatrix.size());
        
        // Calculate the raw GoID
        for (int i = 0; i < attrByOrfFullMatrix.size(); i++) {
            // Added by tdh, from the source code, we need not do this step
            int nonZeroCount = 0;
            String[] tempArray = (String[]) attrByOrfFullMatrix.get(i);
            for (int j = 0; j < tempArray.length; j++) {
            	// System.out.println(Integer.parseInt(tempArray[j].trim()));
                if (tempArray[j].trim().compareToIgnoreCase("1")==0 ) {
                	// System.out.println(Integer.parseInt(tempArray[j].trim()));
                	// System.out.println(tempArray[j].trim().compareToIgnoreCase("1"));//Jingyu added for checking
                    nonZeroCount++;
                    break; // added by tdh, from the source code, we need not do this step//Jingyu notes: the break may help the code running faster.
                    // System.out.println("nonzeroCount =" + nonZeroCount);//Jingyu add
                }
            }
            // System.out.println("nonzeroCount =" + nonZeroCount);//Jingyu add
            if (nonZeroCount >= 0) {
                result = result + Information.relativeEntropy(
                    ((String[]) attrByOrfSubMatrix.get(i)),
                    (String[]) (attrByOrfFullMatrix.get(i)));
            }
            // System.out.println(Information.relativeEntropy(
            // ((String[]) attrByOrfSubMatrix.get(i)), (String[]) (attrByOrfFullMatrix.get(i))));
        }
        // System.out.println("result =" + result);
        return result;
    }

    private ArrayList transpose(ArrayList data) {
        ArrayList result = new ArrayList(data.size());
        // Do transpose here
        int rowSize = data.size();
        int colSize = ((String[]) data.get(0)).length;

        String[][] matrix = new String[colSize][rowSize];
        for (int i = 0; i < rowSize; i++) {
            String[] temp = (String[]) data.get(i);
            for (int j = 0; j < colSize; j++) {
                // System.out.println("j is : " + j);
                matrix[j][i] = temp[j];
            }
        }

        // Convert to ArrayList
        for (int i = 0; i < matrix.length; i++) {
            result.add(matrix[i]);
        }
        return result;
    }

    public double getRandomRawGoID() {
        double result = 0.0;
        this.setClusterGeneList(this.getRandomCluster(this.getOriClusterSize()));
        result = this.getRawGoID();
        if (Double.isNaN(result)) {
            return getRandomRawGoID();
        } else {
            return result;
        }
    }

    private void toFile(HashMap data, String filename) {

        // Output to a file
        try {
            BufferedWriter writer = new BufferedWriter(new FileWriter(filename));
            for (Object key : data.keySet()) {
                writer.write(key.toString() + "\n");
            }
            writer.close();
        } catch (Exception e) {
            System.err.println(e.getStackTrace());
        }

    }
    private static void toFileString(String data, String filename) {

        // Output to a file
        try {
            BufferedWriter writer = new BufferedWriter(new FileWriter(filename,true));
            writer.write(data + "\n");
            writer.close();
        } catch (Exception e) {
            System.err.println(e.getStackTrace());
        }
    }

    private ArrayList getRandomCluster(int clusterSize) {
        ArrayList<String> result = new ArrayList(clusterSize);
        
        // Jingyu: The following segment of code, which is deactivated, is designed to get the random cluster list from a lookuptable-filtered pooltable
        // Jingyu: To do so may cause a bias in average of random raw GOid score by using a smaller pool list
        // get a random cluster with same size of the cluster file and then calculate the Goid
        // 1, get the random orf names to a ArrayList

        // HashMap hm = new HashMap(this.getClusterGeneList().size());
        // while (hm.keySet().size() < clusterSize) {
        //     hm.put(this.getPoolTable().getOrfNames().get(randInt(this.getPoolTable().getOrfNames().size())), "0");
        // }
        // result.addAll(hm.keySet());

        // Get a random cluster with same size of the cluster file from the original ORF pool
        // Extra step added by Jingyu to remove the ORFs not existing in pooltable;
        ArrayList localOriPoolTable = new ArrayList();
        localOriPoolTable = this.getOriPoolOrfsName();

        // Checkpoint
        // System.out.println(localOriPoolTable.size());
        for (int i=0;i<clusterSize;i++){
        	result.add(localOriPoolTable.get(randInt(localOriPoolTable.size())).toString().trim().toLowerCase());       	
        }    
        return result;
    }

    /**
     *
     * @param max the max integer you want to generate
     *
     * @return : a random integar between 0 and max
     */
    private int randInt(int max) {
        Random r = new Random((int) (System.nanoTime()));
        int random = r.nextInt();
        random = Math.abs(random);
        random = random % max;
        // random += 1;
        return random;
    }

    // This method is not used for the final code.
    // private String [] getZeroStringArray(int length) {
    //     String [] tmpStrArray = new String[length];
    //     for (int j=0; j<tmpStrArray.length; j++) {
    //         tmpStrArray[j] = "0";
    //     }
    //     return tmpStrArray;
    // }
}