hartman-server/qhtcp-workflow/apps/java/weka-clustering/src/SGD2AttrTable.java

import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.util.HashMap;
import java.util.Iterator;


/*
 * This program starts by creating an intermediate table and then will load the function from Dr. Brett McKinney to create the attribute table.
 */

/**
 *
 * @author DTian
 */
public class SGD2AttrTable {

    public void createIntermediateTable(String inputFile, String outputFile) {
        HashMap geneToGODict  = new HashMap();
         try {

            FileReader fr = new FileReader(inputFile);
            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) {

                // Check: skip the line if it is a comment line
                if (strRow.trim().charAt(0) != 'S' ) {
                    continue;
                }
                String [] strArray = strRow.trim().split("\\t");
                String key = toKey(strArray[10].toUpperCase());
                if (key.compareToIgnoreCase("") == 0) {
                    continue;
                }
                String value = toValue(strArray[4]);
                if (geneToGODict.containsKey(key)) {
                    geneToGODict.put(key, geneToGODict.get(key)+ "\t" + value);
                } else {
                    geneToGODict.put(key, value);
                }
            }

            br.close();
            fr.close();

            // Write to output file
            FileOutputStream stream; // provides file access
            OutputStreamWriter writer; // writes to the file
            stream = new FileOutputStream(new File(outputFile), true);
            writer = new OutputStreamWriter(stream);
            Iterator it = geneToGODict.keySet().iterator();
            while(it.hasNext()){
                String key = it.next().toString();
                String value = geneToGODict.get(key).toString();
                writer.write(key + "\t" + value + "\n");
            }
            writer.flush();
            writer.close();
            stream.close();
        } catch (IOException e) {
            // Catch possible io errors from readLine()
            System.out.println("IOException error in  'class SGD2AttrTable, method createIntermediateTable'");
        }
    }

    public void createAttrTable(String intermediaFile, String outputFile){
        HashMap geneToGODict  = new HashMap();
         try {

            FileReader fr = new FileReader(intermediaFile);
            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) {

                //check: skip the line if it is a comment line
                if (strRow.trim().charAt(0) != 'S' ) {
                    continue;
                }
                String [] strArray = strRow.trim().split("\\t");
                String key = toKey(strArray[10].toUpperCase());
                if (key.compareToIgnoreCase("") == 0) {
                    continue;
                }
                String value = toValue(strArray[4]);
                if (geneToGODict.containsKey(key)) {
                    geneToGODict.put(key, geneToGODict.get(key)+ "\t" + value);
                } else {
                    geneToGODict.put(key, value);
                }
            }

            br.close();
            fr.close();

            // Write to output file
            FileOutputStream stream; // provides file access
            OutputStreamWriter writer; // writes to the file
            stream = new FileOutputStream(new File(outputFile), true);
            writer = new OutputStreamWriter(stream);
            Iterator it = geneToGODict.keySet().iterator();
            while (it.hasNext()) {
                String key = it.next().toString();
                String value = geneToGODict.get(key).toString();
                writer.write(key + "\t" + value + "\n");
            }
            writer.flush();
            writer.close();
            stream.close();
        } catch (IOException e) {
            // Catch possible io errors from readLine()
            System.out.println("IOException error in  'class SGD2AttrTable, method createIntermediateTable'");
        }
    }

    /**
     * 
     * @param raw  the string need to be get rid of the "GO:0s"
     * @return the string without "GO:00"
     */
    private String toValue(String raw) {
        String result = raw.toUpperCase(); //raw should be like: "GO:0005739"
        // Delete "GO:"
        result = result.substring(3);
        // Delete "lead zeros"
        while (result.charAt(0) == '0') {
            result =result.substring(1);
        }
        return result;
    }

    private String toKey(String raw) {
        String result = raw.toUpperCase(); // raw should be like: "GO:0005739"
        // Find the '|'
        int end = result.indexOf('|');
        // Get the sub string
        if (end < 0) {
            return result;
        } else {
            return result.substring(0, end);
        }
    }
}