Merge files by sum values in columns

[Duy Dinh]

/**
 * Merge files by summing up values from columns
 * 
 * @param files
 *            input files
 * @param output
 *            output file
 * @param header
 *            use header
 * @param startColumnID
 *            sum values of columns starting from a column id
 */
public static void combineResults(List<File> files, File output,
        boolean header, int startColumnID) {
    if (files == null || files.size() == 0) {
        return;
    }

    // an arraylist of arraylist of lines
    ArrayList<ArrayList<String>> lineSetList = new ArrayList<ArrayList<String>>();
    for (int i = 0; i < files.size(); i++)
        lineSetList.add(FileManager.ReadLines(files.get(i)
                .getAbsolutePath()));

    // count the number of column
    int columnCount = lineSetList.get(0).get(0).split("[\t]").length;
    int rowCount = lineSetList.get(0).size();

    String headerString = header == true ? lineSetList.get(0).get(0) : null;
    ArrayList<Double[]> sumValues = ArrayProcessing
            .initializeDoubleArrayList(rowCount, columnCount);

    // merge columns by sum up values from files

    for (int fileID = 0; fileID < files.size(); fileID++) {
        int lineID = header == true ? 1 : 0;

        // parse line
        for (; lineID < lineSetList.get(fileID).size(); lineID++) {
            String[] strValues = lineSetList.get(fileID).get(lineID)
                    .split("[\t]");
            Double[] dblValues = ArrayProcessing.convertDouble(strValues);

            // accumulate value
            // for columns that have the same value, we do not sum values
            int columnID = 0;
            for (; columnID < startColumnID; columnID++) {
                sumValues.get(lineID)[columnID] = dblValues[columnID];
            }

            // sum values of each column in a line
            ArrayProcessing.updateArray(sumValues, lineID, startColumnID,
                    dblValues);
        }
    }

    StringBuilder sb = new StringBuilder();
    System.out.println(sb.append(ArrayProcessing.toString(sumValues,
            headerString)));
    FileManager.WriteToFile(sb.toString(), output.getAbsolutePath());
}

[Duy Dinh]

/**
 * Convert string value into double
 * 
 * @param fields
 *            string
 * @return array of double values
 */
public static Double[] convertDouble(String[] fields) {

    Double[] values = new Double[fields.length];
    for (int i = 0; i < fields.length; i++)
        values[i] = Double.parseDouble(fields[i]);
    return values;
}

public static Double[] initializeDoubleArray(int columnCount) {
    Double[] values = new Double[columnCount];
    for (int i = 0; i < columnCount; i++)
        values[i] = 0.0;
    return values;
}

public static void updateArray(ArrayList<Double[]> list, int lineID,
        int startColumnID, Double[] sum) {
    for (int columnID = startColumnID; columnID < sum.length; columnID++)
        list.get(lineID)[columnID] += sum[columnID];
}

public static ArrayList<Double[]> initializeDoubleArrayList(int rowCount,
        int columnCount) {
    ArrayList<Double[]> doubleArrayList = new ArrayList<Double[]>(rowCount);
    for (int i = 0; i < rowCount; i++)
        doubleArrayList.add(initializeDoubleArray(columnCount));
    return doubleArrayList;
}

public static String toString(ArrayList<Double[]> values,
        String headerString) {
    StringBuilder sb = new StringBuilder();
    int i = headerString == null ? 0 : 1;
    if (i == 1) {
        sb.append(headerString).append("\n");
    }
    for (; i < values.size(); i++) {
        int j = 0;
        for (; j < values.get(i).length - 1; j++)
            sb.append(values.get(i)[j]).append("\t");
        sb.append(values.get(i)[j]).append("\n");
    }
    return sb.toString();
}

public static String toString(ArrayList<Double[]> values) {
    StringBuilder sb = new StringBuilder();
    for (int i = 0; i < values.size(); i++) {
        int j = 0;
        for (; j < values.get(i).length - 1; j++)
            sb.append(values.get(i)[j]).append("\t");
        sb.append(values.get(i)[j]).append("\n");
    }
    return sb.toString();
}