SpectraWithPrecursorMassTable.java

package GeDBIT.type;

import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.util.ArrayList;

import GeDBIT.dist.MSMSMetric;
import GeDBIT.dist.Metric;

public class SpectraWithPrecursorMassTable extends Table {
    /**
     * 
     */
    private static final long serialVersionUID = -6784466397812636659L;

    /**
     * 
     */
    public static final Metric DEFAULT_METRIC = new MSMSMetric();

    /**
     * @param fileName
     * @param maxDataSize
     * @throws FileNotFoundException
     */
    public SpectraWithPrecursorMassTable(String fileName, String indexPrefix,
	    int maxDataSize) throws FileNotFoundException {
	this(fileName, indexPrefix, maxDataSize, DEFAULT_METRIC);
    }

    /**
     * @param fileName
     * @param size
     * @param metric
     * @throws FileNotFoundException
     */
    public SpectraWithPrecursorMassTable(String fileName, String indexPrefix,
	    int size, Metric metric) throws FileNotFoundException {
	super(fileName, indexPrefix, size, metric);

	BufferedReader reader = new java.io.BufferedReader(
		new java.io.FileReader(fileName));
	loadData(reader, size);
    }

    /**
     * @param reader
     * @param size
     */
    private void loadData(BufferedReader reader, int size) {

	String line;
	ArrayList<SpectraWithPrecursorMass> spectraWPM = null;
	ArrayList<Integer> originalRowIDsArrayList = null;
	// System.out.println("Loading... ");
	try {
	    // read sequences from file
	    line = reader.readLine(); // read the first line
	    if (line != null)
		line = line.trim();
	    // get total rows from first line and allocate the ArrayList
	    int numSpectra = java.lang.Integer.parseInt(line);
	    spectraWPM = new ArrayList<SpectraWithPrecursorMass>(numSpectra);
	    originalRowIDsArrayList = new ArrayList<Integer>(numSpectra);

	    // read line byte line
	    line = reader.readLine();
	    if (line != null)
		line = line.trim();

	    int count = 0;
	    while (line != null && count < size) {
		if (count % 1000 == 0) {
		    // System.out.print(count+".. ");
		}
		String[] row = line.split(" ", 3);
		originalRowIDsArrayList.add(count,
			new Integer(row[0]).intValue());
		spectraWPM.add(new SpectraWithPrecursorMass(this, count,
			new Double(row[1]).doubleValue(), row[2]));

		line = reader.readLine();
		if (line != null)
		    line = line.trim();
		count++;
	    }
	} catch (java.io.IOException e) {
	    e.printStackTrace();
	    throw new java.lang.IllegalStateException(
		    "Error occured when reading msms file: " + reader
			    + " error message returned: " + e.getMessage());
	} catch (NumberFormatException e) {
	    e.printStackTrace();
	    /* Ignore strings with invalid characters. */
	}

	// debug
	// System.out.println(seqs);
	spectraWPM.trimToSize();
	data = spectraWPM;

	originalRowIDs = new int[originalRowIDsArrayList.size()];
	for (int i = 0, e = originalRowIDsArrayList.size(); i < e; i++) {
	    originalRowIDs[i] = originalRowIDsArrayList.get(i);
	}
    }

}