DataUtils.java

/*
 * Copyright (c) 2007-2011 by The Broad Institute of MIT and Harvard.  All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
 * Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR
 * WARRANTES OF ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING,
 * WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
 * PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER
 * OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR RESPECTIVE
 * TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES
 * OF ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES,
 * ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER
 * THE BROAD OR MIT SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT
 * SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
 */


/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.data;

//~--- JDK imports ------------------------------------------------------------

import java.io.*;

/**
 * @author jrobinso
 */
public class DataUtils {

    public static int getIndexBefore(int[] values, int x) {
        return getIndexBefore(values, x, 0, values.length);
    }

    public static int getIndexBefore(int[] values, int x, int leftBound, int rightBound) {
        int idx = (leftBound + rightBound) / 2;

        if ((idx == 0) || (idx == values.length - 1)) {
            return idx;
        }
        if (values[idx] == x) {
            return idx;
        }

        if (values[idx] < x) {
            if (values[idx + 1] >= x) {
                return idx;
            } else {
                leftBound = idx;
                return getIndexBefore(values, x, leftBound, rightBound);
            }
        } else {    // values[idx] > x
            if (values[idx - 1] <= x) {
                return idx - 1;
            } else {
                rightBound = idx;
                return getIndexBefore(values, x, leftBound, rightBound);
            }
        }
    }


    /**
     * Estimate the number of rows in an ascii data file.  Estimate is based on
     * the first 100 lines, and assumes the line length is approximately
     * constant.
     *
     * @param textFile
     * @return
     */
    public static AsciiFileMetrics estimateFileMetrics(String textFile) {
        int estRowCount = 0;
        try {

            BufferedReader reader = null;

            File file = new File(textFile);

            reader = new BufferedReader(new FileReader(file));
            String nextLine = reader.readLine();

            double lineCount = 0;
            double nChars = 0;
            while ((nextLine = reader.readLine()) != null && (lineCount < 100)) {
                nChars += nextLine.length();
                lineCount++;
            }

            int columnCount = nextLine.split("\t").length;

            double charsPerLine = ((lineCount > 0) ? nChars / lineCount : 0);
            estRowCount = (int) (file.length() / charsPerLine);
            return new AsciiFileMetrics(estRowCount, columnCount, charsPerLine);

        }
        catch (FileNotFoundException ex) {
            ex.printStackTrace();

        }
        catch (IOException ex) {
            ex.printStackTrace();

        }
        return null;
    }

    /**
     * Method description
     *
     * @param fileMetrics
     * @return
     */
    public static int estimatePreprocessingTime(AsciiFileMetrics fileMetrics) {

        return 8 + (int) ((0.0036 * fileMetrics.getEstRowCount() * fileMetrics.getColumnCount()) / 100);
    }

    /**
     * This class has some useful metrics for optimizing reading of large ascii files
     *
     * @author jrobinso
     */
    public static class AsciiFileMetrics {

        private int estRowCount;

        private int columnCount;

        private double estBytesPerLine;

        public AsciiFileMetrics(int estRowCount, int columnCount, double estBytesPerLine) {
            this.estRowCount = estRowCount;
            this.columnCount = columnCount;
            this.estBytesPerLine = estBytesPerLine;
        }


        public double getEstBytesPerLine() {
            return estBytesPerLine;
        }


        public int getEstRowCount() {
            return estRowCount;
        }


        public int getColumnCount() {
            return columnCount;
        }
    }
}