org.broad.igv.bbfile.ZoomDataBlock Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation
Variant annotation and effect prediction package.
The newest version!
/*
 * 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.
 */

package org.broad.igv.bbfile;

import org.apache.log4j.Logger;
import org.broad.tribble.util.LittleEndianInputStream;
import org.broad.tribble.util.SeekableStream;

import java.io.ByteArrayInputStream;
import java.io.DataInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;

/**
 * Created by IntelliJ IDEA.
 * User: Owner
 * Date: May 5, 2010
 * Time: 8:27:56 PM
 * To change this template use File | Settings | File Templates.
 */
/*
*   Container class for reading and storing a block of zoom level data records.
* */
public class ZoomDataBlock {

    private static Logger log = Logger.getLogger(ZoomDataBlock.class);

    // Bed data block access variables   - for reading in bed records from a file
    private long fileOffset;       // data block file offset
    private long dataBlockSize;    // byte size for data block specified in the R+ leaf
    private boolean isLowToHigh;   // if true, data is low to high byte order; else high to low

    // defines the zoom level source chromosomes
    private int zoomLevel;         // zoom level for the R+ chromosome data location tree
    private HashMap chromosomeMap;  // map of chromosome ID's and corresponding names
    private RPTreeLeafNodeItem leafHitItem;   //R+ leaf item with chromosome region and file data location

    // Provides uncompressed byte stream data reader
    private byte[] zoomBuffer;  // buffer containing leaf block data uncompressed
    private int remDataSize;   // number of unread decompressed data bytes

    // byte stream readers
    private LittleEndianInputStream lbdis = null;    // low to high byte stream reader
    private DataInputStream dis = null;       // high to low byte stream reader

    // Bed data extraction members
    private ArrayList zoomDataList; // array of zoom level data

    /*
    *   Constructor for Bed data block reader.
    *
    *   Parameters:
    *       zoomLevel - zoom level for data block
    *       fis - file input stream handle
    *       leafItem - R+ tree leaf item containing block data file location
    *       chromIDTree - B+ chromosome index tree returns chromosome ID's for names
    *       isLowToHigh - byte order is low to high if true; else high to low
    *       uncompressBufSize - byte size for decompression buffer; else 0 for uncompressed
    * */

    public ZoomDataBlock(int zoomLevel, SeekableStream fis, RPTreeLeafNodeItem leafHitItem,
                         HashMap chromosomeMap, boolean isLowToHigh, int uncompressBufSize) {

        this.zoomLevel = zoomLevel;
        this.leafHitItem = leafHitItem;
        this.chromosomeMap = chromosomeMap;
        this.isLowToHigh = isLowToHigh;

        fileOffset = this.leafHitItem.getDataOffset();
        dataBlockSize = this.leafHitItem.geDataSize();
        byte[] buffer = new byte[(int) dataBlockSize];

        // read Bed data block into a buffer
        try {
            fis.seek(fileOffset);
            fis.readFully(buffer);

            // decompress if necessary - the buffer size is 0 for uncomressed data
            // Note:  BBFile Table C specifies a decompression buffer size
            if (uncompressBufSize > 0)
                zoomBuffer = BBCompressionUtils.decompress(buffer, uncompressBufSize);
            else
                zoomBuffer = buffer;    // use uncompressed read buffer directly

        } catch (IOException ex) {
            log.error("Error reading Zoom level " + this.zoomLevel + " data for leaf item ",  ex);
            String error = String.format("Error reading zoom level %d data for leaf item %d\n", this.zoomLevel);
            throw new RuntimeException(error, ex);
        }

        // wrap the bed buffer as an input stream
        if (this.isLowToHigh)
            lbdis = new LittleEndianInputStream(new ByteArrayInputStream(zoomBuffer));
        else
            dis = new DataInputStream(new ByteArrayInputStream(zoomBuffer));

        // initialize unread data size
        remDataSize = zoomBuffer.length;

        // use method getZoomData to extract block data
    }

    /*
    *   Method returns all zoom level data within the decompressed block buffer
    *
    *   Parameters:
    *       selectionRegion - chromosome region for selecting zoom level data records
    *       contained - indicates selected data must be contained in selection region
    *           if true, else may intersect selection region
    *
    *   Returns:
    *      zoom data records in the data block
    *
    *   Note: Remaining bytes to data block are used to determine end of reading
    *   since a zoom record count for the data block is not known.
    * */

    public ArrayList getZoomData(RPChromosomeRegion selectionRegion,
                                                 boolean contained) {

        int chromID, chromStart, chromEnd, validCount;
        float minVal, maxVal, sumData, sumSquares;
        int itemHitValue;
        int recordNumber = 0;

        // allocate the bed feature array list
        zoomDataList = new ArrayList();

        // check if all leaf items are selection hits
        RPChromosomeRegion itemRegion = new RPChromosomeRegion(leafHitItem.getChromosomeBounds());
        int leafHitValue = itemRegion.compareRegions(selectionRegion);

        try {
            //for(int index = 0; mRemDataSize >= ZoomDataRecord.RECORD_SIZE; ++index) {
            for (int index = 0; remDataSize > 0; ++index) {
                recordNumber = index + 1;

                if (isLowToHigh) {  // buffer stream arranged low to high bytes
                    chromID = lbdis.readInt();
                    chromStart = lbdis.readInt();
                    chromEnd = lbdis.readInt();
                    validCount = lbdis.readInt();
                    minVal = lbdis.readFloat();
                    maxVal = lbdis.readFloat();
                    sumData = lbdis.readFloat();
                    sumSquares = lbdis.readFloat();
                } else { // buffer stream arranged high to low bytes
                    chromID = dis.readInt();
                    chromStart = dis.readInt();
                    chromEnd = dis.readInt();
                    validCount = dis.readInt();
                    minVal = dis.readFloat();
                    maxVal = dis.readFloat();
                    sumData = dis.readFloat();
                    sumSquares = dis.readFloat();
                }

                if (leafHitValue == 0) {     // contained leaf region always a hit
                    String chromName = chromosomeMap.get(chromID);
                    ZoomDataRecord zoomRecord = new ZoomDataRecord(zoomLevel, recordNumber, chromName,
                            chromID, chromStart, chromEnd, validCount, minVal, maxVal, sumData, sumSquares);
                    zoomDataList.add(zoomRecord);
                } else {      // test for hit
                    itemRegion = new RPChromosomeRegion(chromID, chromStart, chromID, chromEnd);
                    itemHitValue = itemRegion.compareRegions(selectionRegion);

                    // itemHitValue < 2 for intersection; itemHitValue == 0 for is contained
                    if (!contained && Math.abs(itemHitValue) < 2 || itemHitValue == 0) {
                        String chromName = chromosomeMap.get(chromID);
                        ZoomDataRecord zoomRecord = new ZoomDataRecord(zoomLevel, recordNumber, chromName,
                                chromID, chromStart, chromEnd, validCount, minVal, maxVal, sumData, sumSquares);
                        zoomDataList.add(zoomRecord);
                    }
                }

                // compute data block remainder fom size item read
                remDataSize -= ZoomDataRecord.RECORD_SIZE;
            }

        } catch (IOException ex) {
            log.error("Read error for zoom level " + zoomLevel + " leaf item " );

            // accept this as an end of block condition unless no items were read
            if (recordNumber == 1)
                throw new RuntimeException("Read error for zoom level " + zoomLevel + " leaf item ");
        }

        return zoomDataList;
    }

    public void print() {
        log.debug("Zoom Level " + zoomLevel + "data for leaf item :");

        for (int index = 0; index <= zoomDataList.size(); ++index) {
            // zoom data records print themselves
            zoomDataList.get(index).print();
        }
    }

}