/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.bbfile;
import htsjdk.samtools.seekablestream.SeekableStream;
import org.apache.log4j.Logger;
import org.broad.igv.util.LittleEndianInputStream;
import java.io.ByteArrayInputStream;
import java.io.DataInputStream;
import java.io.IOException;
/**
* Created by IntelliJ IDEA.
* User: martind
* Date: Dec 17, 2009
* Time: 4:36:21 PM
*
* To change this template use File | Settings | File Templates.
*/
/*
* Container class for holding zoom level header information, BBFile Table D.
*
* Constructed either from BBFile read or by load of header values.
*
* */
public class BBZoomLevelHeader {
private static Logger log = Logger.getLogger(BBZoomLevelHeader.class);
static public final int ZOOM_LEVEL_HEADER_SIZE = 24;
// Defines the Big Binary File (BBFile) access
private SeekableStream fis; // BBFile input stream handle
private long zoomLevelHeaderOffset; // file location for zoom level header
int zoomLevel; // the zoom level for this information
// zoom level header information - BBFile Table D
private int reductionLevel; // number of bases summerized
private int reserved; // reserved, currently 0
private long dataOffset; // file position of zoom data
private long indexOffset; // file position for index of zoomed data
/*
* Constructor reads zoom level header
*
* Parameters:
* fis - File input stream handle
* fileOffset - file byte position for zoom header
* zoomLevel - level of zoom
* isLowToHigh - indicates byte order is low to high, else is high to low
* */
public BBZoomLevelHeader(SeekableStream fis, long fileOffset, int zoomLevel,
boolean isLowToHigh){
this.fis = fis;
zoomLevelHeaderOffset = fileOffset;
this.zoomLevel = zoomLevel;
readZoomLevelHeader(zoomLevelHeaderOffset, this.zoomLevel, isLowToHigh);
}
/*
* Method returns the zoom level.
*
* Returns:
* zoom level
* */
public int getZoomLevel() {
return zoomLevel;
}
/*
* Method returns the reduction level for the zoom level.
*
* Returns:
* reduction level
* * */
public int getReductionLevel() {
return reductionLevel;
}
/*
* Method returns the reserved value.
*
* Returns:
* reserved value
* * */
public int getReserved() {
return reserved;
}
/*
* Method returns the zoom level data file location.
*
* Returns:
* zoom level data file location
* */
public long getDataOffset() {
return dataOffset;
}
/*
* Method returns the zoom level R+ index tree file location.
*
* Returns:
* R+ index tree file location
* */
public long getIndexOffset() {
return indexOffset;
}
/*
* Method prints the zoom level header info.
* */
public void print(){
// Table D - Zoom Level Header information
System.out.println("Zoom level " + zoomLevel + " header Table D: ");
System.out.println("Number of zoom level bases = " + reductionLevel);
System.out.println("Reserved = " + reserved);
System.out.println("Zoom data offset = " + dataOffset);
System.out.println("Zoom index offset = " + indexOffset);
}
/*
* Reads zoom level header information into class data members.
*
* Parameters:
* fileOffset - Byte position in fle for zoom header
* zoomLevel - level of zoom
* isLowToHigh - indicate byte order is low to high, else is high to low
* */
private void readZoomLevelHeader(long fileOffset, int zoomLevel, boolean isLowToHigh) {
LittleEndianInputStream lbdis = null;
DataInputStream bdis = null;
byte[] buffer = new byte[ZOOM_LEVEL_HEADER_SIZE];
try {
// Read zoom header into a buffer
fis.seek(fileOffset);
fis.readFully(buffer);
// decode header
if(isLowToHigh)
lbdis = new LittleEndianInputStream(new ByteArrayInputStream(buffer));
else
bdis = new DataInputStream(new ByteArrayInputStream(buffer));
// Get zoom level information
if(isLowToHigh){
reductionLevel = lbdis.readInt();
reserved = lbdis.readInt();
dataOffset = lbdis.readLong();
indexOffset = lbdis.readLong();
}
else {
reductionLevel = bdis.readInt();
reserved = bdis.readInt();
dataOffset = bdis.readLong();
indexOffset = bdis.readLong();
}
}catch(IOException ex) {
log.error("Error reading zoom level header: " + zoomLevel, ex);
throw new RuntimeException("Error reading zoom header " + zoomLevel, ex);
}
}
}