/*
* 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: Jan 8, 2010
* Time: 3:50:08 PM
* To change this template use File | Settings | File Templates.
*/
/*
* Container class for BBFile B+ Tree header.
* B+ Tree Header can be constructed by reading values in from a BBFile
* ( Table E), or by assigning the values in a constructor.
*
* */
public class BPTreeHeader {
private static Logger log = Logger.getLogger(BPTreeHeader.class);
static public final int BPTREE_HEADER_SIZE = 32;
static public final int BPTREE_MAGIC_LTH = 0x78CA8C91;
static public final int BPTREE_MAGIC_HTL = 0x918CCA78;
private long headerOffset; // BBFile file offset for mChromosome tree
private boolean headerOK; // B+ Tree header OK?
// Chromosome B+ Tree Header - Table E
private int magic; // magic number identifies it as B+ header
private int blockSize; // number of children per block
private int keySize; // min # of charcter bytes for mChromosome name
private int valSize; // size of (bigWig) values - currently 8
private long itemCount; // number of chromosomes/contigs in B+ tree
private long reserved; // Currently 0
/*
* Constructor for reading in a B+ tree header a from a file input stream.
*
* Parameters:
* fis - file input handle
* fileOffset - file offset to the B+ tree header
* isLowToHigh - indicates byte order is low to high, else is high to low
* */
public BPTreeHeader(SeekableStream fis, long fileOffset, boolean isLowToHigh) {
long itemsCount;
// save the seekable file handle and B+ Tree file offset
headerOffset = fileOffset;
// Note: a bad B+ Tree header will result in false returned
headerOK = readHeader(fis, headerOffset, isLowToHigh);
}
public static int getHeaderSize() {
return BPTREE_HEADER_SIZE;
}
public long getHeaderOffset() {
return headerOffset;
}
public boolean isHeaderOK() {
return headerOK;
}
public int getMagic() {
return magic;
}
public int getBlockSize() {
return blockSize;
}
public int getKeySize() {
return keySize;
}
public int getValSize() {
return valSize;
}
public long getItemCount() {
return itemCount;
}
public long getReserved() {
return reserved;
}
// prints out the B+ Tree Header
public void print() {
// Chromosome B+ Tree Header - BBFile Table E
if(headerOK)
log.debug("B+ Tree Header was read from file location " + headerOffset);
log.debug(" Magic ID =" + magic);
log.debug(" Block size = " + blockSize);
log.debug(" Key size = " + keySize);
log.debug(" Indexed value size = " + valSize);
log.debug(" Item Count = " + itemCount);
log.debug(" Reserved = " + reserved);
}
/*
* Reads in the B+ Tree Header.
* Returns status of B+ tree header read; true if read, false if not.
* */
private boolean readHeader(SeekableStream fis, long fileOffset, boolean isLowToHigh) {
LittleEndianInputStream lbdis;
DataInputStream bdis;
byte[] buffer = new byte[BPTREE_HEADER_SIZE];
int bytesRead;
try {
// Read B+ tree header into a buffer
fis.seek(fileOffset);
fis.readFully(buffer);
// decode header
if(isLowToHigh){
lbdis = new LittleEndianInputStream(new ByteArrayInputStream(buffer));
// check for a valid B+ Tree Header
magic = lbdis.readInt();
if(magic != BPTREE_MAGIC_LTH)
return false;
// Get mChromosome B+ header information
blockSize = lbdis.readInt();
keySize = lbdis.readInt();
valSize = lbdis.readInt();
itemCount = lbdis.readLong();
reserved = lbdis.readLong();
}
else {
bdis = new DataInputStream(new ByteArrayInputStream(buffer));
// check for a valid B+ Tree Header
magic = bdis.readInt();
if(magic != BPTREE_MAGIC_HTL)
return false;
// Get mChromosome B+ header information
blockSize = bdis.readInt();
keySize = bdis.readInt();
valSize = bdis.readInt();
itemCount = bdis.readLong();
reserved = bdis.readLong();
}
}catch(IOException ex) {
log.error("Error reading B+ tree header " + ex);
throw new RuntimeException("Error reading B+ tree header \n", ex);
}
// success
return true;
}
}