/*
* 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 18, 2010
* Time: 12:51:25 PM
* To change this template use File | Settings | File Templates.
*/
/*
* Containeer class for file statistics - BBFile Table DD
*
* */
public class BBTotalSummaryBlock {
private static Logger log = Logger.getLogger(BBTotalSummaryBlock.class);
public static final int TOTAL_SUMMARY_BLOCK_SIZE = 40;
// defines the R+ Tree access
private SeekableStream fis; // BBFile handle
private long summaryBlockOffset; // file offset to TotalSummaryBlock
// File data statistics for calculating mean and standard deviation
private long basesCovered; // number of bases with data
private float minVal; // minimum value for file data
private float maxVal; // maximum value for file data
private float sumData; // sum of all squares of file data values
private float sumSquares; // sum of all squares of file data values
/*
* Constructor for reading in TotalSummaryBlock from BBFile
*
* Parameters:
* fis - file input stream handle
* fileOffset - file offset to TotalSummaryBlock
* isLowToHigh - indicates byte order is low to high if true, else is high to low
* */
public BBTotalSummaryBlock(SeekableStream fis, long fileOffset, boolean isLowToHigh)
{
LittleEndianInputStream lbdis = null;
DataInputStream bdis = null;
byte[] buffer = new byte[TOTAL_SUMMARY_BLOCK_SIZE];
// save the seekable file handle and B+ Tree file offset
this.fis = fis;
summaryBlockOffset = fileOffset;
try {
// Read TotalSummaryBlock 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 TotalSummaryBlcok information
if(isLowToHigh){
basesCovered = lbdis.readLong();
minVal = lbdis.readFloat();
maxVal = lbdis.readFloat();
sumData = lbdis.readFloat();
sumSquares = lbdis.readFloat();
}
else {
basesCovered = bdis.readLong();
minVal = bdis.readFloat();
maxVal = bdis.readFloat();
sumData = bdis.readFloat();
sumSquares = bdis.readFloat();
}
}catch(IOException ex) {
log.error("Error reading Total Summary Block ", ex);
throw new RuntimeException("Error reading Total Summary Block", ex);
}
}
/*
* Constructor for filling in TotalSummaryBlock
* */
public BBTotalSummaryBlock(long basesCovered, float minVal, float maxVal,
float sumData, float sumSquares){
this.basesCovered = basesCovered;
this.minVal = minVal;
this.maxVal = maxVal;
this.sumData = sumData;
this.sumSquares = sumSquares;
}
public static int getSummaryBlockSize() {
return TOTAL_SUMMARY_BLOCK_SIZE;
}
public SeekableStream getMBBFis() {
return fis;
}
public long getSummaryBlockOffset() {
return summaryBlockOffset;
}
public long getBasesCovered() {
return basesCovered;
}
public float getMinVal() {
return minVal;
}
public float getMaxVal() {
return maxVal;
}
public float getSumData() {
return sumData;
}
public float getSumSquares() {
return sumSquares;
}
public void printTotalSummaryBlock(){
// Table D - Zoom Level Header information
log.debug("BBFile TotalSummaryBlock (Table DD):");
log.debug("Number of bases covered= " + basesCovered);
log.debug("MinVal = " + minVal);
log.debug("MaxVal = " + maxVal);
log.debug("Sum of data values = "+ sumData);
log.debug("Sum of squares values = " + sumSquares);
}
}