/*
* 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.stream.IGVSeekableBufferedStream;
import java.util.ArrayList;
/**
* Created by IntelliJ IDEA.
* User: martind
* Date: Dec 17, 2009
* Time: 12:36:35 PM
* To change this template use File | Settings | File Templates.
*/
/*
* Container class which reads BBFile zoom information into ArrayLists.
*
* 1) Reads in Zoom Level Header Table D into Zoom Headers and
* loads them into the ZoomLevelHeader array, one for each zoom level.
*
* 2) Reads in Table O overall zoom level format as referenced
* by dataOffset in Table D.
*
* Note: Zoom levels count from Table C is validated by BBZoomLevelHeader,
* which will throw a RuntimeException if header is not found.
*
* */
public class BBZoomLevels {
private static Logger log = Logger.getLogger(BBZoomLevels.class);
// defines the zoom headers access
//private SeekableStream fis; // BBFile handle
private long zoomHeadersOffset; // BBFile first zoom header offset
private int zoomLevelsCount; // BB File header Table C specified zoom levels
// zoom level headers - Table D , one for each zoom level
// Note: array size determines how many zoom levels actually read
private ArrayList<BBZoomLevelHeader> zoomLevelHeaders; // zoom level headers
// zoom level data formats - BBFile Table O
private ArrayList<BBZoomLevelFormat> zoomLevelFormatList;
// zoom level R+ trees - one per level
private ArrayList<RPTree> zoomLevelRPTree;
/*
* constructor - reads zoom level headers and data format from file I/O stream
* for all zoom levels and acts as a container for zoom data records.
*
* Parameters:
* fis - file input stream handle
* fileOffset - file byte location for zoom level headers
* zoomLevels - count of zoom levels from BBFile Table C
* isLowToHigh - boolean flag indicates if values are arranged low to high bytes.
* uncompressBufSize - byte size of the buffer to use for decompression
* */
public BBZoomLevels(SeekableStream is, long fileOffset, int zoomLevels,
boolean isLowToHigh, int uncompressBufSize){
int zoomLevel;
int zoomHeadersRead;
long zoomDataOffset;
long zoomIndexOffset;
// save the seekable file handle and zoom zoomLevel headers file offset
//this.fis = fis;
zoomHeadersOffset = fileOffset;
zoomLevelsCount = zoomLevels;
// We don't know the exact size of the header fields, so use a buffered stream
IGVSeekableBufferedStream fis = new IGVSeekableBufferedStream(is, 512000);
// Note: a bad zoom header will result in a 0 count returned
zoomHeadersRead = readZoomHeaders(fis, zoomHeadersOffset, zoomLevels, isLowToHigh);
if(zoomHeadersRead > 0){
// create zoom level data format containers
zoomLevelFormatList = new ArrayList<BBZoomLevelFormat>();
// for each zoom zoomLevel, get associated zoom data format
for(int index = 0; index < zoomHeadersRead; ++index) {
zoomLevel = index + 1;
// Zoom dataOffset (from Table D) is file location for zoomCount (Table O)
// Note: This dataOffset is zoomFormatLocation in BBZoomLevelFormat.
zoomDataOffset = zoomLevelHeaders.get(index).getDataOffset();
// R+ zoom index offset (Table D) marks end of zoom data in the
// zoom level format (Table O)
long dataSize = zoomLevelHeaders.get(index).getIndexOffset() - zoomDataOffset
- BBZoomLevelFormat.ZOOM_FORMAT_HEADER_SIZE;
// get zoom zoomLevel data records - zoomDataOffset references zoomCount in Table O
// Note: zoom zoomLevel data records read their own data
BBZoomLevelFormat zoomLevelData = new BBZoomLevelFormat(zoomLevel, fis, zoomDataOffset,
dataSize, isLowToHigh, uncompressBufSize);
zoomLevelFormatList.add(zoomLevelData);
}
// create zoom level R+ tree containers
zoomLevelRPTree = new ArrayList<RPTree>();
// for each zoom zoomLevel, get associated R+ tree
for(int index = 0; index < zoomHeadersRead; ++index) {
// Zoom indexOffset (from Table D) is file location
// for Table O zoomIndex for R+ tree zoom data
zoomIndexOffset = zoomLevelHeaders.get(index).getIndexOffset();
// get Zoom Data R+ Tree (Tables K, L, M, N): exists for zoom levels
RPTree zoomRPTree = new RPTree(fis, zoomIndexOffset, isLowToHigh, uncompressBufSize, true);
//if(zoomRPTree.getNodeCount() > 0)
zoomLevelRPTree.add(zoomRPTree);
}
}
}
/*
* Method returns the BBFile's first zoom header file offset.
*
* Note zoom headers immediately follow the BBFile header (Table C)
*
* Returns:
* first zoom header file offset
* */
public long getZoomHeadersOffset() {
return zoomHeadersOffset;
}
/*
* Method returns the number of zoom level headers found.
*
* Note Should match zoomLevels in the BBFile header (Table C)
*
* Returns:
* number of zoom level headers found
* */
public int getZoomHeaderCount() {
return zoomLevelHeaders.size();
}
/*
* Method returns the zoom level headers.
*
* Returns:
* zoom level headers
* */
public ArrayList<BBZoomLevelHeader> getZoomLevelHeaders() {
return zoomLevelHeaders;
}
/*
* Method returns the zoom level header for specified level.
*
* Parameters:
* level - zoom level; level starts at 1
*
* Returns:
* Zoom level header for specified level; or null for bad zoom level.
* */
public BBZoomLevelHeader getZoomLevelHeader(int level) {
if(level < 1 || level > zoomLevelsCount)
return null;
return zoomLevelHeaders.get(level - 1);
}
/*
* Method returns the zoom level formats for zoom data.
*
* Returns:
* zoom level formats for zoom data
* */
public ArrayList<BBZoomLevelFormat> getZoomLevelFormats(){
return zoomLevelFormatList;
}
/*
* Method returns the R+ index tree for the specified zoom level.
*
* Parameters:
* level - zoom level; level starts at 1
*
* Returns:
* R+ index tree for the specified zoom level; or null for bad zoom level
* */
public RPTree getZoomLevelRPTree(int level) {
if(level < 1 || level > zoomLevelsCount)
return null;
return zoomLevelRPTree.get(level - 1);
}
// prints out the zoom level header information
public void printZoomHeaders() {
// note if successfully read - should always be correct
if(zoomLevelHeaders.size() == zoomLevelsCount)
log.debug("Zoom level headers read for " + zoomLevelsCount + " levels:");
else
log.error("Zoom level headers not successfully read for "
+ zoomLevelsCount + "levels.");
for( int index = 0; index < zoomLevelHeaders.size(); ++index) {
// zoom level headers print themselves
zoomLevelHeaders.get(index).print();
}
}
/*
* Reads in all the Zoom Headers.
*
* Parameters:
* fileOffset - File byte location for first zoom level header
* zoomLevels - count of zoom levels to read in
* isLowToHigh - indicate byte order is lwo to high, else is high to low
*
* Returns:
* Count of zoom levels headers read, or 0 for failure to find the
* header information.
* */
private int readZoomHeaders(SeekableStream fis, long fileOffset, int zoomLevels, boolean isLowToHigh) {
int level = 0;
BBZoomLevelHeader zoomLevelHeader;
if(zoomLevels < 1)
return 0;
// create zoom headers and data containers
zoomLevelHeaders = new ArrayList<BBZoomLevelHeader>();
// get zoom header information for each zoom levelsRead
for(int index = 0; index < zoomLevels; ++index) {
level = index + 1;
// read zoom level header - read error is returned as Runtime Exception
zoomLevelHeader = new BBZoomLevelHeader(fis, fileOffset, level, isLowToHigh);
zoomLevelHeaders.add(zoomLevelHeader);
fileOffset += BBZoomLevelHeader.ZOOM_LEVEL_HEADER_SIZE;
}
return level;
}
}