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* Copyright (c) 2007-2015 Broad Institute
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package org.broad.igv.tdf;
import org.broad.igv.util.StringUtils;
import org.broad.igv.util.collections.LRUCache;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
* Represents the data for a particular chromosome and zoom level
*
* @author jrobinso
*/
public class TDFDataset extends TDFEntity {
public enum DataType {
BYTE, SHORT, INT, FLOAT, DOUBLE, STRING
}
DataType dataType;
int tileWidth;
long[] tilePositions; // File position in TDF file
int[] tileSizes; // Tile size in bytes
int nTiles;
LRUCache<String, TDFTile> cache = new LRUCache(20);
// TODO -- refactor this dependency out
TDFReader reader;
public TDFDataset(String name, DataType dataType, int tileWidth, int nTiles) {
super(name);
this.dataType = dataType;
this.tileWidth = tileWidth;
this.nTiles = nTiles;
this.tilePositions = new long[nTiles];
this.tileSizes = new int[nTiles];
// Initialize tile positions to -1. This indicates a blank tile and is the default
Arrays.fill(tilePositions, -1);
}
public TDFDataset(String name, ByteBuffer byteBuffer, TDFReader reader) throws IOException {
super(name);
this.reader = reader;
fill(byteBuffer);
}
public void write(BufferedByteWriter dos) throws IOException {
writeAttributes(dos);
writeString(dos, dataType.toString());
dos.putFloat(tileWidth);
// dos.writeFloat(binWidth);
dos.putInt(tilePositions.length);
for (int i = 0; i < tilePositions.length; i++) {
dos.putLong(tilePositions[i]);
dos.putInt(tileSizes[i]);
}
}
private void fill(ByteBuffer byteBuffer) throws IOException {
// Attributes
readAttributes(byteBuffer);
String typeString = StringUtils.readString(byteBuffer);
dataType = TDFDataset.DataType.valueOf(typeString);
// TODO -- change tileWidth to int ?
tileWidth = (int) byteBuffer.getFloat();
nTiles = byteBuffer.getInt();
tilePositions = new long[nTiles];
tileSizes = new int[nTiles];
for (int i = 0; i < nTiles; i++) {
tilePositions[i] = byteBuffer.getLong();
tileSizes[i] = byteBuffer.getInt();
}
}
// TODO -- this uses an implied linear index. Abstract index or replace
// with general interval index
// TODO -- gather all non-cached tiles and read in one chunk. See BAM
// alignment reader class
public List<TDFTile> getTiles(int startLocation, int endLocation) {
List<TDFTile> tiles = new ArrayList();
int startTile = (int) (startLocation / tileWidth);
int endTile = (int) (endLocation / tileWidth);
for (int t = startTile; t <= endTile; t++) {
TDFTile tile = getTile(t);
if (tile != null && tile.getSize() > 0) {
tiles.add(tile);
}
}
return tiles;
}
public List<TDFTile> getTiles() {
List<TDFTile> tiles = new ArrayList<TDFTile>();
for (int t = 0; t < nTiles; t++) {
TDFTile tile = getTile(t);
if (tile != null) {
tiles.add(tile);
}
}
return tiles;
}
// TDFTile computeTile(TDFDataset ds, int t, List<LocusScore> scores, String chr)
synchronized TDFTile getTile(int t) {
String key = getName() + "_" + t;
TDFTile tile = null;
if (!cache.containsKey(key)) {
tile = reader.readTile(this, t);
cache.put(key, tile);
} else {
tile = cache.get(key);
}
return tile;
}
public void clearCache() {
cache.clear();
}
public DataType getDataType() {
return dataType;
}
public int getTileWidth() {
return tileWidth;
}
}