/*
* 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.tdf;
import java.io.IOException;
import java.nio.ByteBuffer;
/**
* @author jrobinso
*/
public class TDFFixedTile implements TDFTile {
int tileStart;
double span;
int start;
float[][] data;
public TDFFixedTile(ByteBuffer byteBuffer, int nSamples) throws IOException {
this.fill(byteBuffer, nSamples);
}
public TDFFixedTile(int tileStart, int start, double span, float[][] data) {
this.tileStart = tileStart;
this.span = span;
this.data = data;
this.start = start;
}
public int getTileStart() {
return start;
}
public int getTileEnd() {
return getSize() == 0 ? 0 : getEndPosition(getSize() - 1);
}
public int getStartPosition(int idx) {
return start + (int) (idx * span);
}
public int getEndPosition(int idx) {
return start + (int) ((idx + 1) * span);
}
public String getName(int idx) {
return null; //To change body of implemented methods use File | Settings | File Templates.
}
public float getValue(int row, int idx) {
return data[row][idx];
}
public int getSize() {
return (data == null ? 0 : data[0].length);
}
// TODO -- record "type", extent (longest feature), other stuff
public void writeTo(BufferedByteWriter fos) throws IOException {
fos.putNullTerminatedString(TDFTile.Type.fixedStep.toString());
fos.putInt(getSize());
fos.putInt(start);
fos.putFloat((float) span);
for (int i = 0; i < data.length; i++) {
for (int j = 0; j < data[i].length; j++) {
fos.putFloat(data[i][j]);
}
}
}
public void fill(ByteBuffer byteBuffer, int nSamples) throws IOException {
int nPositions = byteBuffer.getInt();
start = byteBuffer.getInt();
span = byteBuffer.getFloat();
data = new float[nSamples][nPositions];
for (int sample = 0; sample < nSamples; sample++) {
data[sample] = new float[nPositions];
for (int i = 0; i < nPositions; i++) {
data[sample][i] = byteBuffer.getFloat();
}
}
}
/**
* This should never be called, but is provided to satisfy the interface
*
* @return
*/
public int[] getStart() {
int nPts = data[0].length;
int[] startArray = new int[nPts];
for (int i = 0; i < nPts; i++) {
startArray[i] = start + (int) (i * span);
}
return startArray;
}
public int[] getEnd() {
int nPts = data[0].length;
int[] endArray = new int[nPts];
for (int i = 0; i < nPts; i++) {
endArray[i] = start + (int) ((i + 1) * span);
}
return endArray;
}
public float[] getData(int trackNumber) {
return data[trackNumber]; //To change body of implemented methods use File | Settings | File Templates.
}
public String[] getNames() {
return null;
}
}