/*
* The MIT License
*
* Copyright (c) 2011 The 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 picard.illumina.parser;
import picard.PicardException;
import java.util.Arrays;
/**
* Holds a 4 short values for each cycle of a read. This is used, to store raw intensities,
* processed intensities, or noise. Note that for Illumina 1.1 and 1.3, these are floating point values,
* but are truncated to shorts to store here.
*
* Indices into the channel arrays are zero-based, i.e. the first cycle is 0.
*
* @author jburke@broadinstitute.org
*/
public class FourChannelIntensityData {
/**
* Major index: channel number; minor index: cycle number (zero based)
*/
private short [] a;
private short [] c;
private short [] g;
private short [] t;
public FourChannelIntensityData(final int numberOfCycles) {
a = new short[numberOfCycles];
c = new short[numberOfCycles];
g = new short[numberOfCycles];
t = new short[numberOfCycles];
}
public short[] getChannel(final IntensityChannel channel) {
switch(channel) {
case A: return a;
case C: return c;
case G: return g;
case T: return t;
}
throw new PicardException("Unexpected intensity channel " + channel);
}
public short[] getA() {
return a;
}
public short[] getC() {
return c;
}
public short[] getG() {
return g;
}
public short[] getT() {
return t;
}
@Override
public boolean equals(final Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
final FourChannelIntensityData that = (FourChannelIntensityData)o;
return Arrays.equals(this.a, that.a) &&
Arrays.equals(this.c, that.c) &&
Arrays.equals(this.g, that.g) &&
Arrays.equals(this.t, that.t);
}
@Override
public int hashCode() {
int ret = 0;
ret = ret * 31 + Arrays.hashCode(a);
ret += ret * 31 + Arrays.hashCode(c);
ret += ret * 31 + Arrays.hashCode(g);
ret += ret * 31 + Arrays.hashCode(t);
return ret;
}
}