/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
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* 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
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*/
package org.broad.igv.feature;
import org.broad.igv.track.WindowFunction;
/**
* Representation of a feature from an Encode "peak" file
* <p/>
* TODO Extending BasicFeature is overkill, no exons for example.
*
* @author jrobinso
* Date: 11/5/13
* Time: 1:11 PM
*/
public class EncodePeakFeature extends BasicFeature implements SignalFeature {
private int peakPosition = -1;
private float signal;
private float PValue;
private float QValue;
public EncodePeakFeature(String chr, int start, int end) {
super(chr, start, end);
}
public int getPeakPosition() {
return peakPosition;
}
public void setPeakPosition(int peakPosition) {
this.peakPosition = peakPosition;
}
public void setSignal(float signal) {
this.signal = signal;
}
public float getSignal() {
return signal;
}
public void setPValue(float PValue) {
this.PValue = PValue;
}
public float getPValue() {
return PValue;
}
public void setQValue(float QValue) {
this.QValue = QValue;
}
public float getQValue() {
return QValue;
}
@Override
public String getValueString(double position, int mouseX, WindowFunction ignored) {
StringBuffer desc = new StringBuffer();
desc.append(super.getValueString(position, mouseX, ignored));
desc.append("<br>Signal Value: " + signal);
desc.append("<br>pValue (-log10): " + PValue);
desc.append("<br>qValue (-log10): " + QValue);
if (peakPosition > 0) {
desc.append("<br>Peak: " + (peakPosition + 1));
}
return desc.toString();
}
}