/*
* 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.data;
//~--- non-JDK imports --------------------------------------------------------
import org.broad.igv.feature.LocusScore;
import org.broad.igv.track.WindowFunction;
/**
* @author jrobinso
*/
public class CompositeScore implements LocusScore {
float[] data;
String[] probes;
float value;
private int start;
private int end;
private WindowFunction windowFunction;
public CompositeScore(int start, int end, float value, float[] data, String[] probes, WindowFunction windowFunction) {
this.start = start;
this.end = end;
this.value = value;
this.probes = probes;
this.data = data;
// Only keep 5 representative values
if (data.length > 5) {
float[] temp = new float[5];
System.arraycopy(data, 0, temp, 0, 5);
this.data = temp;
if (probes != null && probes.length > 5) {
String[] temp2 = new String[5];
System.arraycopy(probes, 0, temp2, 0, 5);
this.probes = temp2;
}
}
}
public CompositeScore(CompositeScore sc) {
this.start = sc.start;
this.end = sc.end;
this.value = sc.value;
this.probes = sc.probes;
this.data = sc.data;
}
public CompositeScore copy() {
return new CompositeScore(this);
}
public float getScore() {
return value;
}
public String getValueString(double position, int mouseX, WindowFunction windowFunction) {
if (data == null) {
return "";
}
StringBuffer buf = new StringBuffer();
buf.append("Composite value = " + value + " (" + windowFunction + ")<br>");
buf.append("-------------------------------<br>");
for (int j = 0; j < data.length; j++) {
buf.append(String.valueOf(data[j]));
String probe = (probes != null && j < probes.length) ? probes[j] : null;
if (probe != null && probe.length() > 0) {
buf.append(" (");
buf.append(probes[j]);
buf.append(")");
}
buf.append("<br>");
}
if (data.length >= 5) {
buf.append("...<br>");
}
return buf.toString();
}
public String getChr() {
return null; //To change body of implemented methods use File | Settings | File Templates.
}
@Override
public String getContig() {
return null;
}
public int getStart() {
return start;
}
public void setStart(int start) {
this.start = start;
}
public int getEnd() {
return end;
}
/**
* Method description
*
* @param end
*/
public void setEnd(int end) {
this.end = end;
}
public int getExtendedStart() {
return getStart();
}
public int getExtendedEnd() {
return getEnd();
}
}