/*
* 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.rnai;
//~--- non-JDK imports --------------------------------------------------------
import org.broad.igv.feature.LocusScore;
import org.broad.igv.feature.NamedFeature;
import org.broad.igv.track.WindowFunction;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
/**
* Class description
*
* @author Enter your name here...
* @version Enter version here..., 08/10/06
*/
public class RNAIGeneScore implements LocusScore {
String batchCondition;
NamedFeature gene;
float geneScore;
int geneConfidence;
boolean hasGeneConfidence;
int numberOfHairpins;
int start;
int end;
/**
* Constructs ...
*
* @param batchId
* @param gene
* @param geneScore
* @param numberOfHairpins
*/
public RNAIGeneScore(String batchId, NamedFeature gene, float geneScore,
int numberOfHairpins) {
this.batchCondition = batchId;
this.gene = gene;
this.geneScore = geneScore;
geneConfidence = 3;
hasGeneConfidence = false;
this.numberOfHairpins = numberOfHairpins;
this.start = gene.getStart();
this.end = gene.getEnd();
}
/**
* Constructs ...
*
* @param batchId
* @param gene
* @param geneScore
* @param confidence
* @param numberOfHairpins
*/
public RNAIGeneScore(String batchId, NamedFeature gene, float geneScore, int confidence,
int numberOfHairpins) {
this.batchCondition = batchId;
this.gene = gene;
this.geneScore = geneScore;
this.geneConfidence = confidence;
hasGeneConfidence = true;
this.numberOfHairpins = numberOfHairpins;
this.start = gene.getStart();
this.end = gene.getEnd();
}
/**
* Copy constructor
*
* @param score
*/
public RNAIGeneScore(RNAIGeneScore score) {
this.batchCondition = score.batchCondition;
this.gene = score.gene;
this.geneScore = score.geneScore;
this.geneConfidence = score.geneConfidence;
this.numberOfHairpins = score.numberOfHairpins;
this.start = score.getStart();
this.end = score.getEnd();
}
/**
* Method description
*
* @return
*/
public RNAIGeneScore copy() {
return new RNAIGeneScore(this);
}
/**
* Checks if there is a confidence value for the gene score
*
* @return
*/
public boolean hasGeneConfidence() {
return hasGeneConfidence;
}
/**
* Method description
*
* @return
*/
public NamedFeature getGene() {
return gene;
}
public String getChr() {
return null; //To change body of implemented methods use File | Settings | File Templates.
}
@Override
public String getContig() {
return null;
}
/**
* Method description
*
* @return
*/
public int getStart() {
return start;
}
/**
* Method description
*
* @return
*/
public int getEnd() {
return end;
}
/**
* Method description
*
* @return
*/
public float getScore() {
return geneScore;
}
public float getConfidence() {
return geneConfidence;
}
public void setStart(int start) {
this.start = start;
}
public void setEnd(int end) {
this.end = end;
}
/**
* Return the list of hairpin scores associated with this gene. Scores are sorted alphabetically
* by haipin name
*
* @return
*/
List<RNAIHairpinValue> hairpinScores = null;
/**
* Method description
*
* @return
*/
public Collection<RNAIHairpinValue> getHairpinValues() {
if (hairpinScores == null) {
Collection<RNAIHairpinValue> tmp =
RNAIHairpinCache.getInstance().getHairpinScores(batchCondition, gene.getName().toUpperCase());
if (tmp != null) {
hairpinScores = new ArrayList(tmp);
}
}
return hairpinScores;
}
/**
* Method description
*
* @param mouseX
* @param ignored
* @return
*/
public String getValueString(double position, int mouseX, WindowFunction ignored) {
StringBuffer buf = new StringBuffer(100);
buf.append("<b>Gene: " + gene.getName() + "</b><br>");
buf.append("<b>Intensity: " + geneScore + "<br></b>");
if (hasGeneConfidence)
buf.append("Confidence: " + geneConfidence + "<br>");
Collection<RNAIHairpinValue> hpins = getHairpinValues();
if ((hpins == null) || hpins.isEmpty()) {
buf.append("# Hairpins: " + numberOfHairpins + "<br>");
} else {
buf.append("Hairpin scores:<br>");
for (RNAIHairpinValue hpScore : hpins) {
if (hpScore.hasScoreSTD()) {
buf.append(hpScore.getName() + ": " + hpScore.getScoreMean() + " ("
+ hpScore.getScoreSTD() + ")<br>");
} else {
buf.append(hpScore.getName() + ": " + hpScore.getScoreMean() + "<br>");
}
}
}
return buf.toString();
}
}