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/*
* Copyright 2013 Brian Tjaden
*
* This file is part of Rockhopper.
*
* Rockhopper is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* any later version.
*
* Rockhopper is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* (in the file gpl.txt) along with Rockhopper.
* If not, see <http://www.gnu.org/licenses/>.
*/
import java.util.ArrayList;
/**
* A Condition keeps track of the RNA-seq data in each
* replicate experiment for a given condition.
*/
public class Condition {
/********************************************
********** INSTANCE VARIABLES **********
********************************************/
private ArrayList<Replicate> replicates;
private int partner; // If there are no replicates, index of most similar other condition.
private int minDiffExpressionLevel; // Used for differentially expressed p-value correction
/*****************************************
********** CLASS VARIABLES **********
*****************************************/
private static long avgUpperQuartile; // Avg upper quartile over all replicates in all conditions
/**************************************
********** CONSTRUCTORS **********
**************************************/
public Condition() {
this.replicates = new ArrayList<Replicate>();
this.partner = -1;
}
/*************************************************
********** PUBLIC INSTANCE METHODS **********
*************************************************/
/**
* Return the Replicate at the specified index.
*/
public Replicate getReplicate(int i) {
if ((i >= 0) && (i < replicates.size()))
return replicates.get(i);
return null;
}
/**
* Adds a replicate to this Condition.
*/
public void addReplicate(Replicate r) {
this.replicates.add(r);
}
/**
* Return the number of Replicates performed for this Condition.
*/
public int numReplicates() {
return replicates.size();
}
/**
* Sets the partner of this Condition, i.e., the index of the other
* condition that is most similar to this Condition.
*/
public void setPartner(int partner) {
this.partner = partner;
}
/**
* Return the partner of this Condition, i.e., the index of the other
* condition that is most similar to this Condition.
*/
public int getPartner() {
return this.partner;
}
/**
* Estimates the minimum expression level, across all replicates,
* necessary to compute a p-value for differential expression.
*/
public int getMinDiffExpressionLevel() {
return minDiffExpressionLevel;
}
/**
* The background probability decreases as the number of reads increases.
* We use this fact to estimate a minimum level of expression necessary
* for us to be able to compute a p-value of differential expression.
* For a given Condition, we ensure that all Replicates meet the
* expression threshold.
* Currently, the expression threshold is set (based on anecdote and
* experience) to 0.005.
*/
public void setMinDiffExpressionLevel() {
double THRESHOLD = 0.005;
minDiffExpressionLevel = 0;
while (true) {
boolean foundThreshold = true;
for (int i=0; i<replicates.size(); i++) {
if (replicates.get(i).getBackgroundProb(minDiffExpressionLevel) >= THRESHOLD)
foundThreshold = false;
}
if (foundThreshold) return;
minDiffExpressionLevel++;
}
}
/**
* Returns a String representation of a this object.
*/
public String toString() {
StringBuilder sb = new StringBuilder();
for (int i=0; i<replicates.size(); i++) {
sb.append(replicates.get(i).toString() + "\n");
}
return sb.toString();
}
/**********************************************
********** PUBLIC CLASS METHODS **********
**********************************************/
/**
* Set the average upper quartile gene expression over
* all replicates in all all conditions.
*/
public static void setAvgUpperQuartile(long avgUpperQuartile) {
Condition.avgUpperQuartile = avgUpperQuartile;
}
/**
* Returns the average upper quartile gene expression over
* all replicates in all conditions.
*/
public static long getAvgUpperQuartile() {
return Condition.avgUpperQuartile;
}
/**************************************************
********** PRIVATE INSTANCE METHODS **********
**************************************************/
/*************************************
********** MAIN METHOD **********
*************************************/
/**
* The main method is used to test the methods of this class.
*/
public static void main(String[] args) {
}
}
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