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package artificialFastqGenerator;
import java.util.ArrayList;
/**
* An instance of the Nucleobase class corresponds to a nucleobase in the human reference genome. It has fields for its
* genotype, unique integer ID, target coverage, covering reads (i.e. those reads in which it is contained), and coverage.
*
* Copyright (C) 2012 The Institute of Cancer Research (ICR).
*
* This file is part of ArtificialFastqGenerator v1.0.0.
*
* ArtificialFastqGenerator 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 (at your option) any
* later version.
*
* This program 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 Public License along with this program. If not, see
* <http://www.gnu.org/licenses/>
*
* Authour's contact email: Matthew.Frampton@icr.ac.uk
*/
public class Nucleobase {
private char genotype;
private long uniqueID;
private int targetCoverage;
private ArrayList<Read> coveringReads;
private int coverage;
/**
* Initialise a new Nucleobase object.
*
* @param genotype - the nucleobase's genotype.
* @param uniqueID - the nucleobase's unique integer ID.
* @param targetCoverage - the nucleobase's target coverage.
*/
public Nucleobase(char genotype, long uniqueID, int targetCoverage) {
this.genotype = genotype;
this.uniqueID = uniqueID;
this.targetCoverage = targetCoverage;
coveringReads = new ArrayList<Read>();
coverage = 0;
}
/**
* Get the nucleobase's genotype.
*
* @return genotype - the nucleobase's genotype.
*/
public char getGenotype() {
return genotype;
}
/***
* GEt the complement of the nucleobase's genotype.
*
* @return complementGenotype - the complement of the nucleobase's genotype.
*/
public char getComplementGenotype() {
if (this.genotype == 'A') {
return 'T';
} else if (this.genotype == 'C') {
return 'G';
} else if (this.genotype == 'G') {
return 'C';
} else if (this.genotype == 'T') {
return 'A';
} else {
return this.genotype;
}
}
/**
* Set the nucleobase's genotype.
*/
public void setGenotype(char genotype) {
this.genotype = genotype;
}
/**
* Add a read to the list of reads which cover this nucleobase.
*
* @param read - the read which covers this nucleobase.
*/
public void addCoveringRead(Read read) {
coveringReads.add(read);
coverage = coverage + 1;
}
/**
* Get the coverage for this nucleobase i.e. the number of reads which include it.
*
* @return coverage - coverage of the nucleobase.
*/
public int getCoverage() {
return coverage;
}
/**
* Get the list of covering reads - the reads which include this nucleobase.
*
* @return coveringReads - the ArrayList containing the reads which cover this nucleobase.
*/
public ArrayList<Read> getCoveringReads() {
return coveringReads;
}
/**
* Get the nucleobase's unique integer ID.
*
* @return uniqueID - the nucleobase's unique integer ID.
*/
public long getUniqueID() {
return uniqueID;
}
/**
* Get the target coverage for this nucleobase (the number of reads that we want to
* include this nucleobase).
*
* @return targetCoverage - the nucleobase's target coverage.
*/
public int getTargetCoverage() {
return targetCoverage;
}
/**
* Set the target coverage for this nucleobase (the number of reads we want to include
* this nucleobase).
*
* @param targetCoverage - the nucleobase's target coverage.
*/
public void setTargetCoverage(int targetCoverage) {
this.targetCoverage = targetCoverage;
}
/**
* Checks whether a nucleobase's coverage matches its target coverage.
*
* @return coverageMatchesTarget - true if the coverage is >= than the target, else false.
*/
public boolean hasTargetCoverage() {
boolean coverageMatchesTarget = false;
if (this.getCoverage() >= this.getTargetCoverage()) {
coverageMatchesTarget = true;}
return coverageMatchesTarget;
}
public String toString() {
if (Main.outputFormat.equals(Main.DEBUG_NUCLEOBASES_NUC_IDS)) {
return genotype + ":" + this.uniqueID + " ";
} else {
return String.valueOf(genotype);
}
}
}
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