94 lines
2.5 KiB
Java
94 lines
2.5 KiB
Java
/*
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* The Broad Institute
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* SOFTWARE COPYRIGHT NOTICE AGREEMENT
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* This software and its documentation are copyright 2009 by the
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* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
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*
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* This software is supplied without any warranty or guaranteed support whatsoever. Neither
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* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
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*/
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package edu.mit.broad.sam;
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import java.util.List;
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import java.util.ArrayList;
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import java.util.Collections;
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/**
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* A list of CigarElements, which describes how a read aligns with the reference.
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* E.g. the Cigar string 10M1D25M means
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* * match or mismatch for 10 bases
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* * deletion of 1 base
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* * match or mismatch for 25 bases
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*/
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public class Cigar {
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private final List<CigarElement> cigarElements = new ArrayList<CigarElement>();
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public Cigar() {
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}
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public Cigar(final List<CigarElement> cigarElements) {
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this.cigarElements.addAll(cigarElements);
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}
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public List<CigarElement> getCigarElements() {
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return Collections.unmodifiableList(cigarElements);
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}
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public CigarElement getCigarElement(final int i) {
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return cigarElements.get(i);
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}
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public void add(final CigarElement cigarElement) {
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cigarElements.add(cigarElement);
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}
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public int numCigarElements() {
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return cigarElements.size();
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}
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public int getReferenceLength() {
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int length = 0;
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for (CigarElement element : cigarElements) {
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switch (element.getOperator()) {
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case M:
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case D:
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case N:
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length += element.getLength();
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}
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}
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return length;
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}
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public int getPaddedReferenceLength() {
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int length = 0;
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for (CigarElement element : cigarElements) {
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switch (element.getOperator()) {
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case M:
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case D:
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case N:
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case P:
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length += element.getLength();
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}
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}
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return length;
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}
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@Override
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public boolean equals(final Object o) {
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if (this == o) return true;
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if (!(o instanceof Cigar)) return false;
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final Cigar cigar = (Cigar) o;
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if (cigarElements != null ? !cigarElements.equals(cigar.cigarElements) : cigar.cigarElements != null)
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return false;
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return true;
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}
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@Override
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public int hashCode() {
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return cigarElements != null ? cigarElements.hashCode() : 0;
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}
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}
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