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/**
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* Copyright (C) 2018 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service.dto;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.util.HashSet;
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import java.util.Set;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.molecular.SequenceString;
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import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
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import eu.etaxonomy.cdm.model.reference.Reference;
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/**
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* @author k.luther
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* @since 02.08.2018
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*
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*/
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public class SequenceDTO {
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private Media contigFile;
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private SequenceString consensusSequence;
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private Boolean isBarcode = null;
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private SequenceString barcodeSequencePart = SequenceString.NewInstance();
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private String geneticAccessionNumber;
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private String boldProcessId;
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private Set<SingleReadAlignment> singleReadAlignments = new HashSet<SingleReadAlignment>();
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private String dnaMarker;
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private String haplotype;
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private Set<Reference> citations = new HashSet<>();
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private URI boldUri;
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private URI ddbjUri;
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private URI emblUri;
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private URI genBankUri;
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public SequenceDTO(Sequence seq){
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contigFile = seq.getContigFile();
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consensusSequence = seq.getConsensusSequence();
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isBarcode = seq.getIsBarcode();
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barcodeSequencePart = seq.getBarcodeSequencePart();
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geneticAccessionNumber = seq.getGeneticAccessionNumber();
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boldProcessId = seq.getBoldProcessId();
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singleReadAlignments = seq.getSingleReadAlignments();
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dnaMarker = seq.getDnaMarker().getLabel();
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haplotype = seq.getHaplotype();
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citations = seq.getCitations();
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try{
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boldUri = seq.getBoldUri();
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ddbjUri = seq.getDdbjUri();
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emblUri = seq.getEmblUri();
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genBankUri = seq.getGenBankUri();
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} catch (URISyntaxException e){
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//TODO
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}
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}
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/**
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* @return the boldUri
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*/
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public URI getBoldUri() {
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return boldUri;
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}
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/**
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* @return the ddbjUri
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*/
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public URI getDdbjUri() {
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return ddbjUri;
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}
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/**
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* @return the emblUri
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*/
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public URI getEmblUri() {
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return emblUri;
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}
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/**
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* @return the genBankUri
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*/
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public URI getGenBankUri() {
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return genBankUri;
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}
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/**
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* @return the contigFile
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*/
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public Media getContigFile() {
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return contigFile;
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}
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/**
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* @return the consensusSequence
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*/
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public SequenceString getConsensusSequence() {
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return consensusSequence;
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}
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/**
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* @return the isBarcode
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*/
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public Boolean getIsBarcode() {
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return isBarcode;
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}
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/**
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* @return the barcodeSequencePart
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*/
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public SequenceString getBarcodeSequencePart() {
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return barcodeSequencePart;
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}
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/**
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* @return the geneticAccessionNumber
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*/
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public String getGeneticAccessionNumber() {
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return geneticAccessionNumber;
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}
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/**
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* @return the boldProcessId
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*/
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public String getBoldProcessId() {
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return boldProcessId;
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}
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/**
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* @return the singleReadAlignments
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*/
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public Set<SingleReadAlignment> getSingleReadAlignments() {
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return singleReadAlignments;
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}
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/**
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* @return the dnaMarker
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*/
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public String getDnaMarker() {
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return dnaMarker;
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}
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/**
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* @return the haplotype
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*/
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public String getHaplotype() {
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return haplotype;
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}
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/**
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* @return the citations
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*/
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public Set<Reference> getCitations() {
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return citations;
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}
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}
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