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/**
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* Copyright (C) 2015 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.io.Serializable;
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import java.net.URISyntaxException;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.List;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
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import eu.etaxonomy.cdm.model.media.MediaUtils;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.molecular.SingleRead;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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/**
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* @author pplitzner
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* @since Mar 26, 2015
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*/
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public class DerivateDataDTO implements Serializable {
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private static final long serialVersionUID = 8329871164348514709L;
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private static final Logger logger = Logger.getLogger(DerivateDataDTO.class);
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private List<Link> specimenScans = new ArrayList<>();
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private List<MolecularData> molecularDataList = new ArrayList<>();
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private List<Link> detailImages = new ArrayList<>();
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private List<UUID> specimenScanUuids = new ArrayList<>();
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private List<UUID> detailImageUuids = new ArrayList<>();
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public static DerivateDataDTO fromEntity(SpecimenOrObservationBase<?> specimenOrObservation, String specimenIdentifier) {
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DerivateDataDTO derivateDataDTO = new DerivateDataDTO();
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Collection<DerivedUnit> childDerivates = specimenOrObservation.collectDerivedUnits();
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for (DerivedUnit childDerivate : childDerivates) {
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// assemble molecular data
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//pattern: DNAMarker [contig1, primer1_1, primer1_2, ...][contig2, primer2_1, ...]...
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if (childDerivate.isInstanceOf(DnaSample.class)) {
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if (childDerivate.getRecordBasis() == SpecimenOrObservationType.TissueSample) {
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// TODO implement TissueSample assembly for web service
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}
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if (childDerivate.getRecordBasis() == SpecimenOrObservationType.DnaSample) {
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DnaSample dna = HibernateProxyHelper.deproxy(childDerivate, DnaSample.class);
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for (Sequence sequence : dna.getSequences()) {
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URI boldUri = null;
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try {
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boldUri = sequence.getBoldUri();
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} catch (URISyntaxException e1) {
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// TODO consider better reporting of this incident
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logger.error("Could not create BOLD URI", e1);
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}
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final DefinedTerm dnaMarker = sequence.getDnaMarker();
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Link providerLink = null;
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if(boldUri!=null && dnaMarker!=null){
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providerLink = new DerivateDataDTO.Link(boldUri, dnaMarker.getLabel());
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}
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MolecularData molecularData = derivateDataDTO.addProviderLink(providerLink);
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//contig file
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ContigFile contigFile = null;
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if (sequence.getContigFile() != null) {
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MediaRepresentationPart contigMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(sequence.getContigFile());
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if (contigMediaRepresentationPart != null) {
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contigFile = molecularData.addContigFile(new Link(contigMediaRepresentationPart.getUri(), "contig"));
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}
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}
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else{
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contigFile = molecularData.addContigFile(null);
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}
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// primer files
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if (sequence.getSingleReads() != null) {
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int readCount = 1;
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for (SingleRead singleRead : sequence.getSingleReads()) {
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MediaRepresentationPart pherogramMediaRepresentationPart = MediaUtils.getFirstMediaRepresentationPart(singleRead.getPherogram());
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if (pherogramMediaRepresentationPart != null && contigFile != null) {
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contigFile.addPrimerLink(pherogramMediaRepresentationPart.getUri(), "read"+readCount++);
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}
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}
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}
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}
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}
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}
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// assemble media data
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else if (childDerivate.isInstanceOf(MediaSpecimen.class)) {
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MediaSpecimen media = HibernateProxyHelper.deproxy(childDerivate, MediaSpecimen.class);
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URI mediaUri = getMediaUri(media);
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if (media.getKindOfUnit() != null) {
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// specimen scan
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if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidSpecimenScan)) {
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derivateDataDTO.addSpecimenScanUuid(media.getMediaSpecimen().getUuid());
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String imageLinkText = "scan";
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imageLinkText = specimenIdentifier;
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derivateDataDTO.addSpecimenScan(mediaUri, imageLinkText);
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}
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// detail image
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else if (media.getKindOfUnit().getUuid().equals(DefinedTerm.uuidDetailImage)) {
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derivateDataDTO.addDetailImageUuid(media.getMediaSpecimen().getUuid());
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String motif = "detail image";
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if (media.getMediaSpecimen()!=null){
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if(CdmUtils.isNotBlank(media.getMediaSpecimen().getTitleCache())) {
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motif = media.getMediaSpecimen().getTitleCache();
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}
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}
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derivateDataDTO.addDetailImage(mediaUri, motif);
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}
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}
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}
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}
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return derivateDataDTO;
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}
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@Deprecated
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private static URI getMediaUri(MediaSpecimen mediaSpecimen) {
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URI mediaUri = null;
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Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
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if (mediaRepresentations != null && !mediaRepresentations.isEmpty()) {
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Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
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if (mediaRepresentationParts != null && !mediaRepresentationParts.isEmpty()) {
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MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
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if (part.getUri() != null) {
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mediaUri = part.getUri();
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}
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}
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}
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return mediaUri;
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}
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/**
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* @return the molecularData
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*/
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public List<MolecularData> getMolecularDataList() {
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return molecularDataList;
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}
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public MolecularData addProviderLink(Link providerLink) {
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MolecularData molecularData = new MolecularData(providerLink);
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this.molecularDataList.add(molecularData);
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return molecularData;
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}
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/**
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* @return the specimenScans
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*/
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public List<Link> getSpecimenScans() {
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return specimenScans;
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}
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public void addSpecimenScan(URI uri, String linkText){
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specimenScans.add(new Link(uri, linkText));
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}
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/**
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* @return the detailImages
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*/
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public List<Link> getDetailImages() {
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return detailImages;
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}
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public void addDetailImage(URI uri, String motif){
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detailImages.add(new Link(uri, motif));
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}
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/**
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* @return the specimenScanUuids
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*/
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public List<UUID> getSpecimenScanUuids() {
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return specimenScanUuids;
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}
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public void addSpecimenScanUuid(UUID uuid){
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specimenScanUuids.add(uuid);
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}
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/**
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* @return the detailImageUuids
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*/
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public List<UUID> getDetailImageUuids() {
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return detailImageUuids;
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}
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public void addDetailImageUuid(UUID uuid){
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detailImageUuids.add(uuid);
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}
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public class MolecularData implements Serializable{
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private static final long serialVersionUID = -3509828381796659200L;
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private final Link providerLink;
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private List<ContigFile> contigFiles;
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public MolecularData(Link providerLink) {
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super();
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this.providerLink = providerLink;
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}
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public ContigFile addContigFile(Link contigLink){
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if(contigFiles==null){
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contigFiles = new ArrayList<ContigFile>();
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}
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ContigFile contigFile = new ContigFile(contigLink);
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contigFiles.add(contigFile);
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return contigFile;
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}
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public synchronized Link getProviderLink() {
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return providerLink;
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}
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public List<ContigFile> getContigFiles() {
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return contigFiles;
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}
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}
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public class ContigFile implements Serializable{
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private final Link contigLink;
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private List<Link> primerLinks;
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public ContigFile(Link contigLink) {
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this.contigLink = contigLink;
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}
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public void addPrimerLink(URI uri, String linkText){
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if(primerLinks==null){
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primerLinks = new ArrayList<Link>();
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}
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primerLinks.add(new Link(uri, linkText));
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}
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public Link getContigLink() {
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return contigLink;
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}
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public List<Link> getPrimerLinks() {
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return primerLinks;
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}
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}
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public static class Link implements Serializable{
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private static final long serialVersionUID = 6635385359662624579L;
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private String linkText;
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private URI uri;
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public Link(URI uri, String linkText) {
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super();
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this.linkText = linkText;
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this.uri = uri;
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}
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/**
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* @return the linkText
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*/
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public synchronized String getLinkText() {
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return linkText;
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}
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/**
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* @param linkText the linkText to set
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*/
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public synchronized void setLinkText(String linkText) {
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this.linkText = linkText;
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}
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/**
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* @return the uri
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*/
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public synchronized URI getUri() {
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return uri;
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}
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/**
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* @param uri the uri to set
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*/
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public synchronized void setUri(URI uri) {
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this.uri = uri;
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}
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@Override
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public int hashCode() {
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final int prime = 31;
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int result = 1;
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result = prime * result + ((linkText == null) ? 0 : linkText.hashCode());
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result = prime * result + ((uri == null) ? 0 : uri.hashCode());
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return result;
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}
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@Override
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public boolean equals(Object obj) {
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if (this == obj) {
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return true;
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}
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if (obj == null) {
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return false;
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}
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if (getClass() != obj.getClass()) {
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return false;
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}
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Link other = (Link) obj;
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if (linkText == null) {
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if (other.linkText != null) {
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return false;
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}
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} else if (!linkText.equals(other.linkText)) {
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return false;
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}
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if (uri == null) {
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if (other.uri != null) {
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return false;
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}
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} else if (!uri.equals(other.uri)) {
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return false;
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}
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return true;
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}
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}
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}
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