cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/dto/SequenceDTO.java

   1 /**
   2 * Copyright (C) 2018 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.api.service.dto;
  10
  11 import java.net.URI;
  12 import java.net.URISyntaxException;
  13 import java.util.HashSet;
  14 import java.util.Set;
  15
  16 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  17 import eu.etaxonomy.cdm.model.media.Media;
  18 import eu.etaxonomy.cdm.model.molecular.Sequence;
  19 import eu.etaxonomy.cdm.model.molecular.SequenceString;
  20 import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
  21 import eu.etaxonomy.cdm.model.reference.Reference;
  22
  23 /**
  24  * @author k.luther
  25  * @since 02.08.2018
  26  *
  27  */
  28 public class SequenceDTO {
  29
  30     private Media contigFile;
  31
  32     private SequenceString consensusSequence = SequenceString.NewInstance();
  33
  34
  35     private Boolean isBarcode = null;
  36
  37
  38     private SequenceString barcodeSequencePart = SequenceString.NewInstance();
  39
  40
  41     private String geneticAccessionNumber;
  42
  43
  44     private String boldProcessId;
  45
  46
  47     private Set<SingleReadAlignment> singleReadAlignments = new HashSet<SingleReadAlignment>();
  48
  49
  50     private DefinedTerm dnaMarker;
  51
  52
  53
  54     private String haplotype;
  55
  56
  57     private Set<Reference> citations = new HashSet<>();
  58
  59     private URI boldUri;
  60     private URI ddbjUri;
  61     private URI emblUri;
  62     private URI genBankUri;
  63
  64     public SequenceDTO(Sequence seq){
  65         contigFile = seq.getContigFile();
  66         consensusSequence = seq.getConsensusSequence();
  67         isBarcode = seq.getIsBarcode();
  68         barcodeSequencePart = seq.getBarcodeSequencePart();
  69         geneticAccessionNumber = seq.getGeneticAccessionNumber();
  70         boldProcessId = seq.getBoldProcessId();
  71         singleReadAlignments = seq.getSingleReadAlignments();
  72         dnaMarker = seq.getDnaMarker();
  73         haplotype = seq.getHaplotype();
  74         citations = seq.getCitations();
  75         try{
  76             boldUri = seq.getBoldUri();
  77             ddbjUri = seq.getDdbjUri();
  78             emblUri = seq.getEmblUri();
  79             genBankUri = seq.getGenBankUri();
  80         } catch (URISyntaxException e){
  81 //TODO
  82         }
  83
  84     }
  85
  86
  87
  88     /**
  89      * @return the boldUri
  90      */
  91     public URI getBoldUri() {
  92         return boldUri;
  93     }
  94
  95
  96     /**
  97      * @return the ddbjUri
  98      */
  99     public URI getDdbjUri() {
 100         return ddbjUri;
 101     }
 102
 103
 104     /**
 105      * @return the emblUri
 106      */
 107     public URI getEmblUri() {
 108         return emblUri;
 109     }
 110
 111
 112     /**
 113      * @return the genBankUri
 114      */
 115     public URI getGenBankUri() {
 116         return genBankUri;
 117     }
 118
 119
 120     /**
 121      * @return the contigFile
 122      */
 123     public Media getContigFile() {
 124         return contigFile;
 125     }
 126
 127
 128     /**
 129      * @return the consensusSequence
 130      */
 131     public SequenceString getConsensusSequence() {
 132         return consensusSequence;
 133     }
 134
 135
 136     /**
 137      * @return the isBarcode
 138      */
 139     public Boolean getIsBarcode() {
 140         return isBarcode;
 141     }
 142
 143
 144     /**
 145      * @return the barcodeSequencePart
 146      */
 147     public SequenceString getBarcodeSequencePart() {
 148         return barcodeSequencePart;
 149     }
 150
 151
 152     /**
 153      * @return the geneticAccessionNumber
 154      */
 155     public String getGeneticAccessionNumber() {
 156         return geneticAccessionNumber;
 157     }
 158
 159
 160     /**
 161      * @return the boldProcessId
 162      */
 163     public String getBoldProcessId() {
 164         return boldProcessId;
 165     }
 166
 167
 168     /**
 169      * @return the singleReadAlignments
 170      */
 171     public Set<SingleReadAlignment> getSingleReadAlignments() {
 172         return singleReadAlignments;
 173     }
 174
 175
 176     /**
 177      * @return the dnaMarker
 178      */
 179     public DefinedTerm getDnaMarker() {
 180         return dnaMarker;
 181     }
 182
 183
 184     /**
 185      * @return the haplotype
 186      */
 187     public String getHaplotype() {
 188         return haplotype;
 189     }
 190
 191
 192     /**
 193      * @return the citations
 194      */
 195     public Set<Reference> getCitations() {
 196         return citations;
 197     }
 198 }