+ /**
+ * @see #getBarcodeSequencePart()
+ */
+ public void setBarcodeSequencePart(SequenceString barcodeSequencePart) {
+ if (barcodeSequencePart == null){
+ barcodeSequencePart = SequenceString.NewInstance();
+ }
+ this.barcodeSequencePart = barcodeSequencePart;
+ }
+
+ /**
+ * Sets the {@link TermType#DnaMarker DNA marker} examined and described by this sequencing.
+ * The marker should usually be similar to the one used in the according {@link Amplification
+ * amplification process}. However, it may slightly differ, or, if multiple amplifications where
+ * used to build this consensus sequence it may be the super set of the markers used in amplification.
+ *
+ * @return
+ */
+ public DefinedTerm getDnaMarker(){
+ return this.dnaMarker;
+ }
+
+ /**
+ * @see #getDnaMarker()
+ * @param marker
+ */
+ public void setDnaMarker(DefinedTerm dnaMarker){
+ this.dnaMarker = dnaMarker;
+ }
+
+ /**
+ * The accession number used in GenBank, EMBL and DDBJ.
+ * @return
+ */
+ public String getGeneticAccessionNumber() {
+ return geneticAccessionNumber;
+ }
+
+ /**
+ * Sets the genetic accession number.
+ * @see #getGeneticAccessionNumber()
+ */
+ public void setGeneticAccessionNumber(String geneticAccessionNumber) {
+ this.geneticAccessionNumber = geneticAccessionNumber;
+ }
+
+
+ /**
+ * The identifier used by the Barcode of Life Data Systems (BOLD, http://www.boldsystems.org/).
+ */
+ public String getBoldProcessId() {
+ return boldProcessId;
+ }
+
+ public void setBoldProcessId(String boldProcessId) {
+ this.boldProcessId = boldProcessId;
+ }
+
+ /**
+ * Returns the name of the haplotype.
+ * A haplotype (haploide genotype) is a variant of nucleotide sequences on the same chromosome.
+ * A certain haplotype may be specific for an individual, a population or a species.
+ * @return
+ */
+ public String getHaplotype() {
+ return haplotype;
+ }
+
+ /**
+ * @see #getHaplotype()
+ */
+ public void setHaplotype(String haplotype) {
+ this.haplotype = haplotype;
+ }
+
+ /**
+ * The contigFile containing all data and data processing for this sequencing.
+ *
+ * @see #getConsensusSequence()
+ * @see #getSingleReads()
+ */
+ public Media getContigFile() {
+ return contigFile;
+ }
+
+ /**
+ * @see #getContigFile()
+ */
+ public void setContigFile(Media contigFile) {
+ this.contigFile = contigFile;
+ }
+
+
+ /**
+ * Citations are the set of references in which this sequence was published.
+ * Unlike taxonomic names the first publication of a sequence
+ * is not so important (maybe because it is required by publishers
+ * that they are all registered at Genbank) therefore we do not have something like an
+ * "original reference" attribute.<BR>
+ * Links to these references are to be stored within the reference itself.
+ * @return the set of references in which this sequence was published.
+ */
+ public Set<Reference> getCitations() {