import eu.etaxonomy.cdm.model.reference.Reference;
/**
- * Alignment of multiple single sequences to a consensus sequence,
- * may also include the extracted barcode sequence.
+ * Alignment of multiple {@link SingleRead single sequences} to a consensus sequence.
+ * This sequence is a part of (or the complete) DNA sequences of the related {@link DnaSample DNA Sample},
+ * while
*
- * This class holds information about both the combining process of
+ * <BR>This class holds information about both the combining process of
* {@link SingleRead single sequences} to one consensus sequence
- * (singleReads, contigFile) as well as sequence related information.
- * The later includes the sequence string itself, important genetic information
- * (marker, haplotype) as well as registration information (genetic accession number)
- * citations and barcoding information.
+ * ({@link #getSingleReads() singleReads} , {@link #getContigFile() contigFile} )
+ * as well as sequence related information.
+ * The later includes the {@link #getConsensusSequence() sequence string} itself,
+ * important genetic information about the DNA that has been sequenced
+ * ({@link #getDnaMarker() marker} , {@link #getHaplotype()} haplotype) as well as
+ * registration information ({@link #getGeneticAccessionNumber() genetic accession number} ),
+ * citations, and barcoding information ({@link #getBoldProcessId() BOLD-id},
+ * {@link #getBarcodeSequencePart() barcode sequence}, ...).
*
* @author m.doering
* @created 08-Nov-2007 13:06:51
private static final long serialVersionUID = 8298983152731241775L;
private static final Logger logger = Logger.getLogger(Sequence.class);
+ //TODO move to cdmlib-ext?
private static final String GENBANK_BASE_URI = "http://www.ncbi.nlm.nih.gov/nuccore/%s";
private static final String EMBL_BASE_URI = "http://www.ebi.ac.uk/ena/data/view/%s";
private static final String DDBJ_BASE_URI = "http://getentry.ddbj.nig.ac.jp/getentry/na/%s/?filetype=html";
@XmlElement(name = "ConsensusSequence")
private SequenceString consensusSequence = SequenceString.NewInstance();
-// /**{@link #getSequence()}*/
-// @XmlElement(name = "Sequence")
-// @Lob
-// private String sequence;
-//
-// @XmlElement(name = "Length")
-// private Integer length;
-
-
@XmlAttribute(name = "isBarcode")
private Boolean isBarcode = null;
}
/**
- * The consensus sequence achieved by this sequencing.
+ * The resulting consensus sequence represened by this {@link Sequence sequence} .
+ * The consensus is usually computed from the {@link SingleRead single reads}.
+ * The result of which is stored in a file called {@link #getContigFile() contig file}
+ *
+ * #see {@link #getContigFile()}
+ * #see {@link #getSingleReads()}
*/
public SequenceString getConsensusSequence() {
return consensusSequence;
/**
* The isBarcode flag should be set to true if this (consensus) sequence is or includes
- * a barcode sequence. If the barcode sequence is only a part of the consensus sequence
- * this part is to be stored as {@link #getBarcodeSequencePart() barcode sequence part}.
+ * a barcoding sequence. If the barcoding sequence is only a part of the consensus sequence
+ * this part shall be stored as {@link #getBarcodeSequencePart() barcoding sequence part}.
* A isBarcode value of <code>null</code> indicates that we do have no knowledge
- * wether the sequence is a barcoding sequence or not.
+ * whether the sequence is a barcoding sequence or not.
*
* @see #getBarcodeSequencePart()
* @see #getSequenceString()
/**
* If the barcode sequence string does not include 100% of the (consensus) sequence
* the part used as barcode is provided here. However, the barcode part
- * should be kept if consensus sequence string and barcode sequence string are equal.
+ * should be kept empty if consensus sequence string and barcode sequence string are equal.
*
* @see #getIsBarcode()
*/
}
/**
- * @see #getBarcodeSequence()
+ * @see #getBarcodeSequencePart()
*/
- public void setBarcodeSequence(SequenceString barcodeSequencePart) {
+ public void setBarcodeSequencePart(SequenceString barcodeSequencePart) {
if (barcodeSequencePart == null){
barcodeSequencePart = SequenceString.NewInstance();
}
}
/**
- * Sets the {@link TermType#DnaMarker marker} examined and described by this sequencing.
+ * 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(){
}
/**
- * The accession number used in GenBank, EMBL and DDBJ.
+ * The accession number used in GenBank, EMBL and DDBJ.
* @return
*/
public String getGeneticAccessionNumber() {
/**
* The contigFile containing all data and data processing for this sequencing.
+ *
+ * @see #getConsensusSequence()
+ * @see #getSingleReads()
*/
public Media getContigFile() {
return contigFile;
}
/**
- * The single reads that where used to create this consensus sequence.
+ * The {@link SingleRead single reads} that were used to build this consensus sequence.
+ *
+ * @see #getConsensusSequence()
+ * @see #getContigFile()
*/
public Set<SingleRead> getSingleReads() {
return singleReads;
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