Package org.biojavax.bio.seq
Class RichSequence.Terms
java.lang.Object
org.biojavax.bio.seq.RichSequence.Terms
- Direct Known Subclasses:
EMBLFormat.Terms
,EMBLxmlFormat.Terms
,GenbankFormat.Terms
,INSDseqFormat.Terms
,UniProtFormat.Terms
,UniProtXMLFormat.Terms
- Enclosing interface:
RichSequence
Stores a number of useful terms used across many sequence formats for
consistency's sake.
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
Holds a reference to the key that must be used to store DOI references.static final String
Holds a reference to the key that must be used to store Medline references.static String
static final String
Holds a reference to the key that must be used to store PubMed references.static String
static String
static String
static String
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic ComparableTerm
Getter for the secondary/tertiary/additional accession termstatic ComparableTerm
Getter for the copyright termstatic ComparableTerm
Getter for the DataClass termstatic ComparableTerm
Getter for the date annotated termstatic ComparableTerm
Getter for the date created termstatic ComparableTerm
Getter for the date updated termstatic ComparableTerm
Getter for the FeatureDesc termstatic ComparableTerm
Getter for the FTId termstatic ComparableTerm
Getter for the GeneName termstatic ComparableTerm
Getter for the GeneSynonym termstatic ComparableTerm
Getter for the keyword termstatic ComparableTerm
getter for the MolType termstatic ComparableTerm
Getter for the OrderedLocusName termstatic ComparableTerm
Getter for the ORFName termstatic ComparableTerm
Getter for the Organelle termstatic ComparableTerm
Getter for the Plasmid termstatic ComparableTerm
Getter for the release annotated termstatic ComparableTerm
Getter for the release created termstatic ComparableTerm
Getter for the release updated termstatic ComparableTerm
Getter for the Species termstatic ComparableTerm
Getter for the Strain termstatic ComparableTerm
Getter for the Strand term; legal values are "single", "double", and "mixed".static ComparableTerm
Getter for the Tissue termstatic ComparableTerm
Getter for the Transposon term
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Field Details
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SPECIES_KEY
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STRAIN_KEY
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TISSUE_KEY
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TRANSPOSON_KEY
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PLASMID_KEY
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PUBMED_KEY
Holds a reference to the key that must be used to store PubMed references.- See Also:
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MEDLINE_KEY
Holds a reference to the key that must be used to store Medline references.- See Also:
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DOI_KEY
Holds a reference to the key that must be used to store DOI references.- See Also:
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Constructor Details
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Terms
public Terms()
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Method Details
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getAdditionalAccessionTerm
Getter for the secondary/tertiary/additional accession term- Returns:
- A Term that represents the secondary accession tag
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getKeywordTerm
Getter for the keyword term- Returns:
- a Term that represents the Keyword tag
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getDateCreatedTerm
Getter for the date created term- Returns:
- a Term
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getDateUpdatedTerm
Getter for the date updated term- Returns:
- a Term
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getDateAnnotatedTerm
Getter for the date annotated term- Returns:
- a Term
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getRelCreatedTerm
Getter for the release created term- Returns:
- a Term
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getRelUpdatedTerm
Getter for the release updated term- Returns:
- a Term
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getRelAnnotatedTerm
Getter for the release annotated term- Returns:
- a Term
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getMolTypeTerm
getter for the MolType term- Returns:
- a Term that represents the molecule type
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getStrandedTerm
Getter for the Strand term; legal values are "single", "double", and "mixed".- Returns:
- a Term that represents the Strand tag
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getOrganelleTerm
Getter for the Organelle term- Returns:
- a Term that represents the Organelle tag
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getGeneNameTerm
Getter for the GeneName term- Returns:
- The GeneName Term
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getGeneSynonymTerm
Getter for the GeneSynonym term- Returns:
- The GeneSynonym Term
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getOrderedLocusNameTerm
Getter for the OrderedLocusName term- Returns:
- The OrderedLocusName Term
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getORFNameTerm
Getter for the ORFName term- Returns:
- The ORFName Term
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getStrainTerm
Getter for the Strain term- Returns:
- The Strain Term
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getSpeciesTerm
Getter for the Species term- Returns:
- The Species Term
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getTissueTerm
Getter for the Tissue term- Returns:
- The Tissue Term
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getTransposonTerm
Getter for the Transposon term- Returns:
- The Transposon Term
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getPlasmidTerm
Getter for the Plasmid term- Returns:
- The plasmid Term
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getDataClassTerm
Getter for the DataClass term- Returns:
- The DataClass Term
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getFTIdTerm
Getter for the FTId term- Returns:
- The FTId Term
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getFeatureDescTerm
Getter for the FeatureDesc term- Returns:
- The FeatureDesc Term
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getCopyrightTerm
Getter for the copyright term- Returns:
- The copyright Term
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