Package org.biojavax.bio.seq.io
Class UniProtXMLFormat.Terms
java.lang.Object
org.biojavax.bio.seq.RichSequence.Terms
org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
- Enclosing class:
UniProtXMLFormat
Implements some UniProtXML-specific terms.
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
static final String
Fields inherited from class org.biojavax.bio.seq.RichSequence.Terms
DOI_KEY, MEDLINE_KEY, PLASMID_KEY, PUBMED_KEY, SPECIES_KEY, STRAIN_KEY, TISSUE_KEY, TRANSPOSON_KEY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic ComparableTerm
Getter for the evidence attr termstatic ComparableTerm
Getter for the evidence category termstatic ComparableTerm
Getter for the evidence date termstatic ComparableTerm
Getter for the evidence type termstatic ComparableTerm
Getter for the feature original termstatic ComparableTerm
Getter for the feature ref termstatic ComparableTerm
Getter for the feature status termstatic ComparableTerm
Getter for the feature variation termstatic ComparableTerm
Getter for the location seq termstatic ComparableTerm
Getter for the protein exists termstatic ComparableTerm
Getter for the protein type termstatic ComparableOntology
Getter for the private uniprot ontology.static ComparableTerm
Getter for the UniProtXML termMethods inherited from class org.biojavax.bio.seq.RichSequence.Terms
getAdditionalAccessionTerm, getCopyrightTerm, getDataClassTerm, getDateAnnotatedTerm, getDateCreatedTerm, getDateUpdatedTerm, getFeatureDescTerm, getFTIdTerm, getGeneNameTerm, getGeneSynonymTerm, getKeywordTerm, getMolTypeTerm, getOrderedLocusNameTerm, getORFNameTerm, getOrganelleTerm, getPlasmidTerm, getRelAnnotatedTerm, getRelCreatedTerm, getRelUpdatedTerm, getSpeciesTerm, getStrainTerm, getStrandedTerm, getTissueTerm, getTransposonTerm
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Field Details
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CONTAINS_PREFIX
- See Also:
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INCLUDES_PREFIX
- See Also:
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GENENAME_KEY
- See Also:
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GENESYNONYM_KEY
- See Also:
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ORDLOCNAME_KEY
- See Also:
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ORFNAME_KEY
- See Also:
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NCBI_TAXON_KEY
- See Also:
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COMMON_NAME_KEY
- See Also:
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FULL_NAME_KEY
- See Also:
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SCIENTIFIC_NAME_KEY
- See Also:
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SYNONYM_NAME_KEY
- See Also:
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ABBREV_NAME_KEY
- See Also:
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LOC_FUZZY_START_KEY
- See Also:
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LOC_FUZZY_END_KEY
- 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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getProteinExistsTerm
Getter for the protein exists term- Returns:
- The protein exists Term
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getUniprotKWOnto
Getter for the private uniprot ontology.- Returns:
- the ontology.
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getUniProtXMLTerm
Getter for the UniProtXML term- Returns:
- The UniProtXML Term
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getProteinTypeTerm
Getter for the protein type term- Returns:
- The protein type Term
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getEvidenceCategoryTerm
Getter for the evidence category term- Returns:
- The evidence category Term
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getEvidenceTypeTerm
Getter for the evidence type term- Returns:
- The evidence type Term
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getEvidenceDateTerm
Getter for the evidence date term- Returns:
- The evidence date Term
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getEvidenceAttrTerm
Getter for the evidence attr term- Returns:
- The evidence attr Term
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getFeatureRefTerm
Getter for the feature ref term- Returns:
- The feature ref Term
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getFeatureStatusTerm
Getter for the feature status term- Returns:
- The feature status Term
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getFeatureOriginalTerm
Getter for the feature original term- Returns:
- The feature original Term
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getFeatureVariationTerm
Getter for the feature variation term- Returns:
- The feature variation Term
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getLocationSequenceTerm
Getter for the location seq term- Returns:
- The location seq Term
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