org.biojavax.bio.seq.io
Class UniProtXMLFormat.Terms

java.lang.Object
  extended by org.biojavax.bio.seq.RichSequence.Terms
      extended by org.biojavax.bio.seq.io.UniProtXMLFormat.Terms
Enclosing class:
UniProtXMLFormat

public static class UniProtXMLFormat.Terms
extends RichSequence.Terms

Implements some UniProtXML-specific terms.


Field Summary
static String ABBREV_NAME_KEY
           
static String COMMON_NAME_KEY
           
static String CONTAINS_PREFIX
           
static String FULL_NAME_KEY
           
static String GENENAME_KEY
           
static String GENESYNONYM_KEY
           
static String INCLUDES_PREFIX
           
static String LOC_FUZZY_END_KEY
           
static String LOC_FUZZY_START_KEY
           
static String NCBI_TAXON_KEY
           
static String ORDLOCNAME_KEY
           
static String ORFNAME_KEY
           
static String SCIENTIFIC_NAME_KEY
           
static String SYNONYM_NAME_KEY
           
 
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
 
Constructor Summary
UniProtXMLFormat.Terms()
           
 
Method Summary
static ComparableTerm getEvidenceAttrTerm()
          Getter for the evidence attr term
static ComparableTerm getEvidenceCategoryTerm()
          Getter for the evidence category term
static ComparableTerm getEvidenceDateTerm()
          Getter for the evidence date term
static ComparableTerm getEvidenceTypeTerm()
          Getter for the evidence type term
static ComparableTerm getFeatureOriginalTerm()
          Getter for the feature original term
static ComparableTerm getFeatureRefTerm()
          Getter for the feature ref term
static ComparableTerm getFeatureStatusTerm()
          Getter for the feature status term
static ComparableTerm getFeatureVariationTerm()
          Getter for the feature variation term
static ComparableTerm getLocationSequenceTerm()
          Getter for the location seq term
static ComparableTerm getProteinExistsTerm()
          Getter for the protein exists term
static ComparableTerm getProteinTypeTerm()
          Getter for the protein type term
static ComparableOntology getUniprotKWOnto()
          Getter for the private uniprot ontology.
static ComparableTerm getUniProtXMLTerm()
          Getter for the UniProtXML term
 
Methods 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
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

CONTAINS_PREFIX

public static final String CONTAINS_PREFIX
See Also:
Constant Field Values

INCLUDES_PREFIX

public static final String INCLUDES_PREFIX
See Also:
Constant Field Values

GENENAME_KEY

public static final String GENENAME_KEY
See Also:
Constant Field Values

GENESYNONYM_KEY

public static final String GENESYNONYM_KEY
See Also:
Constant Field Values

ORDLOCNAME_KEY

public static final String ORDLOCNAME_KEY
See Also:
Constant Field Values

ORFNAME_KEY

public static final String ORFNAME_KEY
See Also:
Constant Field Values

NCBI_TAXON_KEY

public static final String NCBI_TAXON_KEY
See Also:
Constant Field Values

COMMON_NAME_KEY

public static final String COMMON_NAME_KEY
See Also:
Constant Field Values

FULL_NAME_KEY

public static final String FULL_NAME_KEY
See Also:
Constant Field Values

SCIENTIFIC_NAME_KEY

public static final String SCIENTIFIC_NAME_KEY
See Also:
Constant Field Values

SYNONYM_NAME_KEY

public static final String SYNONYM_NAME_KEY
See Also:
Constant Field Values

ABBREV_NAME_KEY

public static final String ABBREV_NAME_KEY
See Also:
Constant Field Values

LOC_FUZZY_START_KEY

public static final String LOC_FUZZY_START_KEY
See Also:
Constant Field Values

LOC_FUZZY_END_KEY

public static final String LOC_FUZZY_END_KEY
See Also:
Constant Field Values
Constructor Detail

UniProtXMLFormat.Terms

public UniProtXMLFormat.Terms()
Method Detail

getProteinExistsTerm

public static ComparableTerm getProteinExistsTerm()
Getter for the protein exists term

Returns:
The protein exists Term

getUniprotKWOnto

public static ComparableOntology getUniprotKWOnto()
Getter for the private uniprot ontology.

Returns:
the ontology.

getUniProtXMLTerm

public static ComparableTerm getUniProtXMLTerm()
Getter for the UniProtXML term

Returns:
The UniProtXML Term

getProteinTypeTerm

public static ComparableTerm getProteinTypeTerm()
Getter for the protein type term

Returns:
The protein type Term

getEvidenceCategoryTerm

public static ComparableTerm getEvidenceCategoryTerm()
Getter for the evidence category term

Returns:
The evidence category Term

getEvidenceTypeTerm

public static ComparableTerm getEvidenceTypeTerm()
Getter for the evidence type term

Returns:
The evidence type Term

getEvidenceDateTerm

public static ComparableTerm getEvidenceDateTerm()
Getter for the evidence date term

Returns:
The evidence date Term

getEvidenceAttrTerm

public static ComparableTerm getEvidenceAttrTerm()
Getter for the evidence attr term

Returns:
The evidence attr Term

getFeatureRefTerm

public static ComparableTerm getFeatureRefTerm()
Getter for the feature ref term

Returns:
The feature ref Term

getFeatureStatusTerm

public static ComparableTerm getFeatureStatusTerm()
Getter for the feature status term

Returns:
The feature status Term

getFeatureOriginalTerm

public static ComparableTerm getFeatureOriginalTerm()
Getter for the feature original term

Returns:
The feature original Term

getFeatureVariationTerm

public static ComparableTerm getFeatureVariationTerm()
Getter for the feature variation term

Returns:
The feature variation Term

getLocationSequenceTerm

public static ComparableTerm getLocationSequenceTerm()
Getter for the location seq term

Returns:
The location seq Term