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

public static class UniProtXMLFormat.Terms
extends RichSequence.Terms

Implements some UniProtXML-specific terms.

Field Summary

Fields

Modifier and Type	Field and Description
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

Constructors

Constructor and Description
UniProtXMLFormat.Terms()

Method Summary

Methods

Modifier and Type	Method and Description
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