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

public static class RichSequence.Terms
extends Object

Stores a number of useful terms used across many sequence formats for consistency's sake.

Field Summary

static String	DOI_KEY Holds a reference to the key that must be used to store DOI references.
static String	MEDLINE_KEY Holds a reference to the key that must be used to store Medline references.
static String	PLASMID_KEY
static String	PUBMED_KEY Holds a reference to the key that must be used to store PubMed references.
static String	SPECIES_KEY
static String	STRAIN_KEY
static String	TISSUE_KEY
static String	TRANSPOSON_KEY

Constructor Summary

RichSequence.Terms()

Method Summary

static ComparableTerm	getAdditionalAccessionTerm() Getter for the secondary/tertiary/additional accession term
static ComparableTerm	getCopyrightTerm() Getter for the copyright term
static ComparableTerm	getDataClassTerm() Getter for the DataClass term
static ComparableTerm	getDateAnnotatedTerm() Getter for the date annotated term
static ComparableTerm	getDateCreatedTerm() Getter for the date created term
static ComparableTerm	getDateUpdatedTerm() Getter for the date updated term
static ComparableTerm	getFeatureDescTerm() Getter for the FeatureDesc term
static ComparableTerm	getFTIdTerm() Getter for the FTId term
static ComparableTerm	getGeneNameTerm() Getter for the GeneName term
static ComparableTerm	getGeneSynonymTerm() Getter for the GeneSynonym term
static ComparableTerm	getKeywordTerm() Getter for the keyword term
static ComparableTerm	getMolTypeTerm() getter for the MolType term
static ComparableTerm	getOrderedLocusNameTerm() Getter for the OrderedLocusName term
static ComparableTerm	getORFNameTerm() Getter for the ORFName term
static ComparableTerm	getOrganelleTerm() Getter for the Organelle term
static ComparableTerm	getPlasmidTerm() Getter for the Plasmid term
static ComparableTerm	getRelAnnotatedTerm() Getter for the release annotated term
static ComparableTerm	getRelCreatedTerm() Getter for the release created term
static ComparableTerm	getRelUpdatedTerm() Getter for the release updated term
static ComparableTerm	getSpeciesTerm() Getter for the Species term
static ComparableTerm	getStrainTerm() Getter for the Strain term
static ComparableTerm	getStrandedTerm() Getter for the Strand term; legal values are "single", "double", and "mixed".
static ComparableTerm	getTissueTerm() Getter for the Tissue term
static ComparableTerm	getTransposonTerm() Getter for the Transposon term

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

SPECIES_KEY

public static String SPECIES_KEY

STRAIN_KEY

public static String STRAIN_KEY

TISSUE_KEY

public static String TISSUE_KEY

TRANSPOSON_KEY

public static String TRANSPOSON_KEY

PLASMID_KEY

public static String PLASMID_KEY

PUBMED_KEY

public static final String PUBMED_KEY

Holds a reference to the key that must be used to store PubMed references.

See Also:

Constant Field Values

MEDLINE_KEY

public static final String MEDLINE_KEY

Holds a reference to the key that must be used to store Medline references.

See Also:

Constant Field Values

DOI_KEY

public static final String DOI_KEY

Holds a reference to the key that must be used to store DOI references.

See Also:

Constant Field Values

Constructor Detail

RichSequence.Terms

public RichSequence.Terms()

Method Detail

getAdditionalAccessionTerm

public static ComparableTerm getAdditionalAccessionTerm()

Getter for the secondary/tertiary/additional accession term

Returns:

A Term that represents the secondary accession tag

getKeywordTerm

public static ComparableTerm getKeywordTerm()

Getter for the keyword term

Returns:

a Term that represents the Keyword tag

getDateCreatedTerm

public static ComparableTerm getDateCreatedTerm()

Getter for the date created term

Returns:

a Term

getDateUpdatedTerm

public static ComparableTerm getDateUpdatedTerm()

Getter for the date updated term

Returns:

a Term

getDateAnnotatedTerm

public static ComparableTerm getDateAnnotatedTerm()

Getter for the date annotated term

Returns:

a Term

getRelCreatedTerm

public static ComparableTerm getRelCreatedTerm()

Getter for the release created term

Returns:

a Term

getRelUpdatedTerm

public static ComparableTerm getRelUpdatedTerm()

Getter for the release updated term

Returns:

a Term

getRelAnnotatedTerm

public static ComparableTerm getRelAnnotatedTerm()

Getter for the release annotated term

Returns:

a Term

getMolTypeTerm

public static ComparableTerm getMolTypeTerm()

getter for the MolType term

Returns:

a Term that represents the molecule type

getStrandedTerm

public static ComparableTerm getStrandedTerm()

Getter for the Strand term; legal values are "single", "double", and "mixed".

Returns:

a Term that represents the Strand tag

getOrganelleTerm

public static ComparableTerm getOrganelleTerm()

Getter for the Organelle term

Returns:

a Term that represents the Organelle tag

getGeneNameTerm

public static ComparableTerm getGeneNameTerm()

Getter for the GeneName term

Returns:

The GeneName Term

getGeneSynonymTerm

public static ComparableTerm getGeneSynonymTerm()

Getter for the GeneSynonym term

Returns:

The GeneSynonym Term

getOrderedLocusNameTerm

public static ComparableTerm getOrderedLocusNameTerm()

Getter for the OrderedLocusName term

Returns:

The OrderedLocusName Term

getORFNameTerm

public static ComparableTerm getORFNameTerm()

Getter for the ORFName term

Returns:

The ORFName Term

getStrainTerm

public static ComparableTerm getStrainTerm()

Getter for the Strain term

Returns:

The Strain Term

getSpeciesTerm

public static ComparableTerm getSpeciesTerm()

Getter for the Species term

Returns:

The Species Term

getTissueTerm

public static ComparableTerm getTissueTerm()

Getter for the Tissue term

Returns:

The Tissue Term

getTransposonTerm

public static ComparableTerm getTransposonTerm()

Getter for the Transposon term

Returns:

The Transposon Term

getPlasmidTerm

public static ComparableTerm getPlasmidTerm()

Getter for the Plasmid term

Returns:

The plasmid Term

getDataClassTerm

public static ComparableTerm getDataClassTerm()

Getter for the DataClass term

Returns:

The DataClass Term

getFTIdTerm

public static ComparableTerm getFTIdTerm()

Getter for the FTId term

Returns:

The FTId Term

getFeatureDescTerm

public static ComparableTerm getFeatureDescTerm()

Getter for the FeatureDesc term

Returns:

The FeatureDesc Term

getCopyrightTerm

public static ComparableTerm getCopyrightTerm()

Getter for the copyright term

Returns:

The copyright Term