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

Fields

Modifier and Type

Field

Description

static final String

DOI_KEY

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

static final String

MEDLINE_KEY

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

static String

PLASMID_KEY

static final 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

Constructors

Constructor

Description

Terms()
Method Summary

Modifier and Type

Method

Description

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 Details
- 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 Details
- Terms
  
  public Terms()
Method Details
- 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

Class RichSequence.Terms

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

SPECIES_KEY

STRAIN_KEY

TISSUE_KEY

TRANSPOSON_KEY

PLASMID_KEY

PUBMED_KEY

MEDLINE_KEY

DOI_KEY

Constructor Details

Terms

Method Details

getAdditionalAccessionTerm

getKeywordTerm

getDateCreatedTerm

getDateUpdatedTerm

getDateAnnotatedTerm

getRelCreatedTerm

getRelUpdatedTerm

getRelAnnotatedTerm

getMolTypeTerm

getStrandedTerm

getOrganelleTerm

getGeneNameTerm

getGeneSynonymTerm

getOrderedLocusNameTerm

getORFNameTerm

getStrainTerm

getSpeciesTerm

getTissueTerm

getTransposonTerm

getPlasmidTerm

getDataClassTerm

getFTIdTerm

getFeatureDescTerm

getCopyrightTerm