RichSequence.Terms (biojava-legacy 1.9.1 API)

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 and Description
`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

Constructors
Constructor and Description

RichSequence.Terms()

Constructors
Constructor and Description
`RichSequence.Terms()`

Method Summary

Methods
Modifier and Type	Method and 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 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

Class RichSequence.Terms

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

SPECIES_KEY

STRAIN_KEY

TISSUE_KEY

TRANSPOSON_KEY

PLASMID_KEY

PUBMED_KEY

MEDLINE_KEY

DOI_KEY

Constructor Detail

RichSequence.Terms

Method Detail

getAdditionalAccessionTerm

getKeywordTerm

getDateCreatedTerm

getDateUpdatedTerm

getDateAnnotatedTerm

getRelCreatedTerm

getRelUpdatedTerm

getRelAnnotatedTerm

getMolTypeTerm

getStrandedTerm

getOrganelleTerm

getGeneNameTerm

getGeneSynonymTerm

getOrderedLocusNameTerm

getORFNameTerm

getStrainTerm

getSpeciesTerm

getTissueTerm

getTransposonTerm

getPlasmidTerm

getDataClassTerm

getFTIdTerm

getFeatureDescTerm

getCopyrightTerm