DATranslation (JEnsembl: A Java API for Ensembl Data Access 1.78 API)

java.lang.Object
- uk.ac.roslin.ensembl.datasourceaware.DAObject
- - uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
  - - uk.ac.roslin.ensembl.datasourceaware.core.DATranslation

All Implemented Interfaces:

Serializable, CoreObject, Translation, VegaFeature, IdentifiableObject, StableID, XRefed
```
public class DATranslation
extends DACoreObject
implements Translation, XRefed, VegaFeature
```
See Also:
Serialized Form

Nested Class Summary
- Nested classes/interfaces inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject
  DAObject.DAComparator

Field Summary

Fields
Modifier and Type Field and Description

protected HashMap<ExternalDBType,Set<DAXRef>> typedXRefs

protected Set<DAXRef> xrefs
- Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
  comparaFactories, creationDate, modificationDate, species, stableID, version
- Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject
  daComparator, daoFactory, dbVersion, id, registry, schemaVersion

Fields
Modifier and Type	Field and Description
`protected HashMap<ExternalDBType,Set<DAXRef>>`	`typedXRefs`
`protected Set<DAXRef>`	`xrefs`

Constructor Summary

Constructors
Constructor and Description

DATranslation()

Constructors
Constructor and Description
`DATranslation()`

Method Summary

Methods
Modifier and Type	Method and Description
`protected void`	`addTypedXRefs(ExternalDBType type, Collection<? extends XRef> xrefs)`
`Integer`	`getAAPositionFromChromosome(Integer chromosomePosition)` Returns the amino acid position on this translation for a given Chromosomal Position
`Integer`	`getAAPositionFromPrimaryTranscript(Integer primaryTranscriptPosition)` Returns the amino acid position on this translation for a given Primary Transcript Position
`Integer`	`getAAPositionFromProcessedTranscript(Integer processedTranscriptPosition)` Returns the amino acid position on this translation for a given Processed Transcript Position
`TreeSet<String>`	`getAllSynonyms()`
`Set<DAXRef>`	`getAllXRefs()`
`Integer`	`getBasePositionFromChromosome(Integer chromosomePosition)` Returns the nucleotide position on this translation sequence for a given Chromosomal Position
`Integer`	`getBasePositionFromPrimaryTranscript(Integer primaryTranscriptPosition)` Returns the nucleotide position on this translation sequence for a given primary Transcript position
`Integer`	`getBasePositionFromProcessedTranscript(Integer processedTranscriptPosition)` Returns the nucleotide position on this translation sequence for a given processed (spliced) transcript position.
`Coordinate`	`getChromosomePositionFromAA(Integer aminoAcidPosition)` Returns the mapped chromosomal coordinates of an amino acid position.
`Integer`	`getChromosomePositionFromBASE(Integer translationBase)` Returns the mapped chromosomal position of a translation (nucleotide) position.
`Date`	`getCreationDate()`
`DAExon`	`getFirstExon()` Returns the first Exon of this Translation.
`Integer`	`getFirstExonID()` Returns the internal database ID of the first Exon for this translation.
`Integer`	`getFirstExonStart()` Returns the (relative) position of the translational start in the first exon of this Translation.
`DAGene`	`getGene()` Gets the Gene associated with this Translation via the associated Transcript.
`Integer`	`getId()`
`DAExon`	`getLastExon()` Returns the last Exon of this Translation.
`Integer`	`getLastExonEnd()` Returns the (relative) position of the translational end in the last exon of this Translation.
`Integer`	`getLastExonID()` Returns the internal database ID of the last Exon for this translation.
`int`	`getLength()` Returns the length of the translated nucleotide sequence, i.e. from first nucleotide of the start codon to end of the stop codon.
`Date`	`getModificationDate()`
`Coordinate`	`getPrimaryTranscriptPositionFromAA(Integer aminoAcidPosition)` Returns the mapped coordinates of an amino acid position on the unprocessed primary transcript that provides this translation.
`Integer`	`getPrimaryTranscriptPositionFromBASE(Integer translationBase)` Returns the mapped position of a translation (nucleotide) position on the unprocessed primary transcript that provides this translation.
`Coordinate`	`getProcessedTranscriptPositionFromAA(Integer aminoAcidPosition)` Returns the mapped coordinates of an amino acid position on the (spliced) processed transcript that provides this translation.
`Integer`	`getProcessedTranscriptPositionFromBASE(Integer translationBase)` Returns the mapped position of a translation (nucleotide) position on the (spliced) processed transcript that provides this translation.
`List<? extends ProteinFeature>`	`getProteinFeatures()`
`ProteinSequence`	`getProteinSequence()` Returns a (BioJava) ProteinSequence for this Translation.
`ProteinSequence`	`getProteinSequence(Integer codonTable)` Returns a (BioJava) ProteinSequence for this Translation using the specified Codon Table ID to retrieve the appropriate (BioJava) TranscriptionEngine.
`ProteinSequence`	`getProteinSequence(TranscriptionEngine trancriptionEngine)` Returns a (BioJava) ProteinSequence for this Translation using the specified (BioJava) TranscriptionEngine.
`String`	`getProteinSequenceAsString()` Convenience method to get the Amino Acid sequence of the protein product of this translation.
`String`	`getProteinSequenceAsString(Integer codonTable)` Convenience method to get the Amino Acid sequence of the protein product of this translation.
`String`	`getProteinSequenceAsString(Integer start, Integer end)` Convenience method to get the Amino Acid sequence of the given range of the protein product of this translation.
`String`	`getProteinSequenceAsString(Integer codonTable, Integer start, Integer end)` Convenience method to get the Amino Acid sequence of the given range of the protein product of this translation.
`String`	`getProteinSequenceAsString(TranscriptionEngine trancriptionEngine)` Convenience method to get the Amino Acid sequence of the protein product of this translation.
`String`	`getProteinSequenceAsString(TranscriptionEngine trancriptionEngine, Integer start, Integer end)` Convenience method to get the Amino Acid sequence of the given range of the protein product of this translation.
`RNASequence`	`getRNASequence()` Returns a (BioJava) RNASequence for this Translation using the default (BioJava) TranscriptionEngine or one assigned to this Gene/Organism.
`RNASequence`	`getRNASequence(TranscriptionEngine engine)` Returns a (BioJava) RNASequence for this Translation using the specified (BioJava) TranscriptionEngine or one assigned to this Gene/Organism.
`String`	`getRNASequenceAsString()`
`String`	`getRNASequenceAsString(Integer start, Integer stop)`
`String`	`getRNASequenceAsString(TranscriptionEngine engine)`
`String`	`getRNASequenceAsString(TranscriptionEngine engine, Integer start, Integer stop)`
`String`	`getStableID()`
`TreeSet<String>`	`getSynonyms(XRef xref)`
`DATranscript`	`getTranscript()`
`Integer`	`getTranscriptID()`
`DNASequence`	`getTranslatedSequence()` Returns a DNASequence object representing the translation.
`String`	`getTranslatedSequenceAsString()` Returns a String representation of this Translation ( i.e. the DNA Sequence...).
`String`	`getTranslatedSequenceAsString(Integer start, Integer stop)` Returns a String representation of this Translation for the given range (i.e. the DNA Sequence...).
`MappingSet`	`getTranslationMappings()` Returns the Set of Mappings between coordinates on this Translation and the Primary transcript.
`ObjectType`	`getType()`
`String`	`getVegaID()` Returns any curated VegaID for the Translation, forcing lazy load if not set, and defaulting to an empty string if absent (e.g. for all the invertebrate species in EnsemblGenomes).
`Set<DAXRef>`	`getVegaXRefs()`
`Integer`	`getVersion()`
`protected Set<DAXRef>`	`getXRefs(ExternalDBType type)` Returns preloaded XRefs of given type: Note - does not lazy load these.
`boolean`	`isCanonical()` Returns whether this Translation is marked as the Canonical Translation for its transcript.
`boolean`	`isInitialized()`
`void`	`setCanonical(boolean canonical)`
`void`	`setFirstExonID(Integer firstExonID)`
`void`	`setFirstExonStart(Integer firstExonStart)`
`void`	`setInitialized(boolean init)`
`void`	`setLastExonEnd(Integer lastExonEnd)`
`void`	`setLastExonID(Integer lastExonID)`
`void`	`setStableID(String stableID)`
`void`	`setTranscript(Transcript transcript)`
`void`	`setTranscriptID(Integer transcriptID)`
`void`	`setVegaProteinID(String vegaProteinID)`

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject
getAssembly, getComparaDivision, getComparaFactory, getComparaFactory, getDaoFactory, getSpecies, setCreationDate, setDBVersion, setModificationDate, setSpecies, setVersion

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject
getDBVersion, getHashID, getRegistry, getSchemaVersion, isLazyloadAllowed, setDaoFactory, setId, setLazyloadAllowed, setRegistry

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject
getDBVersion, getHashID, getSchemaVersion, setId

- Field Detail
  - xrefs
```
protected Set<DAXRef> xrefs
```
  - typedXRefs
```
protected HashMap<ExternalDBType,Set<DAXRef>> typedXRefs
```
- Constructor Detail
  - DATranslation
```
public DATranslation()
```
- Method Detail
  - getProteinFeatures
```
public List<? extends ProteinFeature> getProteinFeatures()
```
    Specified by:
    
    getProteinFeatures in interface Translation
  - getTranscript
```
public DATranscript getTranscript()
```
    Specified by:
    
    getTranscript in interface Translation
  - isInitialized
```
public boolean isInitialized()
```
  - setInitialized
```
public void setInitialized(boolean init)
```
  - setTranscript
```
public void setTranscript(Transcript transcript)
```
    Specified by:
    
    setTranscript in interface Translation
  - getType
```
public ObjectType getType()
```
    Specified by:
    
    getType in interface IdentifiableObject
  - isCanonical
```
public boolean isCanonical()
```
    Returns whether this Translation is marked as the Canonical Translation for its transcript. (Prior to Ensembl57 there was a single translation object for each transcript, which is considered as canonical.)
  - setCanonical
```
public void setCanonical(boolean canonical)
```
  - getFirstExonID
```
public Integer getFirstExonID()
```
    Returns the internal database ID of the first Exon for this translation.
  - setFirstExonID
```
public void setFirstExonID(Integer firstExonID)
```
  - getFirstExonStart
```
public Integer getFirstExonStart()
```
    Returns the (relative) position of the translational start in the first exon of this Translation.
  - setFirstExonStart
```
public void setFirstExonStart(Integer firstExonStart)
```
  - getLastExonID
```
public Integer getLastExonID()
```
    Returns the internal database ID of the last Exon for this translation.
  - setLastExonID
```
public void setLastExonID(Integer lastExonID)
```
  - getStableID
```
public String getStableID()
```
    Specified by:
    
    getStableID in interface StableID
    
    Overrides:
    
    getStableID in class DACoreObject
  - setStableID
```
public void setStableID(String stableID)
```
    Specified by:
    
    setStableID in interface StableID
    
    Overrides:
    
    setStableID in class DACoreObject
  - getFirstExon
```
public DAExon getFirstExon()
```
    Returns the first Exon of this Translation.
  - getGene
```
public DAGene getGene()
```
    Gets the Gene associated with this Translation via the associated Transcript.
  - getLastExon
```
public DAExon getLastExon()
```
    Returns the last Exon of this Translation.
  - getLastExonEnd
```
public Integer getLastExonEnd()
```
    Returns the (relative) position of the translational end in the last exon of this Translation. This is inclusive of the stop codon.
  - setLastExonEnd
```
public void setLastExonEnd(Integer lastExonEnd)
```
  - getProteinSequence
```
public ProteinSequence getProteinSequence(Integer codonTable)
```
    Returns a (BioJava) ProteinSequence for this Translation using the specified Codon Table ID to retrieve the appropriate (BioJava) TranscriptionEngine.
  - getProteinSequence
```
public ProteinSequence getProteinSequence(TranscriptionEngine trancriptionEngine)
```
    Returns a (BioJava) ProteinSequence for this Translation using the specified (BioJava) TranscriptionEngine.
  - getProteinSequence
```
public ProteinSequence getProteinSequence()
```
    Returns a (BioJava) ProteinSequence for this Translation. IF possible it will use a TranscriptionEngine configured to use the Codon table specified by the annotated Chromosome. Otherwise it will use the default Universal codon table.
    
    Specified by:
    
    getProteinSequence in interface Translation
  - getProteinSequenceAsString
```
public String getProteinSequenceAsString()
```
    Convenience method to get the Amino Acid sequence of the protein product of this translation. Wraps BioJava ProteinSequence functionality. Note that no terminator (*) is appended.
  - getProteinSequenceAsString
```
public String getProteinSequenceAsString(Integer codonTable)
```
    Convenience method to get the Amino Acid sequence of the protein product of this translation. Wraps BioJava ProteinSequence functionality, using the specified Codon Table ID to retrieve the appropriate (BioJava) TranscriptionEngine. Note that no terminator (*) is appended.
    
    Parameters:
    codonTable -
  - getProteinSequenceAsString
```
public String getProteinSequenceAsString(TranscriptionEngine trancriptionEngine)
```
    Convenience method to get the Amino Acid sequence of the protein product of this translation. Wraps BioJava ProteinSequence functionality, using the specified (BioJava) TranscriptionEngine. Note that no terminator (*) is appended.
    
    Parameters:
    trancriptionEngine -
  - getProteinSequenceAsString
```
public String getProteinSequenceAsString(Integer start,
                                Integer end)
```
    Convenience method to get the Amino Acid sequence of the given range of the protein product of this translation. Wraps BioJava ProteinSequence functionality. Note that terminators (*) will be appended for positions beyond the end of the peptide, but within the translation (i.e. stop codons).
    
    Parameters:
    start -
    end -
    
    Throws:
    
    RangeException - if position does not lie within the peptide and stop codons.
  - getProteinSequenceAsString
```
public String getProteinSequenceAsString(Integer codonTable,
                                Integer start,
                                Integer end)
```
    Convenience method to get the Amino Acid sequence of the given range of the protein product of this translation. Wraps BioJava ProteinSequence functionality, using the specified Codon Table ID to retrieve the appropriate (BioJava) TranscriptionEngine. For 'start'>'end' the amino acid sequence will be written in reverse. Note that terminators (*) will be appended for positions beyond the end of the peptide, but within the translation (i.e. stop codons).
    
    Parameters:
    start -
    end -
    
    Throws:
    
    RangeException - if position does not lie within the peptide
  - getProteinSequenceAsString
```
public String getProteinSequenceAsString(TranscriptionEngine trancriptionEngine,
                                Integer start,
                                Integer end)
```
    Convenience method to get the Amino Acid sequence of the given range of the protein product of this translation. Wraps BioJava ProteinSequence functionality, using the specified (BioJava) TranscriptionEngine. For 'start'>'end' the amino acid sequence will be written in reverse. Note that terminators (*) will be appended for positions beyond the end of the peptide, but within the translation (i.e. stop codons).
    
    Parameters:
    start -
    end -
    
    Throws:
    
    RangeException - if position does not lie within the peptide
  - getTranslatedSequenceAsString
```
public String getTranslatedSequenceAsString()
```
    Returns a String representation of this Translation ( i.e. the DNA Sequence...).
  - getTranslatedSequenceAsString
```
public String getTranslatedSequenceAsString(Integer start,
                                   Integer stop)
                                     throws RangeException,
                                            IllegalArgumentException
```
    Returns a String representation of this Translation for the given range (i.e. the DNA Sequence...).
    
    Parameters:
    start -
    stop -
    
    Throws:
    
    RangeException
    
    IllegalArgumentException
  - getPrimaryTranscriptPositionFromBASE
```
public Integer getPrimaryTranscriptPositionFromBASE(Integer translationBase)
```
    Returns the mapped position of a translation (nucleotide) position on the unprocessed primary transcript that provides this translation.
    
    Parameters:
    translationBase - a nucleotide position on the translated sequence
  - getProcessedTranscriptPositionFromBASE
```
public Integer getProcessedTranscriptPositionFromBASE(Integer translationBase)
                                               throws DAOException
```
    Returns the mapped position of a translation (nucleotide) position on the (spliced) processed transcript that provides this translation. Querying for upstream or downstream positions is unreliable, and may return null if falling within an intron.
    
    Parameters:
    translationBase - a nucleotide position on the translated sequence
    
    Throws:
    
    DAOException
  - getChromosomePositionFromBASE
```
public Integer getChromosomePositionFromBASE(Integer translationBase)
                                      throws DAOException
```
    Returns the mapped chromosomal position of a translation (nucleotide) position.
    
    Parameters:
    translationBase - a nucleotide position on the translated sequence
    
    Throws:
    
    DAOException
  - getPrimaryTranscriptPositionFromAA
```
public Coordinate getPrimaryTranscriptPositionFromAA(Integer aminoAcidPosition)
                                              throws RangeException
```
    Returns the mapped coordinates of an amino acid position on the unprocessed primary transcript that provides this translation.
    
    Parameters:
    aminoAcidPosition -
    
    Throws:
    
    RangeException - if position does not lie within the peptide
  - getProcessedTranscriptPositionFromAA
```
public Coordinate getProcessedTranscriptPositionFromAA(Integer aminoAcidPosition)
                                                throws DAOException,
                                                       RangeException
```
    Returns the mapped coordinates of an amino acid position on the (spliced) processed transcript that provides this translation. Querying for upstream or downstream positions is unreliable, and may return null if falling within an intron.
    
    Parameters:
    aminoAcidPosition -
    
    Throws:
    
    RangeException - if position does not lie within the peptide
    
    DAOException
  - getChromosomePositionFromAA
```
public Coordinate getChromosomePositionFromAA(Integer aminoAcidPosition)
                                       throws DAOException,
                                              RangeException
```
    Returns the mapped chromosomal coordinates of an amino acid position.
    
    Parameters:
    aminoAcidPosition -
    
    Throws:
    
    DAOException
    
    RangeException - if position does not lie within the peptide
  - getBasePositionFromChromosome
```
public Integer getBasePositionFromChromosome(Integer chromosomePosition)
```
    Returns the nucleotide position on this translation sequence for a given Chromosomal Position
    
    Parameters:
    chromosomePosition -
  - getBasePositionFromPrimaryTranscript
```
public Integer getBasePositionFromPrimaryTranscript(Integer primaryTranscriptPosition)
```
    Returns the nucleotide position on this translation sequence for a given primary Transcript position
    
    Parameters:
    primaryTranscriptPosition -
  - getBasePositionFromProcessedTranscript
```
public Integer getBasePositionFromProcessedTranscript(Integer processedTranscriptPosition)
```
    Returns the nucleotide position on this translation sequence for a given processed (spliced) transcript position.
    
    Parameters:
    processedTranscriptPosition -
  - getAAPositionFromChromosome
```
public Integer getAAPositionFromChromosome(Integer chromosomePosition)
```
    Returns the amino acid position on this translation for a given Chromosomal Position
    
    Parameters:
    chromosomePosition -
  - getAAPositionFromPrimaryTranscript
```
public Integer getAAPositionFromPrimaryTranscript(Integer primaryTranscriptPosition)
```
    Returns the amino acid position on this translation for a given Primary Transcript Position
    
    Parameters:
    primaryTranscriptPosition -
  - getAAPositionFromProcessedTranscript
```
public Integer getAAPositionFromProcessedTranscript(Integer processedTranscriptPosition)
```
    Returns the amino acid position on this translation for a given Processed Transcript Position
    
    Parameters:
    processedTranscriptPosition -
  - getLength
```
public int getLength()
```
    Returns the length of the translated nucleotide sequence, i.e. from first nucleotide of the start codon to end of the stop codon.
  - getTranslatedSequence
```
public DNASequence getTranslatedSequence()
```
    Returns a DNASequence object representing the translation.
  - getTranslationMappings
```
public MappingSet getTranslationMappings()
```
    Returns the Set of Mappings between coordinates on this Translation and the Primary transcript.
  - getRNASequence
```
public RNASequence getRNASequence()
```
    Returns a (BioJava) RNASequence for this Translation using the default (BioJava) TranscriptionEngine or one assigned to this Gene/Organism.
  - getRNASequence
```
public RNASequence getRNASequence(TranscriptionEngine engine)
```
    Returns a (BioJava) RNASequence for this Translation using the specified (BioJava) TranscriptionEngine or one assigned to this Gene/Organism.
  - getRNASequenceAsString
```
public String getRNASequenceAsString()
```
  - getRNASequenceAsString
```
public String getRNASequenceAsString(TranscriptionEngine engine)
```
  - getRNASequenceAsString
```
public String getRNASequenceAsString(Integer start,
                            Integer stop)
```
  - getRNASequenceAsString
```
public String getRNASequenceAsString(TranscriptionEngine engine,
                            Integer start,
                            Integer stop)
```
  - getVegaID
```
public String getVegaID()
```
    Returns any curated VegaID for the Translation, forcing lazy load if not set, and defaulting to an empty string if absent (e.g. for all the invertebrate species in EnsemblGenomes).
    
    Specified by:
    
    getVegaID in interface VegaFeature
  - getVegaXRefs
```
public Set<DAXRef> getVegaXRefs()
```
    Specified by:
    
    getVegaXRefs in interface VegaFeature
  - getXRefs
```
protected Set<DAXRef> getXRefs(ExternalDBType type)
```
    Returns preloaded XRefs of given type: Note - does not lazy load these.
    
    Parameters:
    type -
  - getAllXRefs
```
public Set<DAXRef> getAllXRefs()
```
    Specified by:
    
    getAllXRefs in interface XRefed
  - addTypedXRefs
```
protected void addTypedXRefs(ExternalDBType type,
                 Collection<? extends XRef> xrefs)
```
  - getTranscriptID
```
public Integer getTranscriptID()
```
  - setTranscriptID
```
public void setTranscriptID(Integer transcriptID)
```
  - setVegaProteinID
```
public void setVegaProteinID(String vegaProteinID)
```
  - getId
```
public Integer getId()
```
    Specified by:
    
    getId in interface IdentifiableObject
    
    Overrides:
    
    getId in class DAObject
  - getVersion
```
public Integer getVersion()
```
    Specified by:
    
    getVersion in interface StableID
    
    Overrides:
    
    getVersion in class DACoreObject
  - getModificationDate
```
public Date getModificationDate()
```
    Specified by:
    
    getModificationDate in interface StableID
    
    Overrides:
    
    getModificationDate in class DACoreObject
  - getCreationDate
```
public Date getCreationDate()
```
    Specified by:
    
    getCreationDate in interface StableID
    
    Overrides:
    
    getCreationDate in class DACoreObject
  - getAllSynonyms
```
public TreeSet<String> getAllSynonyms()
```
    Specified by:
    
    getAllSynonyms in interface XRefed
  - getSynonyms
```
public TreeSet<String> getSynonyms(XRef xref)
```
    Specified by:
    
    getSynonyms in interface XRefed

Class DATranslation

Nested Class Summary

Nested classes/interfaces inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject

Field Summary

Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

Fields inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject

Constructor Summary

Method Summary

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.core.DACoreObject

Methods inherited from class uk.ac.roslin.ensembl.datasourceaware.DAObject

Methods inherited from class java.lang.Object

Methods inherited from interface uk.ac.roslin.ensembl.model.IdentifiableObject

Field Detail

xrefs

typedXRefs

Constructor Detail

DATranslation

Method Detail

getProteinFeatures

getTranscript

isInitialized

setInitialized

setTranscript

getType

isCanonical

setCanonical

getFirstExonID

setFirstExonID

getFirstExonStart

setFirstExonStart

getLastExonID

setLastExonID

getStableID

setStableID

getFirstExon

getGene

getLastExon

getLastExonEnd

setLastExonEnd

getProteinSequence

getProteinSequence

getProteinSequence

getProteinSequenceAsString

getProteinSequenceAsString

getProteinSequenceAsString

getProteinSequenceAsString

getProteinSequenceAsString

getProteinSequenceAsString

getTranslatedSequenceAsString

getTranslatedSequenceAsString

getPrimaryTranscriptPositionFromBASE

getProcessedTranscriptPositionFromBASE

getChromosomePositionFromBASE

getPrimaryTranscriptPositionFromAA

getProcessedTranscriptPositionFromAA

getChromosomePositionFromAA

getBasePositionFromChromosome

getBasePositionFromPrimaryTranscript

getBasePositionFromProcessedTranscript

getAAPositionFromChromosome

getAAPositionFromPrimaryTranscript

getAAPositionFromProcessedTranscript

getLength

getTranslatedSequence

getTranslationMappings

getRNASequence

getRNASequence

getRNASequenceAsString

getRNASequenceAsString

getRNASequenceAsString

getRNASequenceAsString

getVegaID

getVegaXRefs

getXRefs

getAllXRefs

addTypedXRefs

getTranscriptID

setTranscriptID

setVegaProteinID

getId