apollo.datamodel
Interface TranslationI

All Known Subinterfaces:

AnnotatedFeatureI, ExonI, FeatureSetI, StrandedFeatureSetI

All Known Implementing Classes:

AnnotatedFeature, AssemblyFeature, Exon, FeatureSet, Protein, SequenceEdit, StrandedFeatureSet, Transcript

public interface TranslationI

im thinking maybe there should be a separate interface for translation methods (yes i know there is - its called a feature set) and seqfeatureI would have this - not be implemented in a subclass (or if it is not have that be noticaeable at the api/interface level) in other words a HASA not a ISA! i think that would be cleaner

Method Summary

void	calcTranslationStartForLongestPeptide()
int	getLastBaseOfStopCodon()
int	getTranslationEnd()
RangeI	getTranslationRange()
int	getTranslationStart()
boolean	hasTranslationEnd()
boolean	hasTranslationStart()
boolean	isMissing3prime()
boolean	isMissing5prime() If true this means there is no real start codon - its missing, rename this isMissing5PrimeStart? or isMissingTranslationStart? hasTranslationStart() can be true while isMissing5prime is true - this means that theres a "contrived" start at the beginning of the transcript
void	setMissing3prime(boolean partial)
void	setMissing5prime(boolean partial)
void	setPeptideValidity(boolean validity) if validity is false the peptide is no longer valid and a new translation needs to be calculated
void	setTranslationEnd(int pos)
void	setTranslationEndFromStart()
boolean	setTranslationStart(int pos)
boolean	setTranslationStart(int pos, boolean set_end)

Method Detail

setTranslationStart

boolean setTranslationStart(int pos)

setTranslationStart

boolean setTranslationStart(int pos,
                            boolean set_end)

setTranslationEnd

void setTranslationEnd(int pos)

hasTranslationStart

boolean hasTranslationStart()

getTranslationStart

int getTranslationStart()

hasTranslationEnd

boolean hasTranslationEnd()

setMissing5prime

void setMissing5prime(boolean partial)

isMissing5prime

boolean isMissing5prime()

If true this means there is no real start codon - its missing, rename this isMissing5PrimeStart? or isMissingTranslationStart? hasTranslationStart() can be true while isMissing5prime is true - this means that theres a "contrived" start at the beginning of the transcript

setMissing3prime

void setMissing3prime(boolean partial)

isMissing3prime

boolean isMissing3prime()

getTranslationEnd

int getTranslationEnd()

calcTranslationStartForLongestPeptide

void calcTranslationStartForLongestPeptide()

setTranslationEndFromStart

void setTranslationEndFromStart()

getLastBaseOfStopCodon

int getLastBaseOfStopCodon()

getTranslationRange

RangeI getTranslationRange()

setPeptideValidity

void setPeptideValidity(boolean validity)

if validity is false the peptide is no longer valid and a new translation needs to be calculated