apollo.datamodel
Interface AnnotatedFeatureI

All Superinterfaces:

java.lang.Cloneable, FeatureSetI, RangeI, SeqFeatureI, java.io.Serializable, TranslationI

All Known Subinterfaces:

ExonI

All Known Implementing Classes:

AnnotatedFeature, AssemblyFeature, Exon, Protein, SequenceEdit, Transcript

public interface AnnotatedFeatureI
extends FeatureSetI

Field Summary

Fields inherited from interface apollo.datamodel.RangeI

NO_NAME, NO_TYPE

Method Summary

void	addComment(Comment comm)
void	addComment(int index, Comment comm)
void	addEvidence(Evidence evidence)
void	addEvidence(java.lang.String evidenceId)
void	addEvidence(java.lang.String evidenceId, int type)
void	addSynonym(int index, java.lang.String syn)
void	addSynonym(java.lang.String syn)
void	addSynonym(Synonym syn)
void	clearComments()
void	clearSynonyms()
AnnotatedFeatureI	cloneAnnot()
void	deleteComment(Comment comm)
void	deleteComment(int index)
int	deleteEvidence(java.lang.String evidenceId)
void	deleteSynonym(java.lang.String syn)
void	deleteSynonym(Synonym syn)
SequenceI	get_cDNASequence() If annotation is a transcript return the transcripts cdna sequence
AnnotatedFeatureI	getAnnotChild(int i) Convenience method.
int	getCommentIndex(Comment comm)
java.util.Vector	getComments()
java.lang.String	getDescription()
java.util.Vector	getEvidence()
EvidenceFinder	getEvidenceFinder()
Identifier	getIdentifier()
int	getNonConsensusAcceptorNum() Returns transcript exon number with non consensus acceptor.
int	getNonConsensusDonorNum() Returns transcript exon number with non consensus donor.
java.lang.String	getOwner() Get owner of annotation.
Synonym	getSynonym(int i)
java.util.Vector	getSynonyms()
java.util.Vector	getSynonyms(boolean excludeInternalSynonyms)
int	getSynonymSize()
boolean	hasSynonym(java.lang.String name)
boolean	isFinished()
boolean	isProblematic()
boolean	nonConsensusSplicingOkay() Return true if non consensus splicing has been deemed ok.
void	nonConsensusSplicingOkay(boolean okay) Set whether its ok to have non-consensus splice site
void	setDescription(java.lang.String desc)
void	setEvidenceFinder(EvidenceFinder ef)
void	setIdentifier(Identifier id)
void	setIsProblematic(boolean isProblematic)
void	setOwner(java.lang.String owner) Set owner of annotation.

Methods inherited from interface apollo.datamodel.FeatureSetI

adjustEdges, adjustEdges, buildEditList, deleteFeature, deleteFeatureAt, findFeaturesByAllNames, findFeaturesByAllNames, findFeaturesByAllNames, findFeaturesByHitName, findFeaturesByName, findFeaturesByName, getHitSequence, getIndexContaining, getPositionFrom, getSequencingErrorAtPosition, getSplicedLength, getStartAA, getStartCodon, hasDescendents, hasNameBeenSet, hasReadThroughStop, isFlagSet, isProteinCodingGene, isSequencingErrorPosition, minus1FrameShiftPosition, plus1FrameShiftPosition, readThroughStopPosition, readThroughStopResidue, setFlag, setHitSequence, setMinus1FrameShiftPosition, setPlus1FrameShiftPosition, setProteinCodingGene, setReadThroughStop, setReadThroughStop, sort, sort, unConventionalStart, withinCDS

Methods inherited from interface apollo.datamodel.SeqFeatureI

accept, addDbXref, addFeature, addFeature, addProperty, addScore, addScore, addScore, addScore, alignmentIsPeptide, clearKids, clearProperties, clone, cloneFeature, compareTo, descendsFrom, flipFlop, get_cDNA, getAlignment, getAnalogousOppositeStrandFeature, getAnnotatedFeature, getCigar, getCloneSource, getCodingDNA, getCodingProperties, getDatabase, getDbXref, getDbXrefs, getEndPhase, getExplicitAlignment, getFeatureAt, getFeatureContaining, getFeatureIndex, getFeaturePosition, getFeatures, getFeatureSequence, getFrame, getGenomicErrors, getGenomicPosForPeptidePos, getGenomicPosition, getHend, getHhigh, getHitFeature, getHlow, getHname, getHstart, getHstrand, getId, getLeafFeatsOver, getNumberOfChildren, getNumberOfDescendents, getParent, getPeptideSequence, getPhase, getProgramName, getProperties, getPropertiesMulti, getProperty, getPropertyMulti, getProteinFeat, getRefFeature, getRefId, getScore, getScore, getScores, getStrandedFeatSetAncestor, getSyntenyLinkInfo, getTopLevelType, getTranslation, getUnpaddedAlignment, getUserObject, hasAlignable, hasAnalogousOppositeStrandFeature, hasAnnotatedFeature, hasHitFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, hasTranslation, haveExplicitAlignment, haveRealAlignment, isAncestorOf, isAnnot, isAnnotTop, isClone, isCodon, isExon, isProtein, isSameFeat, isSequencingError, isTranscript, merge, numberOfGenerations, parseCigar, removeProperty, replaceProperty, setAlignment, setAnalogousOppositeStrandFeature, setCigar, setDatabase, setExplicitAlignment, setId, setPhase, setProgramName, setQueryFeature, setRefFeature, setScore, setSyntenyLinkInfo, setTopLevelType, setUserObject, size, translate

Methods inherited from interface apollo.datamodel.RangeI

canHaveChildren, contains, contains, convertFromBaseOrientedToInterbase, convertFromInterbaseToBaseOriented, getEnd, getFeatureType, getHigh, getLeftOverlap, getLow, getName, getRangeClone, getRefSequence, getResidues, getRightOverlap, getStart, getStrand, hasFeatureType, hasName, hasRefSequence, isContainedByRefSeq, isExactOverlap, isForwardStrand, isIdentical, isSequenceAvailable, length, overlaps, rangeIsUnassigned, sameRange, setEnd, setFeatureType, setHigh, setLow, setName, setRefSequence, setStart, setStrand

Methods inherited from interface apollo.datamodel.TranslationI

calcTranslationStartForLongestPeptide, getLastBaseOfStopCodon, getTranslationEnd, getTranslationRange, getTranslationStart, hasTranslationEnd, hasTranslationStart, isMissing3prime, isMissing5prime, setMissing3prime, setMissing5prime, setPeptideValidity, setTranslationEnd, setTranslationEndFromStart, setTranslationStart, setTranslationStart

Method Detail

getEvidence

java.util.Vector getEvidence()

addEvidence

void addEvidence(java.lang.String evidenceId)

addEvidence

void addEvidence(java.lang.String evidenceId,
                 int type)

addEvidence

void addEvidence(Evidence evidence)

deleteEvidence

int deleteEvidence(java.lang.String evidenceId)

setEvidenceFinder

void setEvidenceFinder(EvidenceFinder ef)

getEvidenceFinder

EvidenceFinder getEvidenceFinder()

getComments

java.util.Vector getComments()

addComment

void addComment(Comment comm)

addComment

void addComment(int index,
                Comment comm)

deleteComment

void deleteComment(Comment comm)

deleteComment

void deleteComment(int index)

clearComments

void clearComments()

getCommentIndex

int getCommentIndex(Comment comm)

getIdentifier

Identifier getIdentifier()

setIdentifier

void setIdentifier(Identifier id)

getSynonyms

java.util.Vector getSynonyms()

getSynonyms

java.util.Vector getSynonyms(boolean excludeInternalSynonyms)

addSynonym

void addSynonym(java.lang.String syn)

addSynonym

void addSynonym(int index,
                java.lang.String syn)

addSynonym

void addSynonym(Synonym syn)

deleteSynonym

void deleteSynonym(java.lang.String syn)

deleteSynonym

void deleteSynonym(Synonym syn)

clearSynonyms

void clearSynonyms()

getSynonymSize

int getSynonymSize()

getSynonym

Synonym getSynonym(int i)

hasSynonym

boolean hasSynonym(java.lang.String name)

isProblematic

boolean isProblematic()

isFinished

boolean isFinished()

setIsProblematic

void setIsProblematic(boolean isProblematic)

getDescription

java.lang.String getDescription()

setDescription

void setDescription(java.lang.String desc)

setOwner

void setOwner(java.lang.String owner)

Set owner of annotation. Currently only Transcript actually uses this.

getOwner

java.lang.String getOwner()

Get owner of annotation. Only used by Transcript.

getNonConsensusAcceptorNum

int getNonConsensusAcceptorNum()

Returns transcript exon number with non consensus acceptor. If top level annot return -1.

getNonConsensusDonorNum

int getNonConsensusDonorNum()

Returns transcript exon number with non consensus donor. -1 for top.

nonConsensusSplicingOkay

boolean nonConsensusSplicingOkay()

Return true if non consensus splicing has been deemed ok. This is set by curator.

nonConsensusSplicingOkay

void nonConsensusSplicingOkay(boolean okay)

Set whether its ok to have non-consensus splice site

cloneAnnot

AnnotatedFeatureI cloneAnnot()

get_cDNASequence

SequenceI get_cDNASequence()

If annotation is a transcript return the transcripts cdna sequence

getAnnotChild

AnnotatedFeatureI getAnnotChild(int i)

Convenience method. The children of annots are always annots.