apollo.datamodel
Interface ExonI

All Superinterfaces:

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

All Known Implementing Classes:

Exon

public interface ExonI
extends AnnotatedFeatureI

Field Summary

Fields inherited from interface apollo.datamodel.RangeI

NO_NAME, NO_TYPE

Method Summary

boolean	containsCoding() Returns true if exon contains any coding region.
int	getCodingProperties()
Transcript	getTranscript()
boolean	isNonConsensusAcceptor() Returns true if exon is nonConsensusAcceptor
boolean	isNonConsensusDonor()

Methods inherited from interface apollo.datamodel.AnnotatedFeatureI

addComment, addComment, addEvidence, addEvidence, addEvidence, addSynonym, addSynonym, addSynonym, clearComments, clearSynonyms, cloneAnnot, deleteComment, deleteComment, deleteEvidence, deleteSynonym, deleteSynonym, get_cDNASequence, getAnnotChild, getCommentIndex, getComments, getDescription, getEvidence, getEvidenceFinder, getIdentifier, getNonConsensusAcceptorNum, getNonConsensusDonorNum, getOwner, getSynonym, getSynonyms, getSynonyms, getSynonymSize, hasSynonym, isFinished, isProblematic, nonConsensusSplicingOkay, nonConsensusSplicingOkay, setDescription, setEvidenceFinder, setIdentifier, setIsProblematic, setOwner

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, 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

containsCoding

boolean containsCoding()

Returns true if exon contains any coding region.

getTranscript

Transcript getTranscript()

getCodingProperties

int getCodingProperties()

Specified by:

getCodingProperties in interface SeqFeatureI

isNonConsensusAcceptor

boolean isNonConsensusAcceptor()

Returns true if exon is nonConsensusAcceptor

isNonConsensusDonor

boolean isNonConsensusDonor()