apollo.datamodel
Class Exon

java.lang.Object
  apollo.datamodel.Range
      apollo.datamodel.SeqFeature
          apollo.datamodel.FeatureSet
              apollo.datamodel.AnnotatedFeature
                  apollo.datamodel.Exon

All Implemented Interfaces:

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

public class Exon
extends AnnotatedFeature
implements ExonI

See Also:

Serialized Form

Field Summary

Fields inherited from class apollo.datamodel.AnnotatedFeature

annotationRoot, logger, owner

Fields inherited from class apollo.datamodel.FeatureSet

features, flags, genericReadThroughStopResidue, hitSequence, minus1_frameshift, missing_3prime, missing_5prime, plus1_frameshift, POLYA_REMOVED, readthrough_stop, standard_start_codon, start_codon, trans_spliced

Fields inherited from class apollo.datamodel.SeqFeature

biotype, edit_offset_adjust, id, phase, properties, ref_features, refFeature, refId, score, scores

Fields inherited from class apollo.datamodel.Range

high, low, name, refSeq, strand, type

Fields inherited from interface apollo.datamodel.RangeI

NO_NAME, NO_TYPE

Constructor Summary

Exon()

Exon(SeqFeatureI sf)

Method Summary

boolean	canHaveChildren() This method determines if there are any child SeqFeatures in this set (FeatureSets are NOT included).
boolean	containsCoding() Convenience function that uses getCodingProperties() and returns true if its codingProperty has coding
java.lang.String	getAcceptor()
java.lang.String	getDonor()
int	getFrame() Overrides SeqFeature.getFrame.
java.lang.String	getTopLevelType() Exon has the same biotype as its gene
Transcript	getTranscript()
boolean	isExon()
boolean	isNonConsensusAcceptor() Returns true if exon is nonConsensusAcceptor
boolean	isNonConsensusDonor()
boolean	isProteinCodingGene() This is the isProteinCodingGene method that really matters--the ones in other classes aren't really used.
java.lang.String	toString() For debugging

Methods inherited from class apollo.datamodel.AnnotatedFeature

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

Methods inherited from class apollo.datamodel.FeatureSet

addFeature, addFeature, adjustEdges, adjustEdges, beforeFivePrimeEnd, buildEditList, buildORFEditList, calcTranslationStartForLongestPeptide, clearKids, deleteFeature, deleteFeatureAt, findFeaturesByAllNames, findFeaturesByAllNames, findFeaturesByAllNames, findFeaturesByHitName, findFeaturesByName, findFeaturesByName, flipFlop, get_cDNA, get_ORF, get_ORF, getFeatureAt, getFeatureContaining, getFeatureIndex, getFeaturePosition, getFeatures, getGenomicPosForPeptidePos, getGenomicPosition, getHitSequence, getIndexContaining, getLastBaseOfStopCodon, getLeafFeatsOver, getName, getNumberOfDescendents, getPeptidePosForGenomicPos, getPositionFrom, getScore, getSequencingErrorAtPosition, getSplicedLength, getSplicedLength, getSplicedTranscript, getStartAA, getStartCodon, getTranslation, getTranslationEnd, getTranslationRange, getTranslationStart, hasDescendents, hasNameBeenSet, hasReadThroughStop, hasTranslation, hasTranslationEnd, hasTranslationStart, insertFeatureAt, isFlagSet, isMissing3prime, isMissing5prime, isSequencingErrorPosition, isTransSpliced, minus1FrameShiftPosition, pastThreePrimeEnd, plus1FrameShiftPosition, rangeIsUnassigned, readThroughStopPosition, readThroughStopResidue, setFlag, setHitSequence, setMinus1FrameShiftPosition, setMissing3prime, setMissing5prime, setPeptideValidity, setPhases, setPlus1FrameShiftPosition, setProteinCodingGene, setReadThroughStop, setReadThroughStop, setRefSequence, setTranslationEnd, setTranslationEndFromStart, setTranslationEndNoPhase, setTranslationStart, setTranslationStart, size, sort, sort, translate, unConventionalStart, withinCDS

Methods inherited from class apollo.datamodel.SeqFeature

addDbXref, addProperty, addRefFeature, addScore, addScore, addScore, addScore, alignmentIsPeptide, amend_RNA, buildmRNAEditList, clearProperties, cloneFeature, compareTo, descendsFrom, getAlignment, getAnalogousOppositeStrandFeature, getCigar, getCloneSource, getCodingDNA, getCodingProperties, getDatabase, getDbXref, getDbXrefs, getEndPhase, getExplicitAlignment, getFeatureSequence, getGenomicErrors, getHend, getHhigh, getHitFeature, getHlow, getHname, getHstart, getHstrand, getId, getIdentifier, getNumberOfChildren, getParent, getPeptideSequence, getPhase, getPrimaryDbXref, getProgramName, getProperties, getPropertiesMulti, getProperty, getPropertyMulti, getProteinFeat, getRefFeature, getRefFeature, getRefId, getScore, getScores, getStrandedFeatSetAncestor, getSubSequence, getSyntenyLinkInfo, getUnpaddedAlignment, getUserObject, hasAlignable, hasAnalogousOppositeStrandFeature, hasCigar, hasHitFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, haveExplicitAlignment, haveRealAlignment, initWithSeqFeat, isAncestorOf, isAnnot, isClone, isCodon, isProtein, isSameFeat, isSequencingError, isTranscript, main, merge, na2aa, numberOfGenerations, parseCigar, removeProperty, replaceProperty, setAlignment, setAnalogousOppositeStrandFeature, setCigar, setDatabase, setExplicitAlignment, setId, setIdentifier, setPhase, setProgramName, setQueryFeature, setRefFeature, setScore, setSyntenyLinkInfo, setTopLevelType, setUserObject

Methods inherited from class apollo.datamodel.Range

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

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface apollo.datamodel.ExonI

getCodingProperties

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, 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, 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, getTranslation, getUnpaddedAlignment, getUserObject, hasAlignable, hasAnalogousOppositeStrandFeature, hasAnnotatedFeature, hasHitFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, hasTranslation, haveExplicitAlignment, haveRealAlignment, isAncestorOf, isAnnot, isAnnotTop, isClone, isCodon, 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

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

Constructor Detail

Exon

public Exon(SeqFeatureI sf)

Exon

public Exon()

Method Detail

isExon

public boolean isExon()

Specified by:

isExon in interface SeqFeatureI

Overrides:

isExon in class SeqFeature

canHaveChildren

public boolean canHaveChildren()

Description copied from class: FeatureSet

This method determines if there are any child SeqFeatures in this set (FeatureSets are NOT included).

Specified by:

canHaveChildren in interface RangeI

Overrides:

canHaveChildren in class FeatureSet

getFrame

public int getFrame()

Overrides SeqFeature.getFrame.

Specified by:

getFrame in interface SeqFeatureI

Overrides:

getFrame in class SeqFeature

Returns:

1, 2, or 3 for frames, -1 if not in coding. The frame is relative to the ref sequence, not the feature start. In contrast getPhase returns 0,1,2 in relation to beginning of feature.

See Also:

should this return -1 if outside of region?

toString

public java.lang.String toString()

Description copied from class: FeatureSet

For debugging

Overrides:

toString in class AnnotatedFeature

getAcceptor

public java.lang.String getAcceptor()

getDonor

public java.lang.String getDonor()

isNonConsensusAcceptor

public boolean isNonConsensusAcceptor()

Description copied from interface: ExonI

Returns true if exon is nonConsensusAcceptor

Specified by:

isNonConsensusAcceptor in interface ExonI

isNonConsensusDonor

public boolean isNonConsensusDonor()

Specified by:

isNonConsensusDonor in interface ExonI

containsCoding

public boolean containsCoding()

Convenience function that uses getCodingProperties() and returns true if its codingProperty has coding

Specified by:

containsCoding in interface ExonI

getTopLevelType

public java.lang.String getTopLevelType()

Exon has the same biotype as its gene

Specified by:

getTopLevelType in interface SeqFeatureI

Overrides:

getTopLevelType in class SeqFeature

getTranscript

public Transcript getTranscript()

Specified by:

getTranscript in interface ExonI

isProteinCodingGene

public boolean isProteinCodingGene()

Description copied from class: AnnotatedFeature

This is the isProteinCodingGene method that really matters--the ones in other classes aren't really used.

Specified by:

isProteinCodingGene in interface FeatureSetI

Specified by:

isProteinCodingGene in interface SeqFeatureI

Overrides:

isProteinCodingGene in class AnnotatedFeature

See Also:

FeatureSet.setProteinCodingGene(boolean)