AssemblyFeature

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apollo.datamodel
Class AssemblyFeature

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

All Implemented Interfaces:: AnnotatedFeatureI, AssemblyFeatureI, Comparable, FeatureSetI, RangeI, SeqFeatureI, TranslationI, java.io.Serializable, java.lang.Cloneable

public class AssemblyFeature
extends AnnotatedFeature
implements AssemblyFeatureI
extends AnnotatedFeature
implements AssemblyFeatureI

A class to represent SeqFeatures which have been mapped to a static golden path- the usual start/end is assumed to be in chromosome coords, but the assembly start/end specific to this subclass are in coords relative to the feature.

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
`AssemblyFeature()`
`AssemblyFeature(int theFragmentOffset, java.lang.String theChromosome)`

Method Summary
`void`	`accept(Visitor visitor)` General implementation of Visitor pattern.
`void`	`addKeyword(java.lang.String keyword)`
`void`	`addRemark(java.lang.String remark)`
`java.lang.String`	`getAccession()`
`java.lang.String`	`getChromosome()`
`int`	`getFragmentOffset()`
`java.util.Vector`	`getKeywords()`
`java.util.Vector`	`getRemarks()`
`int`	`getVersion()`
`void`	`setAccession(java.lang.String acc)`
`void`	`setChromosome(java.lang.String chr)`
`void`	`setFragmentOffset(int start)`
`void`	`setVersion(int ver)`

Methods inherited from class apollo.datamodel.AnnotatedFeature
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, isProteinCodingGene, nonConsensusSplicingOkay, nonConsensusSplicingOkay, setDescription, setEvidenceFinder, setIsProblematic, setOwner, toString

Methods inherited from class apollo.datamodel.AnnotatedFeature

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, isProteinCodingGene, nonConsensusSplicingOkay, nonConsensusSplicingOkay, setDescription, setEvidenceFinder, setIsProblematic, setOwner, toString

Methods inherited from class apollo.datamodel.FeatureSet
addFeature, addFeature, adjustEdges, adjustEdges, beforeFivePrimeEnd, buildEditList, buildORFEditList, calcTranslationStartForLongestPeptide, canHaveChildren, 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.FeatureSet

addFeature, addFeature, adjustEdges, adjustEdges, beforeFivePrimeEnd, buildEditList, buildORFEditList, calcTranslationStartForLongestPeptide, canHaveChildren, 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, getFrame, 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, getTopLevelType, getUnpaddedAlignment, getUserObject, hasAlignable, hasAnalogousOppositeStrandFeature, hasCigar, hasHitFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, haveExplicitAlignment, haveRealAlignment, initWithSeqFeat, isAncestorOf, isAnnot, isClone, isCodon, isExon, 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.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, getFrame, 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, getTopLevelType, getUnpaddedAlignment, getUserObject, hasAlignable, hasAnalogousOppositeStrandFeature, hasCigar, hasHitFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, haveExplicitAlignment, haveRealAlignment, initWithSeqFeat, isAncestorOf, isAnnot, isClone, isCodon, isExon, 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 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.AnnotatedFeatureI
`getIdentifier, setIdentifier`

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.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
addDbXref, addFeature, addFeature, addProperty, addScore, addScore, addScore, addScore, alignmentIsPeptide, clearKids, clearProperties, cloneFeature, compareTo, descendsFrom, flipFlop, get_cDNA, getAlignment, getAnalogousOppositeStrandFeature, 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, hasHitFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, hasTranslation, haveExplicitAlignment, haveRealAlignment, isAncestorOf, isAnnot, 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.SeqFeatureI

addDbXref, addFeature, addFeature, addProperty, addScore, addScore, addScore, addScore, alignmentIsPeptide, clearKids, clearProperties, cloneFeature, compareTo, descendsFrom, flipFlop, get_cDNA, getAlignment, getAnalogousOppositeStrandFeature, 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, hasHitFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, hasTranslation, haveExplicitAlignment, haveRealAlignment, isAncestorOf, isAnnot, 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.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`

Constructor Detail