apollo.datamodel
Class SequenceEdit

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

All Implemented Interfaces:

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

public class SequenceEdit
extends AnnotatedFeature
implements java.io.Serializable

seq edits are really seq features (very tiny ones) arent they so subclass seq feature? do we still need seq edit? or seq edit has a seq feature? chado models indels as features which makes sense so why not apollo? needs to be annotated feat for chado transaction transformer sake - to be consistent with other annots

See Also:

Serialized Form

Field Summary

protected static org.apache.log4j.Logger

logger

Fields inherited from class apollo.datamodel.AnnotatedFeature

annotationRoot, 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, strand, type

Fields inherited from interface apollo.datamodel.RangeI

NO_NAME, NO_TYPE

Constructor Summary

SequenceEdit(SequenceI refSeq, java.lang.String edit_type, int position, java.lang.String residue)

SequenceEdit(java.lang.String res)

SequenceEdit(java.lang.String edit_type, int position, java.lang.String residue)

Method Summary

java.lang.String	getEditType() phase out for getFeatureType? yes! same thing - although actually CLEAR_EDIT/NOP is really the deletion of the indel - hmmm
int	getPosition()
SequenceI	getRefSequence() Retrieve the SequenceI that this feature annotates.
java.lang.String	getResidue()
boolean	isDeletion()
boolean	isInsertion()
boolean	isSequencingError()
boolean	isSubstitution()
void	setRefSequence(SequenceI refSeq) This is presently used to locate features that have a drawable.
static boolean	typeIsSeqError(java.lang.String type) should come from config/SO - used in jdbc adapter

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, 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, 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, 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, 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.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, 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, getResidues, getRightOverlap, getStart, getStrand, hasFeatureType, hasName, hasRefSequence, isContainedByRefSeq, isExactOverlap, isForwardStrand, isIdentical, isSequenceAvailable, length, overlaps, rangeIsUnassigned, sameRange, setEnd, setFeatureType, setHigh, setLow, setName, 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

Field Detail

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

SequenceEdit

public SequenceEdit(SequenceI refSeq,
                    java.lang.String edit_type,
                    int position,
                    java.lang.String residue)

SequenceEdit

public SequenceEdit(java.lang.String edit_type,
                    int position,
                    java.lang.String residue)

SequenceEdit

public SequenceEdit(java.lang.String res)

Method Detail

getPosition

public int getPosition()

getResidue

public java.lang.String getResidue()

getRefSequence

public SequenceI getRefSequence()

Description copied from interface: RangeI

Retrieve the SequenceI that this feature annotates.

Specified by:

getRefSequence in interface RangeI

Overrides:

getRefSequence in class Range

Returns:

the current parent SequenceI

setRefSequence

public void setRefSequence(SequenceI refSeq)

Description copied from class: FeatureSet

This is presently used to locate features that have a drawable. If the feature can't be found then the drawable is removed. Called after FeatureChangeEvent.SYNC occurs. And this happens when additional features are added - move to SeqFeatureUtil? rename containsFeature?

Specified by:

setRefSequence in interface RangeI

Overrides:

setRefSequence in class FeatureSet

Parameters:

refSeq - the new parent SequenceI

getEditType

public java.lang.String getEditType()

phase out for getFeatureType? yes! same thing - although actually CLEAR_EDIT/NOP is really the deletion of the indel - hmmm

typeIsSeqError

public static boolean typeIsSeqError(java.lang.String type)

should come from config/SO - used in jdbc adapter

isInsertion

public boolean isInsertion()

isDeletion

public boolean isDeletion()

isSubstitution

public boolean isSubstitution()

isSequencingError

public boolean isSequencingError()

Specified by:

isSequencingError in interface SeqFeatureI

Overrides:

isSequencingError in class SeqFeature