apollo.datamodel
Class StrandedFeatureSet

java.lang.Object
  apollo.datamodel.Range
      apollo.datamodel.SeqFeature
          apollo.datamodel.FeatureSet
              apollo.datamodel.StrandedFeatureSet

All Implemented Interfaces:

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

public class StrandedFeatureSet
extends FeatureSet
implements StrandedFeatureSetI

It may well be that any FeatureSet for which the strand is not explicitly set to either 1 or -1 (in other words the strand is 0) should be treated as a mixed set of features that may be on either strand

See Also:

Serialized Form

Field Summary

protected FeatureSetI	forward
protected static org.apache.log4j.Logger	logger
protected FeatureSetI	reverse

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

StrandedFeatureSet()

StrandedFeatureSet(FeatureSetI forward_set, FeatureSetI reverse_set)

Method Summary

void	accept(Visitor visitor) General implementation of Visitor pattern.
void	addFeature(SeqFeatureI feature) Features must be added in sort order, if this turns out to be too slow, then we will need to figure out another way to keep them all sorted (5prime to 3prime that is)
void	addFeature(SeqFeatureI feature, boolean sortFlag) no-op - overridden by FeatureSet
void	deleteFeature(SeqFeatureI feature) The number of directly containd features.
SeqFeatureI	deleteFeatureAt(int i)
int	getEnd()
FeatureSetI	getFeatSetForStrand(int strand)
SeqFeatureI	getFeatureAt(int i) This actually returns not forward feature set and reverse feature set, but the children of forward and reverse.
java.util.Vector	getFeatures() This actually returns not forward feature set and reverse feature set, but the children of forward and reverse.
FeatureSetI	getForwardSet()
FeatureList	getLeafFeatsOver(int pos) This is used in the base editor to find the sub features that overlap a base with a sequence edit on it
FeatureSetI	getReverseSet()
SeqFeatureI	getSeqFeat(int strand, java.lang.String type) Returns seq feat grandchildren (tier level) of type & strand.
int	getStart()
StrandedFeatureSetI	getStrandedFeatSetAncestor()
void	setRefSequence(SequenceI seq) This is presently used to locate features that have a drawable.
int	size() FeatureSet overrides - merge with getNumberOfChildren

Methods inherited from class apollo.datamodel.FeatureSet

adjustEdges, adjustEdges, beforeFivePrimeEnd, buildEditList, buildORFEditList, calcTranslationStartForLongestPeptide, canHaveChildren, clearKids, clone, findFeaturesByAllNames, findFeaturesByAllNames, findFeaturesByAllNames, findFeaturesByHitName, findFeaturesByName, findFeaturesByName, flipFlop, get_cDNA, get_ORF, get_ORF, getFeatureContaining, getFeatureIndex, getFeaturePosition, getGenomicPosForPeptidePos, getGenomicPosition, getHitSequence, getIndexContaining, getLastBaseOfStopCodon, 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, isProteinCodingGene, isSequencingErrorPosition, isTransSpliced, minus1FrameShiftPosition, pastThreePrimeEnd, plus1FrameShiftPosition, rangeIsUnassigned, readThroughStopPosition, readThroughStopResidue, setFlag, setHitSequence, setMinus1FrameShiftPosition, setMissing3prime, setMissing5prime, setPeptideValidity, setPhases, setPlus1FrameShiftPosition, setProteinCodingGene, setReadThroughStop, setReadThroughStop, setTranslationEnd, setTranslationEndFromStart, setTranslationEndNoPhase, setTranslationStart, setTranslationStart, sort, sort, toString, 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, getAnnotatedFeature, 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, getSubSequence, getSyntenyLinkInfo, getTopLevelType, getUnpaddedAlignment, getUserObject, hasAlignable, hasAnalogousOppositeStrandFeature, hasAnnotatedFeature, hasCigar, hasHitFeature, hasId, hasKids, hasPeptideSequence, hasSyntenyLinkInfo, haveExplicitAlignment, haveRealAlignment, initWithSeqFeat, isAncestorOf, isAnnot, isAnnotTop, 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, getEndAsString, getFeatureType, getHigh, getLeftOverlap, getLow, getRangeClone, getRefSequence, getResidues, getRightOverlap, 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.FeatureSetI

adjustEdges, adjustEdges, buildEditList, 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

addDbXref, 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, getFeatureContaining, getFeatureIndex, getFeaturePosition, getFeatureSequence, getFrame, getGenomicErrors, getGenomicPosForPeptidePos, getGenomicPosition, getHend, getHhigh, getHitFeature, getHlow, getHname, getHstart, getHstrand, getId, getNumberOfChildren, getNumberOfDescendents, getParent, getPeptideSequence, getPhase, getProgramName, getProperties, getPropertiesMulti, getProperty, getPropertyMulti, getProteinFeat, getRefFeature, getRefId, getScore, getScore, getScores, 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, translate

Methods inherited from interface apollo.datamodel.RangeI

canHaveChildren, contains, contains, convertFromBaseOrientedToInterbase, convertFromInterbaseToBaseOriented, getFeatureType, getHigh, getLeftOverlap, getLow, getName, getRangeClone, getRefSequence, getResidues, getRightOverlap, 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

forward

protected FeatureSetI forward

reverse

protected FeatureSetI reverse

logger

protected static final org.apache.log4j.Logger logger

Constructor Detail

StrandedFeatureSet

public StrandedFeatureSet(FeatureSetI forward_set,
                          FeatureSetI reverse_set)

StrandedFeatureSet

public StrandedFeatureSet()

Method Detail

getForwardSet

public FeatureSetI getForwardSet()

Specified by:

getForwardSet in interface StrandedFeatureSetI

getReverseSet

public FeatureSetI getReverseSet()

Specified by:

getReverseSet in interface StrandedFeatureSetI

size

public int size()

Description copied from class: SeqFeature

FeatureSet overrides - merge with getNumberOfChildren

Specified by:

size in interface SeqFeatureI

Overrides:

size in class FeatureSet

addFeature

public void addFeature(SeqFeatureI feature)

Features must be added in sort order, if this turns out to be too slow, then we will need to figure out another way to keep them all sorted (5prime to 3prime that is)

Specified by:

addFeature in interface SeqFeatureI

Overrides:

addFeature in class FeatureSet

addFeature

public void addFeature(SeqFeatureI feature,
                       boolean sortFlag)

Description copied from class: SeqFeature

no-op - overridden by FeatureSet

Specified by:

addFeature in interface SeqFeatureI

Overrides:

addFeature in class FeatureSet

deleteFeature

public void deleteFeature(SeqFeatureI feature)

Description copied from interface: FeatureSetI

The number of directly containd features.

Specified by:

deleteFeature in interface FeatureSetI

Overrides:

deleteFeature in class FeatureSet

deleteFeatureAt

public SeqFeatureI deleteFeatureAt(int i)

Specified by:

deleteFeatureAt in interface FeatureSetI

Overrides:

deleteFeatureAt in class FeatureSet

getFeatureAt

public SeqFeatureI getFeatureAt(int i)

This actually returns not forward feature set and reverse feature set, but the children of forward and reverse. In other words it retrieves the grandchildren of the StrandedFeatureSet

Specified by:

getFeatureAt in interface SeqFeatureI

Overrides:

getFeatureAt in class FeatureSet

getFeatures

public java.util.Vector getFeatures()

This actually returns not forward feature set and reverse feature set, but the children of forward and reverse. In other words it retrieves the grandchildren of the StrandedFeatureSet

Specified by:

getFeatures in interface SeqFeatureI

Overrides:

getFeatures in class FeatureSet

getLeafFeatsOver

public FeatureList getLeafFeatsOver(int pos)

Description copied from interface: SeqFeatureI

This is used in the base editor to find the sub features that overlap a base with a sequence edit on it

Specified by:

getLeafFeatsOver in interface SeqFeatureI

Overrides:

getLeafFeatsOver in class FeatureSet

getStart

public int getStart()

Specified by:

getStart in interface RangeI

Overrides:

getStart in class Range

getEnd

public int getEnd()

Specified by:

getEnd in interface RangeI

Overrides:

getEnd in class Range

setRefSequence

public void setRefSequence(SequenceI seq)

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:

seq - the new parent SequenceI

getSeqFeat

public SeqFeatureI getSeqFeat(int strand,
                              java.lang.String type)

Returns seq feat grandchildren (tier level) of type & strand. returns null if not present

getFeatSetForStrand

public FeatureSetI getFeatSetForStrand(int strand)

Specified by:

getFeatSetForStrand in interface StrandedFeatureSetI

getStrandedFeatSetAncestor

public StrandedFeatureSetI getStrandedFeatSetAncestor()

Specified by:

getStrandedFeatSetAncestor in interface SeqFeatureI

Overrides:

getStrandedFeatSetAncestor in class SeqFeature

accept

public void accept(Visitor visitor)

General implementation of Visitor pattern. (see apollo.util.Visitor).

Specified by:

accept in interface SeqFeatureI

Overrides:

accept in class FeatureSet