apollo.datamodel
Interface FeatureSetI

All Superinterfaces:

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

All Known Subinterfaces:

AnnotatedFeatureI, ExonI, StrandedFeatureSetI

All Known Implementing Classes:

AnnotatedFeature, AssemblyFeature, Exon, FeatureSet, Protein, SequenceEdit, StrandedFeatureSet, Transcript

public interface FeatureSetI
extends SeqFeatureI, TranslationI

Field Summary

Fields inherited from interface apollo.datamodel.RangeI

NO_NAME, NO_TYPE

Method Summary

void	adjustEdges()
void	adjustEdges(SeqFeatureI sf)
SequenceEdit[]	buildEditList()
void	deleteFeature(SeqFeatureI feature) The number of directly containd features.
SeqFeatureI	deleteFeatureAt(int i)
FeatureList	findFeaturesByAllNames(java.lang.String name) Search for names and hit names
FeatureList	findFeaturesByAllNames(java.lang.String name, boolean useRegExp)
FeatureList	findFeaturesByAllNames(java.lang.String searchString, boolean useRegExp, boolean kidNamesOverParent) searchString is pattern to search, useRegExp - whether pattern is reg exp, kidNamesOverParent if descendants match then ignore self match
FeatureList	findFeaturesByHitName(java.lang.String hname)
FeatureList	findFeaturesByName(java.lang.String name)
FeatureList	findFeaturesByName(java.lang.String name, boolean kidNamesOverParent)
SequenceI	getHitSequence() If feat has hit feat, or children with hit feat, then this is the seq associated with the hit or kid hits
int	getIndexContaining(int pos)
int	getPositionFrom(int at_pos, int offset)
SequenceEdit	getSequencingErrorAtPosition(int base_position)
int	getSplicedLength()
java.lang.String	getStartAA()
java.lang.String	getStartCodon()
boolean	hasDescendents() returns true if the count of the number of leaf features (those that can't have child features themselves) is > 0.
boolean	hasNameBeenSet()
boolean	hasReadThroughStop()
boolean	isFlagSet(int flag) some useful flags, hopefully using minimal space, to pass information about handling through from the parser to the filter when running bop.
boolean	isProteinCodingGene() returns true if this can encode a protein.
boolean	isSequencingErrorPosition(int base_position)
int	minus1FrameShiftPosition()
int	plus1FrameShiftPosition()
int	readThroughStopPosition()
java.lang.String	readThroughStopResidue()
void	setFlag(boolean state, byte mask)
void	setHitSequence(SequenceI seq)
boolean	setMinus1FrameShiftPosition(int shift_pos)
boolean	setPlus1FrameShiftPosition(int shift_pos) returns false of the frame shift position is unworkable
void	setProteinCodingGene(boolean isProteinCodingGene) A setter is needed for some featureSet, like gene prediction results, which can have translation start and stop whithout being instances of transcripts
void	setReadThroughStop(boolean readthrough)
void	setReadThroughStop(java.lang.String residue)
void	sort(int sortStrand)
void	sort(int sortStrand, boolean byLow)
boolean	unConventionalStart()
boolean	withinCDS(int pos) Returns true if the position is within the CDS of this feature

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, 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, 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

deleteFeature

void deleteFeature(SeqFeatureI feature)

The number of directly containd features.

deleteFeatureAt

SeqFeatureI deleteFeatureAt(int i)

getIndexContaining

int getIndexContaining(int pos)

hasDescendents

boolean hasDescendents()

returns true if the count of the number of leaf features (those that can't have child features themselves) is > 0. That is, this feature isn't merely a collection of feature sets which are empty themselves

adjustEdges

void adjustEdges()

adjustEdges

void adjustEdges(SeqFeatureI sf)

sort

void sort(int sortStrand)

sort

void sort(int sortStrand,
          boolean byLow)

hasNameBeenSet

boolean hasNameBeenSet()

findFeaturesByHitName

FeatureList findFeaturesByHitName(java.lang.String hname)

findFeaturesByName

FeatureList findFeaturesByName(java.lang.String name)

findFeaturesByName

FeatureList findFeaturesByName(java.lang.String name,
                               boolean kidNamesOverParent)

findFeaturesByAllNames

FeatureList findFeaturesByAllNames(java.lang.String name)

Search for names and hit names

findFeaturesByAllNames

FeatureList findFeaturesByAllNames(java.lang.String name,
                                   boolean useRegExp)

findFeaturesByAllNames

FeatureList findFeaturesByAllNames(java.lang.String searchString,
                                   boolean useRegExp,
                                   boolean kidNamesOverParent)

searchString is pattern to search, useRegExp - whether pattern is reg exp, kidNamesOverParent if descendants match then ignore self match

getPositionFrom

int getPositionFrom(int at_pos,
                    int offset)

withinCDS

boolean withinCDS(int pos)

Returns true if the position is within the CDS of this feature

isProteinCodingGene

boolean isProteinCodingGene()

returns true if this can encode a protein. This was just for annotated features originally, but since the translation code is in FeatureSet it needs to reside here. The default is to return true;

Specified by:

isProteinCodingGene in interface SeqFeatureI

setProteinCodingGene

void setProteinCodingGene(boolean isProteinCodingGene)

A setter is needed for some featureSet, like gene prediction results, which can have translation start and stop whithout being instances of transcripts

unConventionalStart

boolean unConventionalStart()

getStartCodon

java.lang.String getStartCodon()

getStartAA

java.lang.String getStartAA()

hasReadThroughStop

boolean hasReadThroughStop()

readThroughStopResidue

java.lang.String readThroughStopResidue()

setReadThroughStop

void setReadThroughStop(boolean readthrough)

setReadThroughStop

void setReadThroughStop(java.lang.String residue)

readThroughStopPosition

int readThroughStopPosition()

plus1FrameShiftPosition

int plus1FrameShiftPosition()

minus1FrameShiftPosition

int minus1FrameShiftPosition()

setPlus1FrameShiftPosition

boolean setPlus1FrameShiftPosition(int shift_pos)

returns false of the frame shift position is unworkable

setMinus1FrameShiftPosition

boolean setMinus1FrameShiftPosition(int shift_pos)

isSequencingErrorPosition

boolean isSequencingErrorPosition(int base_position)

getSequencingErrorAtPosition

SequenceEdit getSequencingErrorAtPosition(int base_position)

buildEditList

SequenceEdit[] buildEditList()

getHitSequence

SequenceI getHitSequence()

Description copied from interface: SeqFeatureI

If feat has hit feat, or children with hit feat, then this is the seq associated with the hit or kid hits

Specified by:

getHitSequence in interface SeqFeatureI

setHitSequence

void setHitSequence(SequenceI seq)

getSplicedLength

int getSplicedLength()

isFlagSet

boolean isFlagSet(int flag)

some useful flags, hopefully using minimal space, to pass information about handling through from the parser to the filter when running bop.

setFlag

void setFlag(boolean state,
             byte mask)