apollo.datamodel
Interface RangeI

All Superinterfaces:

java.lang.Cloneable, java.io.Serializable

All Known Subinterfaces:

AnnotatedFeatureI, ExonI, FeaturePairI, FeatureSetI, SeqFeatureI, StrandedFeatureSetI

All Known Implementing Classes:

AnnotatedFeature, AssemblyFeature, CurationSet, CutSite, Exon, FeaturePair, FeatureSet, GenomicRange, Protein, Range, SeqFeature, SequenceEdit, StrandedFeatureSet, Transcript

public interface RangeI
extends java.io.Serializable, java.lang.Cloneable

Field Summary

static java.lang.String	NO_NAME The type String to use for features that have no other name.
static java.lang.String	NO_TYPE The type String to use for features that have no other type.

Method Summary

boolean	canHaveChildren() If RangeI is an instanceof FeatureSetI and FeatureSetI.hasChildFeatures is true then return true.
boolean	contains(int position)
boolean	contains(RangeI sf) Returns true if range of sf is entierly within this RangeI
void	convertFromBaseOrientedToInterbase() Converts base oriented range to interbase range
void	convertFromInterbaseToBaseOriented() Converts interbase range to base oriented range
int	getEnd()
java.lang.String	getFeatureType() getType is not the "visual" type, ie the type one sees in the EvidencePanel.
int	getHigh()
int	getLeftOverlap(RangeI sf)
int	getLow()
java.lang.String	getName() In the case where the range is chromosomal the name is the chromosome name
RangeI	getRangeClone() Returns clone of self
SequenceI	getRefSequence() Retrieve the SequenceI that this feature annotates.
java.lang.String	getResidues()
int	getRightOverlap(RangeI sf)
int	getStart()
int	getStrand()
boolean	hasFeatureType() convenience method returns !getType()==NO_TYPE
boolean	hasName() return true if name !equal NO_NAME
boolean	hasRefSequence() return false if no ref seq, ranges should generally have ref seq, only during initialization might it not
boolean	isContainedByRefSeq() Return true if ref seq contains this range
boolean	isExactOverlap(RangeI sf)
boolean	isForwardStrand()
boolean	isIdentical(RangeI range) Returns true if same start,end,type and name.
boolean	isSequenceAvailable(int position)
int	length()
boolean	overlaps(RangeI sf)
boolean	rangeIsUnassigned() Return true if range has been assigned high & low
boolean	sameRange(RangeI r) Return true if start and end are equal
void	setEnd(int end)
void	setFeatureType(java.lang.String type)
void	setHigh(int high)
void	setLow(int low)
void	setName(java.lang.String name)
void	setRefSequence(SequenceI refSeq) Set the SequenceI that this feature annotates.
void	setStart(int start)
void	setStrand(int strand)

Field Detail

NO_NAME

static final java.lang.String NO_NAME

The type String to use for features that have no other name.

See Also:

Constant Field Values

NO_TYPE

static final java.lang.String NO_TYPE

The type String to use for features that have no other type.

See Also:

Constant Field Values

Method Detail

getName

java.lang.String getName()

In the case where the range is chromosomal the name is the chromosome name

setName

void setName(java.lang.String name)

hasName

boolean hasName()

return true if name !equal NO_NAME

getFeatureType

java.lang.String getFeatureType()

getType is not the "visual" type, ie the type one sees in the EvidencePanel. getType returns the "logical" type(the type from the data). These are the types in the squiggly brackets in the tiers file that map to the visual type listed before the squigglies. gui.scheme.FeatureProperty maps logical types to visual types (convenience function in DetailInfo.getPropertyType)

setFeatureType

void setFeatureType(java.lang.String type)

hasFeatureType

boolean hasFeatureType()

convenience method returns !getType()==NO_TYPE

getStart

int getStart()

setStart

void setStart(int start)

getEnd

int getEnd()

setEnd

void setEnd(int end)

getLow

int getLow()

setLow

void setLow(int low)

getHigh

int getHigh()

setHigh

void setHigh(int high)

isSequenceAvailable

boolean isSequenceAvailable(int position)

getRefSequence

SequenceI getRefSequence()

Retrieve the SequenceI that this feature annotates.

Returns:

the current parent SequenceI

hasRefSequence

boolean hasRefSequence()

return false if no ref seq, ranges should generally have ref seq, only during initialization might it not

setRefSequence

void setRefSequence(SequenceI refSeq)

Set the SequenceI that this feature annotates.

Parameters:

refSeq - the new parent SequenceI

isContainedByRefSeq

boolean isContainedByRefSeq()

Return true if ref seq contains this range

getResidues

java.lang.String getResidues()

getStrand

int getStrand()

Returns:

1 for forward strand, -1 for reverse strand, 0 for strandless

setStrand

void setStrand(int strand)

isForwardStrand

boolean isForwardStrand()

length

int length()

getLeftOverlap

int getLeftOverlap(RangeI sf)

getRightOverlap

int getRightOverlap(RangeI sf)

isExactOverlap

boolean isExactOverlap(RangeI sf)

contains

boolean contains(RangeI sf)

Returns true if range of sf is entierly within this RangeI

contains

boolean contains(int position)

overlaps

boolean overlaps(RangeI sf)

sameRange

boolean sameRange(RangeI r)

Return true if start and end are equal

canHaveChildren

boolean canHaveChildren()

If RangeI is an instanceof FeatureSetI and FeatureSetI.hasChildFeatures is true then return true. Basically convenience method that does the awkward instanceof for you.

getRangeClone

RangeI getRangeClone()

Returns clone of self

isIdentical

boolean isIdentical(RangeI range)

Returns true if same start,end,type and name. This could potentially be changed to equals, theres implications there for hashing. A range and its clone will be identical barring modifications.

rangeIsUnassigned

boolean rangeIsUnassigned()

Return true if range has been assigned high & low

convertFromBaseOrientedToInterbase

void convertFromBaseOrientedToInterbase()

Converts base oriented range to interbase range

convertFromInterbaseToBaseOriented

void convertFromInterbaseToBaseOriented()

Converts interbase range to base oriented range