apollo.datamodel
Class Range

java.lang.Object
  apollo.datamodel.Range

All Implemented Interfaces:

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

Direct Known Subclasses:

CutSite, GenomicRange, SeqFeature

public class Range
extends java.lang.Object
implements RangeI, java.io.Serializable

See Also:

Serialized Form

Field Summary

protected int	high
protected static org.apache.log4j.Logger	logger
protected int	low
protected java.lang.String	name
protected SequenceI	refSeq
protected byte	strand
protected java.lang.String	type

Fields inherited from interface apollo.datamodel.RangeI

NO_NAME, NO_TYPE

Constructor Summary

Range()

Range(int start, int end)
Range with NO_NAME name

Range(java.lang.String name, int start, int end)

Method Summary

boolean	canHaveChildren() If SeqFeature is an instanceof FeatureSetI and FeatureSetI.hasChildFeatures is true then 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	getEndAsString()
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()
java.lang.String	getStartAsString()
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() Convenience method for getStrand() == 1
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 not 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 sequence) Set the SequenceI that this feature annotates.
void	setStart(int start)
void	setStrand(int strand)
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

logger

protected static final org.apache.log4j.Logger logger

low

protected int low

high

protected int high

strand

protected byte strand

name

protected java.lang.String name

type

protected java.lang.String type

refSeq

protected SequenceI refSeq

Constructor Detail

Range

public Range()

Range

public Range(int start,
             int end)

Range with NO_NAME name

Range

public Range(java.lang.String name,
             int start,
             int end)

Method Detail

getRangeClone

public RangeI getRangeClone()

returns clone of self

Specified by:

getRangeClone in interface RangeI

isIdentical

public 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.

Specified by:

isIdentical in interface RangeI

setName

public void setName(java.lang.String name)

Specified by:

setName in interface RangeI

getName

public java.lang.String getName()

Description copied from interface: RangeI

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

Specified by:

getName in interface RangeI

hasName

public boolean hasName()

Description copied from interface: RangeI

return true if name !equal NO_NAME

Specified by:

hasName in interface RangeI

getFeatureType

public 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)

Specified by:

getFeatureType in interface RangeI

setFeatureType

public void setFeatureType(java.lang.String type)

Specified by:

setFeatureType in interface RangeI

hasFeatureType

public boolean hasFeatureType()

Description copied from interface: RangeI

convenience method returns !getType()==NO_TYPE

Specified by:

hasFeatureType in interface RangeI

getStrand

public int getStrand()

Specified by:

getStrand in interface RangeI

Returns:

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

isForwardStrand

public boolean isForwardStrand()

Convenience method for getStrand() == 1

Specified by:

isForwardStrand in interface RangeI

setStrand

public void setStrand(int strand)

Specified by:

setStrand in interface RangeI

setStart

public void setStart(int start)

Specified by:

setStart in interface RangeI

getStart

public int getStart()

Specified by:

getStart in interface RangeI

setEnd

public void setEnd(int end)

Specified by:

setEnd in interface RangeI

getEnd

public int getEnd()

Specified by:

getEnd in interface RangeI

getLow

public int getLow()

Specified by:

getLow in interface RangeI

setLow

public void setLow(int low)

Specified by:

setLow in interface RangeI

getHigh

public int getHigh()

Specified by:

getHigh in interface RangeI

setHigh

public void setHigh(int high)

Specified by:

setHigh in interface RangeI

getStartAsString

public java.lang.String getStartAsString()

getEndAsString

public java.lang.String getEndAsString()

getRefSequence

public SequenceI getRefSequence()

Description copied from interface: RangeI

Retrieve the SequenceI that this feature annotates.

Specified by:

getRefSequence in interface RangeI

Returns:

the current parent SequenceI

hasRefSequence

public boolean hasRefSequence()

Description copied from interface: RangeI

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

Specified by:

hasRefSequence in interface RangeI

isContainedByRefSeq

public boolean isContainedByRefSeq()

Description copied from interface: RangeI

Return true if ref seq contains this range

Specified by:

isContainedByRefSeq in interface RangeI

setRefSequence

public void setRefSequence(SequenceI sequence)

Description copied from interface: RangeI

Set the SequenceI that this feature annotates.

Specified by:

setRefSequence in interface RangeI

Parameters:

sequence - the new parent SequenceI

getResidues

public java.lang.String getResidues()

Specified by:

getResidues in interface RangeI

getLeftOverlap

public int getLeftOverlap(RangeI sf)

Specified by:

getLeftOverlap in interface RangeI

getRightOverlap

public int getRightOverlap(RangeI sf)

Specified by:

getRightOverlap in interface RangeI

isExactOverlap

public boolean isExactOverlap(RangeI sf)

Specified by:

isExactOverlap in interface RangeI

contains

public boolean contains(RangeI sf)

Description copied from interface: RangeI

Returns true if range of sf is entierly within this RangeI

Specified by:

contains in interface RangeI

contains

public boolean contains(int position)

Specified by:

contains in interface RangeI

overlaps

public boolean overlaps(RangeI sf)

Specified by:

overlaps in interface RangeI

sameRange

public boolean sameRange(RangeI r)

Return true if start and end are equal

Specified by:

sameRange in interface RangeI

length

public int length()

Specified by:

length in interface RangeI

isSequenceAvailable

public boolean isSequenceAvailable(int position)

Specified by:

isSequenceAvailable in interface RangeI

canHaveChildren

public boolean canHaveChildren()

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

Specified by:

canHaveChildren in interface RangeI

rangeIsUnassigned

public boolean rangeIsUnassigned()

Return true if range has not been assigned high & low

Specified by:

rangeIsUnassigned in interface RangeI

convertFromBaseOrientedToInterbase

public void convertFromBaseOrientedToInterbase()

Description copied from interface: RangeI

Converts base oriented range to interbase range

Specified by:

convertFromBaseOrientedToInterbase in interface RangeI

convertFromInterbaseToBaseOriented

public void convertFromInterbaseToBaseOriented()

Description copied from interface: RangeI

Converts interbase range to base oriented range

Specified by:

convertFromInterbaseToBaseOriented in interface RangeI

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object