io.repseq.core

Class GeneFeature

java.lang.Object

io.repseq.core.GeneFeature

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<GeneFeature>, java.lang.Iterable<GeneFeature.ReferenceRange>

public final class GeneFeature
extends java.lang.Object
implements java.lang.Iterable<GeneFeature.ReferenceRange>, java.lang.Comparable<GeneFeature>, java.io.Serializable

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GeneFeature.Deserializer
static class	GeneFeature.ReferenceRange
static class	GeneFeature.Serializer

Field Summary

Fields

Modifier and Type	Field and Description
static GeneFeature	CDR1
static GeneFeature	CDR2
static GeneFeature	CDR3
static GeneFeature	CExon1
static GeneFeature	CRegion
static GeneFeature	DCDR3Part
static GeneFeature	DJJunction
static GeneFeature	DLeftPSegment
static GeneFeature	DRegion
static GeneFeature	DRegionTrimmed
static GeneFeature	DRegionWithP
static GeneFeature	DRightPSegment
static GeneFeature	Exon1
static GeneFeature	Exon2
static GeneFeature	FR1
static GeneFeature	FR2
static GeneFeature	FR3
static GeneFeature	FR4
static GeneFeature	GermlineDPSegment
static GeneFeature	GermlineJCDR3Part
static GeneFeature	GermlineJPSegment
static int	GermlinePRegionSize
static GeneFeature	GermlineVCDR3Part
static GeneFeature	GermlineVPSegment
static GeneFeature	JCDR3Part
static GeneFeature	JPSegment
static GeneFeature	JRegion
static GeneFeature	JRegionTrimmed
static GeneFeature	JRegionWithP
static GeneFeature	L
static GeneFeature	L1
static GeneFeature	L2
static GeneFeature	ShortCDR3
static GeneFeature	V5UTR
static GeneFeature	V5UTRGermline
static GeneFeature	VCDR3Part
static GeneFeature	VDJRegion
static GeneFeature	VDJTranscript
static GeneFeature	VDJTranscriptWithout5UTR
static GeneFeature	VDJunction
static GeneFeature	VExon2
static GeneFeature	VExon2Trimmed
static GeneFeature	VGene
static GeneFeature	VGeneWithP
static GeneFeature	VIntron
static GeneFeature	VJJunction
static GeneFeature	VLIntronL
static GeneFeature	VPSegment
static GeneFeature	VRegion
static GeneFeature	VRegionTrimmed
static GeneFeature	VRegionWithP
static GeneFeature	VTranscript
static GeneFeature	VTranscriptWithout5UTR
static GeneFeature	VTranscriptWithout5UTRWithP
static GeneFeature	VTranscriptWithP

Constructor Summary

Constructors

Constructor and Description
GeneFeature(GeneFeature... features)
GeneFeature(GeneFeature feature, int leftOffset, int rightOffset)
GeneFeature(ReferencePoint referencePoint, int leftOffset, int rightOffset)
GeneFeature(ReferencePoint begin, ReferencePoint end)

Method Summary

Modifier and Type	Method and Description
GeneFeature	append(GeneFeature gf)
int	compareTo(GeneFeature o)
boolean	contains(GeneFeature geneFeature)
static java.lang.String	encode(GeneFeature feature)
boolean	equals(java.lang.Object o)
static GeneFeature	getCodingGeneFeature(GeneFeature feature) Returns coding gene feature contained in input gene feature
static GeneFeature	getFeatureByName(java.lang.String pointName)
static java.util.Map<java.lang.String,GeneFeature>	getFeaturesByName()
ReferencePoint	getFirstPoint()
static ReferencePoint	getFrameReference(GeneFeature feature) Returns reference point that is triplet boundary (so defines reading frame) inside provided gene feature or returns null.
GeneType	getGeneType()
ReferencePoint	getLastPoint()
static java.util.Map<GeneFeature,java.lang.String>	getNameByFeature()
static java.lang.String	getNameByFeature(GeneFeature point)
GeneFeature.ReferenceRange	getReferenceRange(int i)
static GeneFeature	getRegion(GeneType type)
int	hashCode()
boolean	hasReversedRegions()
static GeneFeature	intersection(GeneFeature gf1, GeneFeature gf2)
static GeneFeature	intersection(GeneFeature gf1, GeneFeature gf2, boolean strict)
static GeneFeature	intersectionStrict(GeneFeature gf1, GeneFeature gf2)
boolean	isAlignmentAttached() Return true if contains at least one alignment attached point
boolean	isComposite() Return true if this gene feature contains more then one disjoint region
java.util.Iterator<GeneFeature.ReferenceRange>	iterator()
static boolean	match(GeneFeature.ReferenceRange a, GeneFeature b)
static GeneFeature	parse(java.lang.String string)
GeneFeature	reverse()
int	size()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

GermlinePRegionSize

public static final int GermlinePRegionSize

See Also:

Constant Field Values

VPSegment

@Doc(value="P-segment of V gene")
public static final GeneFeature VPSegment

JPSegment

@Doc(value="P-segment of J gene")
public static final GeneFeature JPSegment

DLeftPSegment

@Doc(value="Left P-segment of D gene")
public static final GeneFeature DLeftPSegment

DRightPSegment

@Doc(value="Right P-segment of D gene")
public static final GeneFeature DRightPSegment

GermlineVPSegment

@Doc(value="P-segment of V gene to be used as alignment reference")
public static final GeneFeature GermlineVPSegment

GermlineJPSegment

@Doc(value="P-segment of J gene to be used as alignment reference")
public static final GeneFeature GermlineJPSegment

GermlineDPSegment

@Doc(value="P-segment of D gene to be used as alignment reference")
public static final GeneFeature GermlineDPSegment

VRegion

@Doc(value="Full V Region; germline")
public static final GeneFeature VRegion

VRegionWithP

@Doc(value="Full V Region with P-segment; to be used as alignment reference")
public static final GeneFeature VRegionWithP

VRegionTrimmed

@Doc(value="Full V Region in rearranged sequence, e.g. after trimming")
public static final GeneFeature VRegionTrimmed

DRegion

@Doc(value="Full D Region; germline")
public static final GeneFeature DRegion

DRegionWithP

@Doc(value="Full D Region with P-segment; germline; to be used as alignment reference")
public static final GeneFeature DRegionWithP

DCDR3Part

@Doc(value="Full D Region in rearranged sequence, e.g. after trimming; same as DRegionTrimmed")
public static final GeneFeature DCDR3Part

DRegionTrimmed

@Doc(value="Full D Region in rearranged sequence, e.g. after trimming; same as DCDR3Part")
public static final GeneFeature DRegionTrimmed

JRegion

@Doc(value="Full J Region; germline")
public static final GeneFeature JRegion

JRegionWithP

@Doc(value="Full J Region with P-segment; to be used as alignment reference")
public static final GeneFeature JRegionWithP

JRegionTrimmed

@Doc(value="Full J Region in rearranged sequence, e.g. after trimming")
public static final GeneFeature JRegionTrimmed

V5UTRGermline

@Doc(value="5\'UTR; germline")
public static final GeneFeature V5UTRGermline

V5UTR

@Doc(value="5\'UTR in aligned sequence; trimmed")
public static final GeneFeature V5UTR

L1

@Doc(value="Part of lider sequence in first exon. The same as ``Exon1``.")
public static final GeneFeature L1

VIntron

@Doc(value="Intron in V region.")
public static final GeneFeature VIntron

L2

@Doc(value="Part of lider sequence in second exon.")
public static final GeneFeature L2

VLIntronL

@Doc(value="``L1`` + ``VIntron`` + ``L2``")
public static final GeneFeature VLIntronL

FR1

@Doc(value="Framework 1")
public static final GeneFeature FR1

CDR1

@Doc(value="CDR1 (Complementarity determining region 1)")
public static final GeneFeature CDR1

FR2

@Doc(value="Framework 2")
public static final GeneFeature FR2

CDR2

@Doc(value="CDR2 (Complementarity determining region 2)")
public static final GeneFeature CDR2

FR3

@Doc(value="Framework 2")
public static final GeneFeature FR3

CDR3

@Doc(value="CDR3 (Complementarity determining region 3). Cys from V region and Phe/Trp from J region included.")
public static final GeneFeature CDR3

ShortCDR3

@Doc(value="CDR3 (Complementarity determining region 3). Cys from V region and Phe/Trp from J region excluded.")
public static final GeneFeature ShortCDR3

FR4

@Doc(value="Framework 4 (J region after CDR3)")
public static final GeneFeature FR4

VCDR3Part

@Doc(value="Part of V region inside CDR3 (commonly starts from Cys)")
public static final GeneFeature VCDR3Part

JCDR3Part

@Doc(value="Part of J region inside CDR3 (commonly ends with Phe/Trp)")
public static final GeneFeature JCDR3Part

GermlineVCDR3Part

@Doc(value="Part of V region inside CDR3 (commonly starts from Cys)")
public static final GeneFeature GermlineVCDR3Part

GermlineJCDR3Part

@Doc(value="Part of J region inside CDR3 (commonly ends with Phe/Trp)")
public static final GeneFeature GermlineJCDR3Part

VDJunction

@Doc(value="N region between V and D genes; not defined for loci without D genes and for V(D)J rearrangement with unidentified D region.")
public static final GeneFeature VDJunction

DJJunction

@Doc(value="N region between V and D genes; not defined for loci without D genes and for V(D)J rearrangement with unidentified D region.")
public static final GeneFeature DJJunction

VJJunction

@Doc(value="Region between V and J regions. For loci without D genes - fully composed from non-template nucleotides. May contain D region.")
public static final GeneFeature VJJunction

Exon1

@Doc(value="First exon. The same as ``L1``.")
public static final GeneFeature Exon1

Exon2

@Doc(value="Full second exon of IG/TCR gene.")
public static final GeneFeature Exon2

VExon2

@Doc(value="Second exon of V gene.")
public static final GeneFeature VExon2

VExon2Trimmed

@Doc(value="Second exon of V gene trimmed. Ends within CDR3 in V(D)J rearrangement.")
public static final GeneFeature VExon2Trimmed

CExon1

@Doc(value="First exon of C Region")
public static final GeneFeature CExon1

CRegion

@Doc(value="Full C region")
public static final GeneFeature CRegion

L

@Doc(value="Full leader sequence")
public static final GeneFeature L

VTranscriptWithout5UTR

@Doc(value="``Exon1`` + ``VExon2``. Common reference feature used in alignments for mRNA data obtained without 5\'RACE.")
public static final GeneFeature VTranscriptWithout5UTR

VTranscript

@Doc(value="``V5UTR`` + ``Exon1`` + ``VExon2``. Common reference feature used in alignments for cDNA data obtained using 5\'RACE (that may contain UTRs).")
public static final GeneFeature VTranscript

VGene

@Doc(value="``{V5UTRBegin:VEnd}``. Common reference feature used in alignments for genomic DNA data.")
public static final GeneFeature VGene

VTranscriptWithout5UTRWithP

@Doc(value="``Exon1`` + ``VExon2``. Common reference feature used in alignments for mRNA data obtained without 5\'RACE. Contains reference for P region.")
public static final GeneFeature VTranscriptWithout5UTRWithP

VTranscriptWithP

@Doc(value="``V5UTR`` + ``Exon1`` + ``VExon2``. Common reference feature used in alignments for cDNA data obtained using 5\'RACE (that may contain UTRs). Contains reference for P region.")
public static final GeneFeature VTranscriptWithP

VGeneWithP

@Doc(value="``{V5UTRBegin:VEnd}``. Common reference feature used in alignments for genomic DNA data. Contains reference for P region.")
public static final GeneFeature VGeneWithP

VDJTranscriptWithout5UTR

@Doc(value="First two exons of IG/TCR gene.")
public static final GeneFeature VDJTranscriptWithout5UTR

VDJTranscript

@Doc(value="First two exons with 5\'UTR of IG/TCR gene.")
public static final GeneFeature VDJTranscript

VDJRegion

@Doc(value="Full V, D, J assembly without 5\'UTR and leader sequence.")
public static final GeneFeature VDJRegion

Constructor Detail

GeneFeature

public GeneFeature(GeneFeature... features)

GeneFeature

public GeneFeature(ReferencePoint begin,
                   ReferencePoint end)

GeneFeature

public GeneFeature(GeneFeature feature,
                   int leftOffset,
                   int rightOffset)

GeneFeature

public GeneFeature(ReferencePoint referencePoint,
                   int leftOffset,
                   int rightOffset)

Method Detail

getReferenceRange

public GeneFeature.ReferenceRange getReferenceRange(int i)

append

public GeneFeature append(GeneFeature gf)

size

public int size()

hasReversedRegions

public boolean hasReversedRegions()

reverse

public GeneFeature reverse()

getGeneType

public GeneType getGeneType()

isComposite

public boolean isComposite()

Return true if this gene feature contains more then one disjoint region

isAlignmentAttached

public boolean isAlignmentAttached()

Return true if contains at least one alignment attached point

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

intersectionStrict

public static GeneFeature intersectionStrict(GeneFeature gf1,
                                             GeneFeature gf2)

intersection

public static GeneFeature intersection(GeneFeature gf1,
                                       GeneFeature gf2)

intersection

public static GeneFeature intersection(GeneFeature gf1,
                                       GeneFeature gf2,
                                       boolean strict)

getFirstPoint

public ReferencePoint getFirstPoint()

getLastPoint

public ReferencePoint getLastPoint()

contains

public boolean contains(GeneFeature geneFeature)

getFrameReference

public static ReferencePoint getFrameReference(GeneFeature feature)

Returns reference point that is triplet boundary (so defines reading frame) inside provided gene feature or returns null.

Parameters:

feature - gene feature

Returns:

reference point that is triplet boundary (so defines reading frame) inside provided gene feature or null

getCodingGeneFeature

public static GeneFeature getCodingGeneFeature(GeneFeature feature)

Returns coding gene feature contained in input gene feature

Parameters:

feature - input gene feature

Returns:

coding gene feature contained in input gene feature or null

compareTo

public int compareTo(GeneFeature o)

Specified by:

compareTo in interface java.lang.Comparable<GeneFeature>

iterator

public java.util.Iterator<GeneFeature.ReferenceRange> iterator()

Specified by:

iterator in interface java.lang.Iterable<GeneFeature.ReferenceRange>

getRegion

public static GeneFeature getRegion(GeneType type)

getFeatureByName

public static GeneFeature getFeatureByName(java.lang.String pointName)

getNameByFeature

public static java.lang.String getNameByFeature(GeneFeature point)

parse

public static GeneFeature parse(java.lang.String string)

getFeaturesByName

public static java.util.Map<java.lang.String,GeneFeature> getFeaturesByName()

getNameByFeature

public static java.util.Map<GeneFeature,java.lang.String> getNameByFeature()

encode

public static java.lang.String encode(GeneFeature feature)

match

public static boolean match(GeneFeature.ReferenceRange a,
                            GeneFeature b)