io.repseq.dto

Class VDJCGeneData

java.lang.Object

io.repseq.dto.VDJCGeneData

All Implemented Interfaces:

java.lang.Comparable<VDJCGeneData>

public class VDJCGeneData
extends java.lang.Object
implements java.lang.Comparable<VDJCGeneData>

DTO for VDJC Gene

Constructor Summary

Constructors

Constructor and Description
VDJCGeneData(BaseSequence baseSequence, java.lang.String name, GeneType geneType, boolean isFunctional, Chains chains, java.util.SortedMap<java.lang.String,java.util.SortedSet<java.lang.String>> meta, java.util.SortedMap<ReferencePoint,java.lang.Long> anchorPoints)

Method Summary

Modifier and Type	Method and Description
VDJCGeneData	addMetaValue(java.lang.String key, java.lang.String value) Add value to the list of values associated with the key.
VDJCGeneData	clone() Clone this object
int	compareTo(VDJCGeneData o)
boolean	equals(java.lang.Object o)
java.util.Map<ReferencePoint,java.lang.Long>	getAnchorPoints() Map of anchor points
BaseSequence	getBaseSequence()
Chains	getChains() Chains of immunological receptors that this segment can be a part of
java.lang.String	getFamilyName() Gene family name (e.g.
java.lang.String	getGeneName() Name without allele index (e.g.
GeneType	getGeneType() Gene type (V / D / J / C)
java.util.SortedMap<java.lang.String,java.util.SortedSet<java.lang.String>>	getMeta() Free form meta information for the gene, raw meta map
java.lang.String	getMetaValue(java.lang.String key) Returns single value associated with the key from meta section of the gene record
java.util.SortedSet<java.lang.String>	getMetaValueSet(java.lang.String key) Returns list of values associated with the key from meta section of the gene record
java.lang.String	getName() Full gene name
int	hashCode()
boolean	isFunctional() Returns true if this gene is marked as functional in the library file
VDJCGeneData	setMetaValue(java.lang.String key, java.lang.String newValue) Overrides value of field with the specified key.

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

VDJCGeneData

public VDJCGeneData(BaseSequence baseSequence,
                    java.lang.String name,
                    GeneType geneType,
                    boolean isFunctional,
                    Chains chains,
                    java.util.SortedMap<java.lang.String,java.util.SortedSet<java.lang.String>> meta,
                    java.util.SortedMap<ReferencePoint,java.lang.Long> anchorPoints)

Method Detail

getBaseSequence

public BaseSequence getBaseSequence()

getName

public java.lang.String getName()

Full gene name

Returns:

full gene name

getGeneName

public java.lang.String getGeneName()

Name without allele index (e.g. TRBV12-3 for TRBV12-3*01).

Returns:

without allele index (e.g. TRBV12-3 for TRBV12-3*01)

getFamilyName

public java.lang.String getFamilyName()

Gene family name (e.g. TRBV12 for TRBV12-3*01).

Returns:

gene family name (e.g. TRBV12 for TRBV12-3*01)

getGeneType

public GeneType getGeneType()

Gene type (V / D / J / C)

isFunctional

public boolean isFunctional()

Returns true if this gene is marked as functional in the library file

getChains

public Chains getChains()

Chains of immunological receptors that this segment can be a part of

getAnchorPoints

public java.util.Map<ReferencePoint,java.lang.Long> getAnchorPoints()

Map of anchor points

getMeta

public java.util.SortedMap<java.lang.String,java.util.SortedSet<java.lang.String>> getMeta()

Free form meta information for the gene, raw meta map

getMetaValueSet

public java.util.SortedSet<java.lang.String> getMetaValueSet(java.lang.String key)

Returns list of values associated with the key from meta section of the gene record

Parameters:

key - key

getMetaValue

public java.lang.String getMetaValue(java.lang.String key)

Returns single value associated with the key from meta section of the gene record

Parameters:

key - key

setMetaValue

public VDJCGeneData setMetaValue(java.lang.String key,
                                 java.lang.String newValue)

Overrides value of field with the specified key. All previous values (even if several were associated with the field) will be dropped.

Parameters:

key - key

newValue - new value

addMetaValue

public VDJCGeneData addMetaValue(java.lang.String key,
                                 java.lang.String value)

Add value to the list of values associated with the key.

Parameters:

key - key

value - value

clone

public VDJCGeneData clone()

Clone this object

Overrides:

clone in class java.lang.Object

compareTo

public int compareTo(VDJCGeneData o)

Specified by:

compareTo in interface java.lang.Comparable<VDJCGeneData>

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