public class VDJCGeneData extends java.lang.Object implements java.lang.Comparable<VDJCGeneData>
| 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) |
| 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.
|
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)
public BaseSequence getBaseSequence()
public java.lang.String getName()
public java.lang.String getGeneName()
public java.lang.String getFamilyName()
public GeneType getGeneType()
public boolean isFunctional()
public Chains getChains()
public java.util.Map<ReferencePoint,java.lang.Long> getAnchorPoints()
public java.util.SortedMap<java.lang.String,java.util.SortedSet<java.lang.String>> getMeta()
public java.util.SortedSet<java.lang.String> getMetaValueSet(java.lang.String key)
key - keypublic java.lang.String getMetaValue(java.lang.String key)
key - keypublic VDJCGeneData setMetaValue(java.lang.String key, java.lang.String newValue)
key - keynewValue - new valuepublic VDJCGeneData addMetaValue(java.lang.String key, java.lang.String value)
key - keyvalue - valuepublic VDJCGeneData clone()
clone in class java.lang.Objectpublic int compareTo(VDJCGeneData o)
compareTo in interface java.lang.Comparable<VDJCGeneData>public boolean equals(java.lang.Object o)
equals in class java.lang.Objectpublic int hashCode()
hashCode in class java.lang.Object