io.repseq.gen.dist

Class MarkovInsertModel

java.lang.Object

io.repseq.gen.dist.MarkovInsertModel

All Implemented Interfaces:

InsertModel, Model

Direct Known Subclasses:

MarkovInsertModel.Model3, MarkovInsertModel.Model5

public abstract class MarkovInsertModel
extends java.lang.Object
implements InsertModel

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MarkovInsertModel.Model3
static class	MarkovInsertModel.Model5

Field Summary

Fields

Modifier and Type	Field and Description
java.util.Map<java.lang.String,java.lang.Double>	distribution Map like: "A>C": 0.3, "A>A": 0.1
IndependentIntModel	lengthDistribution

Method Summary

Modifier and Type	Method and Description
InsertGenerator	create(org.apache.commons.math3.random.RandomGenerator random, boolean v, java.util.List<VDJCGene> vGenes, java.util.List<VDJCGene> dGenes, java.util.List<VDJCGene> jGenes, java.util.List<VDJCGene> cGenes) Initialize insert generator

Methods inherited from class java.lang.Object

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

Field Detail

lengthDistribution

public final IndependentIntModel lengthDistribution

distribution

public final java.util.Map<java.lang.String,java.lang.Double> distribution

Map like: "A>C": 0.3, "A>A": 0.1

Method Detail

create

public InsertGenerator create(org.apache.commons.math3.random.RandomGenerator random,
                              boolean v,
                              java.util.List<VDJCGene> vGenes,
                              java.util.List<VDJCGene> dGenes,
                              java.util.List<VDJCGene> jGenes,
                              java.util.List<VDJCGene> cGenes)

Description copied from interface: InsertModel

Initialize insert generator

Specified by:

create in interface InsertModel

Parameters:

random - source of random data

v - true for V(J/D) insert, false for DJ insert

Returns:

insert generator