net.maizegenetics.pangenome.processAssemblyGenomes

Class MAFToGVCFPlugin.AssemblyVariantInfo

net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo

Enclosing class:

MAFToGVCFPlugin

public static class MAFToGVCFPlugin.AssemblyVariantInfo

Constructor Detail

AssemblyVariantInfo

public AssemblyVariantInfo(@NotNull
                           java.lang.String chr,
                           int startPos,
                           int endPos,
                           @NotNull
                           java.lang.String genotype,
                           @NotNull
                           java.lang.String refAllele,
                           @NotNull
                           java.lang.String altAllele,
                           boolean isVariant,
                           @NotNull
                           kotlin.Array[] alleleDepths,
                           @NotNull
                           java.lang.String asmChrom,
                           int asmStart,
                           int asmEnd,
                           @NotNull
                           java.lang.String asmStrand)

Method Detail

getChr

@NotNull
public java.lang.String getChr()

setChr

public void setChr(@NotNull
                   java.lang.String p)

getStartPos

public int getStartPos()

setStartPos

public void setStartPos(int p)

getEndPos

public int getEndPos()

setEndPos

public void setEndPos(int p)

getGenotype

@NotNull
public java.lang.String getGenotype()

setGenotype

public void setGenotype(@NotNull
                        java.lang.String p)

getRefAllele

@NotNull
public java.lang.String getRefAllele()

setRefAllele

public void setRefAllele(@NotNull
                         java.lang.String p)

getAltAllele

@NotNull
public java.lang.String getAltAllele()

setAltAllele

public void setAltAllele(@NotNull
                         java.lang.String p)

isVariant

public boolean isVariant()

setVariant

public void setVariant(boolean p)

getAlleleDepths

@NotNull
public kotlin.Array[] getAlleleDepths()

setAlleleDepths

public void setAlleleDepths(@NotNull
                            kotlin.Array[] p)

getAsmChrom

@NotNull
public java.lang.String getAsmChrom()

setAsmChrom

public void setAsmChrom(@NotNull
                        java.lang.String p)

getAsmStart

public int getAsmStart()

setAsmStart

public void setAsmStart(int p)

getAsmEnd

public int getAsmEnd()

setAsmEnd

public void setAsmEnd(int p)

getAsmStrand

@NotNull
public java.lang.String getAsmStrand()

setAsmStrand

public void setAsmStrand(@NotNull
                         java.lang.String p)

component1

@NotNull
public java.lang.String component1()

component2

public int component2()

component3

public int component3()

component4

@NotNull
public java.lang.String component4()

component5

@NotNull
public java.lang.String component5()

component6

@NotNull
public java.lang.String component6()

component7

public boolean component7()

component8

@NotNull
public kotlin.Array[] component8()

component9

@NotNull
public java.lang.String component9()

component10

public int component10()

component11

public int component11()

component12

@NotNull
public java.lang.String component12()

copy

@NotNull
public net.maizegenetics.pangenome.processAssemblyGenomes.MAFToGVCFPlugin.AssemblyVariantInfo copy(@NotNull
                                                                                                            java.lang.String chr,
                                                                                                            int startPos,
                                                                                                            int endPos,
                                                                                                            @NotNull
                                                                                                            java.lang.String genotype,
                                                                                                            @NotNull
                                                                                                            java.lang.String refAllele,
                                                                                                            @NotNull
                                                                                                            java.lang.String altAllele,
                                                                                                            boolean isVariant,
                                                                                                            @NotNull
                                                                                                            kotlin.Array[] alleleDepths,
                                                                                                            @NotNull
                                                                                                            java.lang.String asmChrom,
                                                                                                            int asmStart,
                                                                                                            int asmEnd,
                                                                                                            @NotNull
                                                                                                            java.lang.String asmStrand)

toString

@NotNull
public java.lang.String toString()

hashCode

public int hashCode()

equals

public boolean equals(@Nullable
                      java.lang.Object p)