org.pharmgkb.parser.vcf.model.genotype

Class VcfAllele

java.lang.Object

org.pharmgkb.parser.vcf.model.genotype.VcfAllele

@Immutable
public class VcfAllele
extends java.lang.Object

An Allele matching the VCF 4.2 specification for the ALT and REF columns. For example:

• ATgggcN
• <IDxx>
• ]34]ATGC
• ]34:55]<IDxx>

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	VcfAllele.PrimaryType

Constructor Summary

Constructors

Constructor and Description
VcfAllele(java.lang.String string)

Method Summary

Modifier and Type	Method and Description
boolean	containsBase(char... bases)
boolean	equals(java.lang.Object o)
boolean	equalsIgnoreCase(VcfAllele allele)
VcfAllele.PrimaryType	getPrimaryType()
int	hashCode()
boolean	isAmbigious()
boolean	isBreakpoint()
boolean	isDeleted()
boolean	isSimple()
boolean	isSymbolic()
int	length() Before calling, verify that this VcfAllele is not a breakpoint or a symbolic name.
java.lang.String	toString()
java.lang.String	withLowercaseBases()

Methods inherited from class java.lang.Object

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

Constructor Detail

VcfAllele

public VcfAllele(@Nonnull
                 java.lang.String string)

Parameters:

string - A string following the VCF specification for the REF or ALT columns

Method Detail

toString

@Nonnull
public java.lang.String toString()

Overrides:

toString in class java.lang.Object

Returns:

The allele string from the constructor

length

public int length()
           throws java.lang.IllegalArgumentException

Before calling, verify that this VcfAllele is not a breakpoint or a symbolic name.

Returns:

The number of bases in this Allele

Throws:

java.lang.IllegalArgumentException - If this Allele is a breakpoint or symbolic name

isBreakpoint

public boolean isBreakpoint()

Returns:

Whether this Allele is defined using breakpoints (see the VCF spec)

isSymbolic

public boolean isSymbolic()

Returns:

Whether this Allele contains a symbolic name like <IDxx>

isAmbigious

public boolean isAmbigious()

Returns:

Whether this Allele contains 'N' or 'n' as a base (does not include symbolic names)

isDeleted

public boolean isDeleted()

Returns:

Whether this Allele is '*', indicating a deletion upstream

isSimple

public boolean isSimple()

Returns:

Whether this Allele is not symbolic, deleted, or a breakpoint

getPrimaryType

public VcfAllele.PrimaryType getPrimaryType()

withLowercaseBases

@Nonnull
public java.lang.String withLowercaseBases()

Returns:

A string where every base is in lowercase; symbolic names (e.g. <IDxx>) will not be lowercased

equalsIgnoreCase

public boolean equalsIgnoreCase(@Nullable
                                VcfAllele allele)

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

containsBase

public boolean containsBase(@Nonnull
                            char... bases)

Returns:

Whether this Allele contains one or more of the characters (case-sensitive) in bases, restricted to bases (i.e. symbolic names like <IDxx> are excluded)