htsjdk.variant.variantcontext

Class SimpleAllele

java.lang.Object

htsjdk.variant.variantcontext.SimpleAllele

All Implemented Interfaces:

Allele, java.io.Serializable, java.lang.Comparable<Allele>

public class SimpleAllele
extends java.lang.Object
implements Allele

An implementation of Allele which includes a byte[] of the bases in the allele or the symbolic name. This has been made public as a base for classes which need to subclass Allele. Most users should create alleles using Allele.create(byte[]) instead of interacting with this class directly.

See Also:

Serialized Form

Field Summary

Fields inherited from interface htsjdk.variant.variantcontext.Allele

ALT_A, ALT_C, ALT_G, ALT_N, ALT_T, BREAKEND_EXTENDING_LEFT, BREAKEND_EXTENDING_RIGHT, NO_CALL, NO_CALL_STRING, NON_REF_ALLELE, NON_REF_STRING, REF_A, REF_C, REF_G, REF_N, REF_T, SINGLE_BREAKEND_INDICATOR, SPAN_DEL, SPAN_DEL_STRING, SV_SIMPLE_CNV, SV_SIMPLE_DEL, SV_SIMPLE_DUP, SV_SIMPLE_INS, SV_SIMPLE_INV, SYMBOLIC_ALLELE_END, SYMBOLIC_ALLELE_START, UNSPECIFIED_ALTERNATE_ALLELE, UNSPECIFIED_ALTERNATE_ALLELE_STRING

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	SimpleAllele(byte[] bases, boolean isRef)
protected	SimpleAllele(SimpleAllele allele, boolean ignoreRefState) Creates a new allele based on the provided one.
protected	SimpleAllele(java.lang.String bases, boolean isRef)

Method Summary

Modifier and Type	Method and Description
boolean	basesMatch(Allele test)
boolean	basesMatch(byte[] test)
boolean	basesMatch(java.lang.String test)
int	compareTo(Allele other)
boolean	equals(Allele other, boolean ignoreRefState) Returns true if this and other are equal.
boolean	equals(java.lang.Object other)
byte[]	getBases() Return the DNA bases segregating in this allele.
java.lang.String	getBaseString() Return the DNA bases segregating in this allele in String format.
byte[]	getDisplayBases() Same as #getDisplayString() but returns the result as byte[].
java.lang.String	getDisplayString() Return the printed representation of this allele.
int	hashCode()
boolean	isBreakpoint()
boolean	isCalled()
boolean	isNoCall()
boolean	isNonRefAllele()
boolean	isNonReference()
boolean	isPrefixOf(Allele other)
boolean	isReference()
boolean	isSingleBreakend()
boolean	isSymbolic()
int	length()
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.variant.variantcontext.Allele

acceptableAlleleBases, acceptableAlleleBases, acceptableAlleleBases, acceptableAlleleBases, create, create, create, create, create, create, create, extend, oneIsPrefixOfOther, wouldBeBreakpoint, wouldBeNoCallAllele, wouldBeNullAllele, wouldBeSingleBreakend, wouldBeStarAllele, wouldBeSymbolicAllele

Constructor Detail

SimpleAllele

protected SimpleAllele(byte[] bases,
                       boolean isRef)

SimpleAllele

protected SimpleAllele(java.lang.String bases,
                       boolean isRef)

SimpleAllele

protected SimpleAllele(SimpleAllele allele,
                       boolean ignoreRefState)

Creates a new allele based on the provided one. Ref state will be copied unless ignoreRefState is true (in which case the returned allele will be non-Ref). This method is efficient because it can skip the validation of the bases (since the original allele was already validated)

Parameters:

allele - the allele from which to copy the bases

ignoreRefState - should we ignore the reference state of the input allele and use the default ref state?

Method Detail

isPrefixOf

public boolean isPrefixOf(Allele other)

Specified by:

isPrefixOf in interface Allele

isNoCall

public boolean isNoCall()

Specified by:

isNoCall in interface Allele

Returns:

true if this is the NO_CALL allele

isCalled

public boolean isCalled()

Specified by:

isCalled in interface Allele

isReference

public boolean isReference()

Specified by:

isReference in interface Allele

Returns:

true if this Allele is the reference allele

isNonReference

public boolean isNonReference()

Specified by:

isNonReference in interface Allele

Returns:

true if this Allele is not the reference allele

isSymbolic

public boolean isSymbolic()

Specified by:

isSymbolic in interface Allele

Returns:

true if this Allele is symbolic (i.e. no well-defined base sequence), this includes breakpoints and breakends

isBreakpoint

public boolean isBreakpoint()

Specified by:

isBreakpoint in interface Allele

Returns:

true if this Allele is a breakpoint ( ex: G]17:198982] or ]13:123456]T )

isSingleBreakend

public boolean isSingleBreakend()

Specified by:

isSingleBreakend in interface Allele

Returns:

true if this Allele is a single breakend (ex: .A or A.)

toString

public java.lang.String toString()

Specified by:

toString in interface Allele

Overrides:

toString in class java.lang.Object

getBases

public byte[] getBases()

Return the DNA bases segregating in this allele. Note this isn't reference polarized, so the Null allele is represented by a vector of length 0

Specified by:

getBases in interface Allele

Returns:

the segregating bases

getBaseString

public java.lang.String getBaseString()

Return the DNA bases segregating in this allele in String format. This is useful, because toString() adds a '*' to reference alleles and getBases() returns garbage when you call toString() on it.

Specified by:

getBaseString in interface Allele

Returns:

the segregating bases

getDisplayString

public java.lang.String getDisplayString()

Return the printed representation of this allele. Same as getBaseString(), except for symbolic alleles. For symbolic alleles, the base string is empty while the display string contains <TAG>.

Specified by:

getDisplayString in interface Allele

Returns:

the allele string representation

getDisplayBases

public byte[] getDisplayBases()

Same as #getDisplayString() but returns the result as byte[]. Slightly faster then getDisplayString()

Specified by:

getDisplayBases in interface Allele

Returns:

the allele string representation

equals

public boolean equals(java.lang.Object other)

Specified by:

equals in interface Allele

Overrides:

equals in class java.lang.Object

Parameters:

other - the other allele

Returns:

true if these alleles are equal

hashCode

public int hashCode()

Specified by:

hashCode in interface Allele

Overrides:

hashCode in class java.lang.Object

Returns:

hash code

equals

public boolean equals(Allele other,
                      boolean ignoreRefState)

Returns true if this and other are equal. If ignoreRefState is true, then doesn't require both alleles has the same ref tag

Specified by:

equals in interface Allele

Parameters:

other - allele to compare to

ignoreRefState - if true, ignore ref state in comparison

Returns:

true if this and other are equal

basesMatch

public boolean basesMatch(byte[] test)

Specified by:

basesMatch in interface Allele

Parameters:

test - bases to test against

Returns:

true if this Allele contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles

basesMatch

public boolean basesMatch(java.lang.String test)

Specified by:

basesMatch in interface Allele

Parameters:

test - bases to test against

Returns:

true if this Allele contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles

basesMatch

public boolean basesMatch(Allele test)

Specified by:

basesMatch in interface Allele

Parameters:

test - allele to test against

Returns:

true if this Allele contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles

length

public int length()

Specified by:

length in interface Allele

Returns:

the length of this allele. Null and NO_CALL alleles have 0 length.

compareTo

public int compareTo(Allele other)

Specified by:

compareTo in interface java.lang.Comparable<Allele>

isNonRefAllele

public boolean isNonRefAllele()

Specified by:

isNonRefAllele in interface Allele

Returns:

true if Allele is either <NON_REF> or <*>