de.charite.compbio.jannovar.hgvs.nts

Class NucleotideSeqDescription

java.lang.Object

de.charite.compbio.jannovar.hgvs.nts.NucleotideSeqDescription

All Implemented Interfaces:

ConvertibleToHGVSString

public class NucleotideSeqDescription
extends Object
implements ConvertibleToHGVSString

Specification for a nucleotide sequence, e.g. deleted or inserted. This can be either just a count or a nucleotide sequence.

Author:

Manuel Holtgrewe

Field Summary

Fields

Modifier and Type	Field and Description
static int	INVALID_NT_COUNT sentinel value for invalid nucleotide count

Constructor Summary

Constructors

Constructor and Description
NucleotideSeqDescription() Construct as reporting the empty string.
NucleotideSeqDescription(int ntCount) Construct with nucleotide string length and null string.
NucleotideSeqDescription(String nts) Construct with nucleotide string length.

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
String	getNucleotides() Get nucleotidestring, only available if hasNucleotides() returns true.
int	hashCode()
boolean	hasNucleotides()
boolean	isBlank()
int	length()
String	toHGVSString() Return HGVS representation in three-letter amino acid code.
String	toHGVSString(AminoAcidCode code) Return HGVS representation using the given amino acid code.
String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Field Detail

INVALID_NT_COUNT

public static final int INVALID_NT_COUNT

sentinel value for invalid nucleotide count

See Also:

Constant Field Values

Constructor Detail

NucleotideSeqDescription

public NucleotideSeqDescription()

Construct as reporting the empty string.

NucleotideSeqDescription

public NucleotideSeqDescription(int ntCount)

Construct with nucleotide string length and null string.

NucleotideSeqDescription

public NucleotideSeqDescription(String nts)

Construct with nucleotide string length.

Method Detail

hasNucleotides

public boolean hasNucleotides()

Returns:

true if the nucleotide sequence was specified

getNucleotides

public String getNucleotides()

Get nucleotidestring, only available if hasNucleotides() returns true.

Returns:

String of nucleotides in 1-character encoding

isBlank

public boolean isBlank()

Returns:

true if nothing is to be printed.

length

public int length()

Returns:

length of amino acids

toHGVSString

public String toHGVSString()

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation in three-letter amino acid code.

Specified by:

toHGVSString in interface ConvertibleToHGVSString

Returns:

HGVS representation, e.g. "133L" for an ProteinPointLocation

toHGVSString

public String toHGVSString(AminoAcidCode code)

Description copied from interface: ConvertibleToHGVSString

Return HGVS representation using the given amino acid code.

Specified by:

toHGVSString in interface ConvertibleToHGVSString

Parameters:

code - AminoAcidCode to use

Returns:

HGVS representation, e.g. "133L" for an ProteinPointLocation

toString

public String toString()

Overrides:

toString in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object