Package de.charite.compbio.jannovar.hgvs.protein

Class ProteinRange

java.lang.Object

de.charite.compbio.jannovar.hgvs.protein.ProteinRange

All Implemented Interfaces:

ConvertibleToHGVSString

public class ProteinRange
extends Object
implements ConvertibleToHGVSString

Represent a range in a protein.

Note that contrary to Java-style, we represent the first and last character of the range instead of the begin and end position. Thus, we use inclusive positions. This is also reflected by the members being named first and last instead of begin and end.

In the case of the first position being equal to the last one, the ProteinRange degrades to a point when toHGVSString() is called.

Author:

Manuel Holtgrewe

Constructor Summary

Constructors

Constructor	Description
ProteinRange(ProteinPointLocation first, ProteinPointLocation last)

Method Summary

Modifier and Type	Method	Description
static ProteinRange	build(String firstAA, int first, String lastAA, int last)
static ProteinRange	buildDownstreamOfTerminal(String firstAA, int first, String lastAA, int last)
static ProteinRange	buildWithOffset(String firstAA, int first, int firstOffset, String lastAA, int last, int lastOffset)
boolean	equals(Object obj)
ProteinPointLocation	getFirst()
ProteinPointLocation	getLast()
int	hashCode()
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

Constructor Detail

ProteinRange

public ProteinRange(ProteinPointLocation first,
                    ProteinPointLocation last)

Parameters:

first - first position of the range

last - last position of the range

Method Detail

build

public static ProteinRange build(String firstAA,
                                 int first,
                                 String lastAA,
                                 int last)

buildWithOffset

public static ProteinRange buildWithOffset(String firstAA,
                                           int first,
                                           int firstOffset,
                                           String lastAA,
                                           int last,
                                           int lastOffset)

buildDownstreamOfTerminal

public static ProteinRange buildDownstreamOfTerminal(String firstAA,
                                                     int first,
                                                     String lastAA,
                                                     int last)

getFirst

public ProteinPointLocation getFirst()

Returns:

location of the first amino acid in the range

getLast

public ProteinPointLocation getLast()

Returns:

location of the last amino acid in the range

length

public int length()

Returns:

length of the range

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