org.expasy.mzjava.proteomics.mol

Class Protein

java.lang.Object

org.expasy.mzjava.proteomics.mol.Protein

All Implemented Interfaces:

SymbolSequence<AminoAcid>

public class Protein
extends Object
implements SymbolSequence<AminoAcid>

Author:

fnikitin, Oliver Horlacher Date: 12/2/13

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Protein.Builder

Constructor Summary

Constructors

Constructor and Description
Protein(String accessionId, AminoAcid... aas) Create an instance from a list of AminoAcids
Protein(String accessionId, String sequence) Create an instance from a sequence string

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object o)
String	getAccessionId()
PeptideBuilder	getPeptideBuilder(int fromInclusive, int toExclusive) Create a PeptideBuilder that has the sequence initialised by copying this Protein's amino acids starting at fromInclusive to toExclusive.
AminoAcid	getSymbol(int index) Returns the symbol at the specified position in this symbol sequence.
int	hashCode()
int	size() Returns the number of symbols in this symbol sequence.
String	toString()
String	toSymbolString() String containing the Symbols

Methods inherited from class java.lang.Object

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

Constructor Detail

Protein

public Protein(String accessionId,
       String sequence)

Create an instance from a sequence string

Parameters:

sequence - the string to create a Protein from

Throws:

IllegalArgumentException - if the amino-acid sequence is invalid

Protein

public Protein(String accessionId,
       AminoAcid... aas)

Create an instance from a list of AminoAcids

Parameters:

aas - the list of amino-acids

Method Detail

getAccessionId

public String getAccessionId()

getPeptideBuilder

public PeptideBuilder getPeptideBuilder(int fromInclusive,
                               int toExclusive)

Create a PeptideBuilder that has the sequence initialised by copying this Protein's amino acids starting at fromInclusive to toExclusive.

Parameters:

fromInclusive - from index protein

toExclusive - to index protein

Returns:

a new PeptideBuilder

getSymbol

public AminoAcid getSymbol(int index)

Description copied from interface: SymbolSequence

Returns the symbol at the specified position in this symbol sequence.

Specified by:

getSymbol in interface SymbolSequence<AminoAcid>

Parameters:

index - index of the symbol to return

Returns:

the symbol at the specified position in this symbol sequence

toSymbolString

public String toSymbolString()

Description copied from interface: SymbolSequence

String containing the Symbols

Specified by:

toSymbolString in interface SymbolSequence<AminoAcid>

Returns:

String containing the Symbols

size

public int size()

Description copied from interface: SymbolSequence

Returns the number of symbols in this symbol sequence. If this symbol sequence contains more than Integer.MAX_VALUE symbols, returns Integer.MAX_VALUE.

Specified by:

size in interface SymbolSequence<AminoAcid>

Returns:

the number of symbols in this symbol sequence

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Overrides:

toString in class Object