Package com.compomics.util.experiment.biology.proteins

Class Protein

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.biology.proteins.Protein

All Implemented Interfaces:

Serializable

public class Protein
extends ExperimentObject

This class models a protein.

Author:

Marc Vaudel, Harald Barsnes

See Also:

• Serialized Form

Field Summary

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor	Description
Protein()	Constructor for a protein.
Protein(String accession)	Simplistic constructor for a protein (typically used when loading identification files).
Protein(String accession, String sequence)	Constructor for a protein.
Protein(String accession, String sequence, boolean isDecoy)	Constructor for a protein.

Method Summary

Modifier and Type	Method	Description
String	getAccession()	Getter for the protein accession.
int	getLength()	Returns the number of amino acids in the sequence.
String	getProteinKey()	Returns the key for protein indexing.
String	getSequence()	Getter for the protein sequence.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

Protein

public Protein()

Constructor for a protein.

Protein

public Protein(String accession)

Simplistic constructor for a protein (typically used when loading identification files).

Parameters:

accession - The protein accession

Protein

public Protein(String accession,
 String sequence)

Constructor for a protein.

Parameters:

accession - The protein accession

sequence - The protein sequence

Protein

public Protein(String accession,
 String sequence,
 boolean isDecoy)

Constructor for a protein.

Parameters:

accession - The protein accession

sequence - The protein sequence

isDecoy - boolean indicating whether the protein is a decoy

Method Details

getAccession

public String getAccession()

Getter for the protein accession.

Returns:

the protein accession

getSequence

public String getSequence()

Getter for the protein sequence.

Returns:

the protein sequence

getProteinKey

public String getProteinKey()

Returns the key for protein indexing. For now the protein accession.

Returns:

the key for protein indexing.

getLength

public int getLength()

Returns the number of amino acids in the sequence.

Returns:

the number of amino acids in the sequence