com.compomics.util.experiment.biology
Class Protein

java.lang.Object
  extended by com.compomics.util.experiment.personalization.ExperimentObject
      extended by com.compomics.util.experiment.biology.Protein
All Implemented Interfaces:
Serializable, Cloneable

public class Protein
extends ExperimentObject

This class models a protein. Created by IntelliJ IDEA. User: Marc Date: Jun 18, 2010 Time: 8:56:22 AM

See Also:
Serialized Form

Constructor Summary
Protein()
          Constructor for a protein
Protein(String accession, boolean isDecoy)
          Simplistic constructor for a protein (typically used when loading identification files).
Protein(String accession, Header.DatabaseType databaseType, String sequence, boolean isDecoy)
          Constructor for a protein.
Protein(String accession, String sequence, boolean isDecoy)
          Constructor for a protein.
 
Method Summary
 String getAccession()
          Getter for the protein accession
 Header.DatabaseType getDatabaseType()
          Getter for the protein database type.
 int getNPossiblePeptides(Enzyme enzyme)
          Returns the number of possible peptides (not accounting PTMs nor missed cleavages) with the selected enzyme
 String getProteinKey()
          Returns the key for protein indexing.
 String getSequence()
          Getter for the protein sequence
 boolean isDecoy()
          Indicates if the protein is factice (from a decoy database for instance)
 boolean isSameAs(Protein anotherProtein)
          A method to compare proteins.
 
Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, getParameterKey, getUrParam
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Protein

public Protein()
Constructor for a protein


Protein

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

Parameters:
accession - The protein accession
isDecoy - boolean indicating whether the protein is a decoy

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

Protein

public Protein(String accession,
               Header.DatabaseType databaseType,
               String sequence,
               boolean isDecoy)
Constructor for a protein.

Parameters:
accession - The protein accession
databaseType - The protein database the protein comes from
sequence - The protein sequence
isDecoy - boolean indicating whether the protein is a decoy
Method Detail

isDecoy

public boolean isDecoy()
Indicates if the protein is factice (from a decoy database for instance)

Returns:
a boolean indicating if the protein is factice

getAccession

public String getAccession()
Getter for the protein accession

Returns:
the protein accession

getDatabaseType

public Header.DatabaseType getDatabaseType()
Getter for the protein database type.

Returns:
the protein database type

getSequence

public String getSequence()
Getter for the protein sequence

Returns:
the protein sequence

isSameAs

public boolean isSameAs(Protein anotherProtein)
A method to compare proteins. For now accession based.

Parameters:
anotherProtein - an other protein
Returns:
a boolean indicating if the proteins are identical

getProteinKey

public String getProteinKey()
Returns the key for protein indexing. For now the protein accession.

Returns:
the key for protein indexing.

getNPossiblePeptides

public int getNPossiblePeptides(Enzyme enzyme)
Returns the number of possible peptides (not accounting PTMs nor missed cleavages) with the selected enzyme

Parameters:
enzyme - The selected enzyme
Returns:
the number of possible peptides


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