com.compomics.util.experiment.biology

Class Protein

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.biology.Protein

All Implemented Interfaces:

Serializable, Cloneable

public class Protein
extends ExperimentObject

This class models a protein.

Author:

Marc Vaudel, Harald Barsnes

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
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

Methods

Modifier and Type	Method and Description
double	computeMolecularWeight() Returns the protein's molecular weight.
String	getAccession() Getter for the protein accession.
Header.DatabaseType	getDatabaseType() Getter for the protein database type.
int	getLength() Returns the number of amino acids in the sequence.
int	getNCleavageSites(Enzyme enzyme) Returns the number of cleavage sites.
int	getObservableLength(Enzyme enzyme, double pepMaxLength) Returns the number of observable amino acids in the sequence.
ArrayList<Integer>	getPeptideStart(String peptideSequence, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns the list of indexes where a peptide can be found in the protein sequence.
String	getProteinKey() Returns the key for protein indexing.
String	getSequence() Getter for the protein sequence.
HashMap<Integer,String[]>	getSurroundingAA(String peptide, int nAA, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns the amino acids surrounding a peptide in the sequence of the given protein in a map: peptide start index -> (amino acids before, amino acids after).
boolean	isCTerm(String peptideSequence, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns a boolean indicating whether the protein ends with the given peptide.
boolean	isDecoy() Indicates if the protein is factice (from a decoy database for instance).
boolean	isEnzymaticPeptide(String peptideSequence, Enzyme enzyme, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns true of the peptide is non-enzymatic, i.e., has one or more end points that cannot be caused by the enzyme alone.
boolean	isNTerm(String peptideSequence, AminoAcidPattern.MatchingType matchingType, Double massTolerance) Returns a boolean indicating whether the protein starts with the given peptide.
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.

getLength

public int getLength()

Returns the number of amino acids in the sequence.

Returns:

the number of amino acids in the sequence

getObservableLength

public int getObservableLength(Enzyme enzyme,
                      double pepMaxLength)

Returns the number of observable amino acids in the sequence.

Parameters:

enzyme - the enzyme to use

pepMaxLength - the max peptide length

Returns:

the number of observable amino acids of the sequence

getNCleavageSites

public int getNCleavageSites(Enzyme enzyme)

Returns the number of cleavage sites.

Parameters:

enzyme - The selected enzyme

Returns:

the number of possible peptides

computeMolecularWeight

public double computeMolecularWeight()

Returns the protein's molecular weight. (Note that when using a SequenceFactory it is recommended to use the SequenceFactory's computeMolecularWeight method instead, as that method stored the computed molecular weights instead of recalculating them every time.)

Returns:

the protein's molecular weight

getPeptideStart

public ArrayList<Integer> getPeptideStart(String peptideSequence,
                                 AminoAcidPattern.MatchingType matchingType,
                                 Double massTolerance)

Returns the list of indexes where a peptide can be found in the protein sequence. 1 is the first amino acid.

Parameters:

peptideSequence - the sequence of the peptide of interest

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

the list of indexes where a peptide can be found in a protein sequence

isNTerm

public boolean isNTerm(String peptideSequence,
              AminoAcidPattern.MatchingType matchingType,
              Double massTolerance)

Returns a boolean indicating whether the protein starts with the given peptide.

Parameters:

peptideSequence - the peptide sequence

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

a boolean indicating whether the protein starts with the given peptide

isCTerm

public boolean isCTerm(String peptideSequence,
              AminoAcidPattern.MatchingType matchingType,
              Double massTolerance)

Returns a boolean indicating whether the protein ends with the given peptide.

Parameters:

peptideSequence - the peptide sequence

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

a boolean indicating whether the protein ends with the given peptide

isEnzymaticPeptide

public boolean isEnzymaticPeptide(String peptideSequence,
                         Enzyme enzyme,
                         AminoAcidPattern.MatchingType matchingType,
                         Double massTolerance)
                           throws IOException

Returns true of the peptide is non-enzymatic, i.e., has one or more end points that cannot be caused by the enzyme alone. False means that both the endpoints of the peptides could be caused by the selected enzyme, or that it is a terminal peptide (where one end point is most likely not enzymatic). Note that if a peptide maps to multiple locations in the protein sequence this method returns true if one or more of these peptides are enzymatic, even if not all mappings are enzymatic.

Parameters:

peptideSequence - the peptide sequence to check

enzyme - the enzyme to use

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

true of the peptide is non-enzymatic

Throws:

IOException

getSurroundingAA

public HashMap<Integer,String[]> getSurroundingAA(String peptide,
                                         int nAA,
                                         AminoAcidPattern.MatchingType matchingType,
                                         Double massTolerance)
                                           throws IOException

Returns the amino acids surrounding a peptide in the sequence of the given protein in a map: peptide start index -> (amino acids before, amino acids after).

Parameters:

peptide - the sequence of the peptide of interest

nAA - the number of amino acids to include

matchingType - the type of sequence matching

massTolerance - the mass tolerance for matching type 'indistiguishibleAminoAcids'. Can be null otherwise

Returns:

the amino acids surrounding a peptide in the protein sequence

Throws:

IOException - Exception thrown whenever an error occurred while parsing the protein sequence