Package com.compomics.util.experiment.identification.utils

Class ProteinUtils

java.lang.Object

com.compomics.util.experiment.identification.utils.ProteinUtils

public class ProteinUtils
extends Object

Convenience functions for the handling of proteins.

Author:

Marc Vaudel

Constructor Summary

Constructors

Constructor	Description
ProteinUtils()	Empty default constructor.

Method Summary

Modifier and Type	Method	Description
static double	computeMolecularWeight(String sequence)	Returns the protein's molecular weight.
static int	getNCleavageSites(String sequence, ArrayList<Enzyme> enzymes)	Returns the number of cleavage sites.
static int[]	getObservableAminoAcids(String sequence, ArrayList<Enzyme> enzymes, double pepMaxLength)	Returns the observable amino acids in the sequence when using the given enzymes with the given maximal peptide length.
static int	getObservableLength(String sequence, ArrayList<Enzyme> enzymes, double pepMaxLength)	Returns the number of observable amino acids in the sequence.
static boolean	isDecoy(String accession, FastaParameters fastaParameters)	Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given FASTA parameters.
static boolean	isDecoy(String accession, SequenceProvider sequenceProvider)	Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given sequence provider.

Methods inherited from class java.lang.Object

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

Constructor Details

ProteinUtils

public ProteinUtils()

Empty default constructor.

Method Details

isDecoy

public static boolean isDecoy(String accession,
 FastaParameters fastaParameters)

Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given FASTA parameters.

Parameters:

accession - the protein accession

fastaParameters - the FASTA parameters

Returns:

a boolean indicating whether the given accession corresponds to a decoy sequence

isDecoy

public static boolean isDecoy(String accession,
 SequenceProvider sequenceProvider)

Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given sequence provider.

Parameters:

accession - the protein accession

sequenceProvider - the sequence provider

Returns:

a boolean indicating whether the given accession corresponds to a decoy sequence

getObservableAminoAcids

public static int[] getObservableAminoAcids(String sequence,
 ArrayList<Enzyme> enzymes,
 double pepMaxLength)

Returns the observable amino acids in the sequence when using the given enzymes with the given maximal peptide length.

Parameters:

sequence - the protein sequence

enzymes - the enzymes to use

pepMaxLength - the max peptide length

Returns:

the number of observable amino acids of the sequence

getObservableLength

public static int getObservableLength(String sequence,
 ArrayList<Enzyme> enzymes,
 double pepMaxLength)

Returns the number of observable amino acids in the sequence.

Parameters:

sequence - the protein sequence

enzymes - the enzymes to use

pepMaxLength - the max peptide length

Returns:

the number of observable amino acids of the sequence

getNCleavageSites

public static int getNCleavageSites(String sequence,
 ArrayList<Enzyme> enzymes)

Returns the number of cleavage sites.

Parameters:

sequence - the protein sequence

enzymes - the enzymes to use

Returns:

the number of possible peptides

computeMolecularWeight

public static double computeMolecularWeight(String sequence)

Returns the protein's molecular weight.

Parameters:

sequence - the protein sequence

Returns:

the protein's molecular weight in kDa