com.compomics.util.experiment.identification.identification_parameters.tool_specific

Class PNovoParameters

java.lang.Object

com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters

All Implemented Interfaces:

IdentificationAlgorithmParameter, Serializable

public class PNovoParameters
extends Object
implements IdentificationAlgorithmParameter

pNovo specific parameters.

Author:

Harald Barsnes

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PNovoParameters() Constructor.

Method Summary

Modifier and Type	Method and Description
boolean	equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) Indicates whether another identificationAlgorithmParameter has the same parameters.
String	getActicationType() Returns the activation type.
Advocate	getAlgorithm() Returns the identification algorithm.
int	getLowerPrecursorMass() Returns the lower precursor mass.
int	getNumberOfPeptides() Returns the number of peptides to report per spectrum.
HashMap<Character,String>	getPNovoPtmMap() Returns the pNovo to utilities PTM map.
HashMap<Character,Character>	getPNovoPtmResiduesMap() Returns the pNovo to original amino acids residue map.
Character	getPtmResidue(Character pNovoPtmCharacter) Returns the original amino acids residue corresponding to the given pNovo PTM character.
int	getUpperPrecursorMass() Returns the upper precursor mass.
String	getUtilitiesPtmName(Character pNovoPtmCharacter) Returns the utilities PTM name corresponding to the given pNovo PTM character.
void	setActicationType(String acticationType) Sets the activation type.
void	setLowerPrecursorMass(int lowerPrecursorMass) Set the lower precursor mass.
void	setNumberOfPeptides(int numberOfPeptides) Set the number of peptides to report per spectrum.
void	setPNovoPtmMap(HashMap<Character,String> pNovoPtmMap) Set the pNovo to utilities PTM map.
void	setPNovoPtmResiduesMap(HashMap<Character,Character> pNovoResidueMap) Set the pNovo to original amino acids residue map.
void	setUpperPrecursorMass(int upperPrecursorMass) Set the upper precursor mass.
String	toString(boolean html) Returns the parameters as a string.

Methods inherited from class java.lang.Object

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

Constructor Detail

PNovoParameters

public PNovoParameters()

Constructor.

Method Detail

getAlgorithm

public Advocate getAlgorithm()

Description copied from interface: IdentificationAlgorithmParameter

Returns the identification algorithm.

Specified by:

getAlgorithm in interface IdentificationAlgorithmParameter

Returns:

the identification algorithm

equals

public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)

Description copied from interface: IdentificationAlgorithmParameter

Indicates whether another identificationAlgorithmParameter has the same parameters.

Specified by:

equals in interface IdentificationAlgorithmParameter

Parameters:

identificationAlgorithmParameter - the other identificationAlgorithmParameter

Returns:

true if the algorithm and parameters are the same

toString

public String toString(boolean html)

Description copied from interface: IdentificationAlgorithmParameter

Returns the parameters as a string.

Specified by:

toString in interface IdentificationAlgorithmParameter

Parameters:

html - use HTML formatting

Returns:

the parameters as a string

getNumberOfPeptides

public int getNumberOfPeptides()

Returns the number of peptides to report per spectrum.

Returns:

the number of peptides to report per spectrum

setNumberOfPeptides

public void setNumberOfPeptides(int numberOfPeptides)

Set the number of peptides to report per spectrum.

Parameters:

numberOfPeptides - the number of peptides to report per spectrum

getLowerPrecursorMass

public int getLowerPrecursorMass()

Returns the lower precursor mass.

Returns:

the lowerPrecursorMass

setLowerPrecursorMass

public void setLowerPrecursorMass(int lowerPrecursorMass)

Set the lower precursor mass.

Parameters:

lowerPrecursorMass - the lowerPrecursorMass to set

getUpperPrecursorMass

public int getUpperPrecursorMass()

Returns the upper precursor mass.

Returns:

the upperPrecursorMass

setUpperPrecursorMass

public void setUpperPrecursorMass(int upperPrecursorMass)

Set the upper precursor mass.

Parameters:

upperPrecursorMass - the upperPrecursorMass to set

getActicationType

public String getActicationType()

Returns the activation type.

Returns:

the acticationType

setActicationType

public void setActicationType(String acticationType)

Sets the activation type.

Parameters:

acticationType - the acticationType to set

getPNovoPtmMap

public HashMap<Character,String> getPNovoPtmMap()

Returns the pNovo to utilities PTM map. Null if not set.

Returns:

the pNovo to utilities PTM map, null if not set

getUtilitiesPtmName

public String getUtilitiesPtmName(Character pNovoPtmCharacter)

Returns the utilities PTM name corresponding to the given pNovo PTM character. Null if not found.

Parameters:

pNovoPtmCharacter - the pNovo PTM character

Returns:

the utilities PTM name

setPNovoPtmMap

public void setPNovoPtmMap(HashMap<Character,String> pNovoPtmMap)

Set the pNovo to utilities PTM map.

Parameters:

pNovoPtmMap - the pNovoPtmMap to set

getPNovoPtmResiduesMap

public HashMap<Character,Character> getPNovoPtmResiduesMap()

Returns the pNovo to original amino acids residue map. Null if not set.

Returns:

the pNovo to original amino acids residue map, null if not set

getPtmResidue

public Character getPtmResidue(Character pNovoPtmCharacter)

Returns the original amino acids residue corresponding to the given pNovo PTM character. Null if not found.

Parameters:

pNovoPtmCharacter - the pNovo PTM character

Returns:

the original amino acids residue

setPNovoPtmResiduesMap

public void setPNovoPtmResiduesMap(HashMap<Character,Character> pNovoResidueMap)

Set the pNovo to original amino acids residue map.

Parameters:

pNovoResidueMap - the pNovoResidueMap to set