com.compomics.util.experiment.identification.identification_parameters

Class PepnovoParameters

java.lang.Object

com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters

All Implemented Interfaces:

IdentificationAlgorithmParameter, java.io.Serializable

public class PepnovoParameters
extends java.lang.Object
implements IdentificationAlgorithmParameter

PepNovo specific parameters.

Author:

Marc Vaudel

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
PepnovoParameters() Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(IdentificationAlgorithmParameter identificationAlgorithmParameter) Indicates whether another identificationAlgorithmParameter has the same parameters.
java.lang.Boolean	generateQuery() Returns a boolean indicating whether a blast query shall be generated.
Advocate	getAlgorithm() Returns the identification algorithm.
java.lang.Boolean	getDiscardLowQualitySpectra() Returns a boolean indicating whether low quality spectra shall be discarded.
java.lang.String	getFragmentationModel() Returns the name of the fragmentation model.
java.lang.Integer	getHitListLength() Returns the length of the hit list.
java.util.Map<java.lang.String,java.lang.String>	getPepNovoPtmMap() Returns the PepNovo to utilities PTM map.
java.lang.Boolean	isCorrectPrecursorMass() Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).
java.lang.Boolean	isEstimateCharge() Indicates whether the precursor charge shall be estimated for OMSSA.
void	setCorrectPrecursorMass(java.lang.Boolean correctPrecursorMass) Sets whether the precursor mass shall be corrected (TagDB setting).
void	setDiscardLowQualitySpectra(java.lang.Boolean discardLowQualitySpectra) Sets whether low quality spectra shall be discarded.
void	setEstimateCharge(java.lang.Boolean estimateCharge) Sets whether the precursor charge shall be estimated for OMSSA.
void	setFragmentationModel(java.lang.String fragmentationModel) Sets the name of the fragmentation model.
void	setGenerateQuery(java.lang.Boolean generateQuery) Sets a boolean indicating whether a blast query shall be generated.
void	setHitListLength(java.lang.Integer hitListLength) Sets the length of the hit list.
void	setPepNovoPtmMap(java.util.Map<java.lang.String,java.lang.String> pepNovoPtmMap) Set the PepNovo to utilities PTM map.
java.lang.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

PepnovoParameters

public PepnovoParameters()

Constructor.

Method Detail

getHitListLength

public java.lang.Integer getHitListLength()

Returns the length of the hit list.

Returns:

the length of the hit list

setHitListLength

public void setHitListLength(java.lang.Integer hitListLength)

Sets the length of the hit list.

Parameters:

hitListLength - the length of the hit list

isEstimateCharge

public java.lang.Boolean isEstimateCharge()

Indicates whether the precursor charge shall be estimated for OMSSA.

Returns:

a boolean indicating whether the precursor charge shall be estimated for OMSSA

setEstimateCharge

public void setEstimateCharge(java.lang.Boolean estimateCharge)

Sets whether the precursor charge shall be estimated for OMSSA.

Parameters:

estimateCharge - a boolean indicating whether the precursor charge shall be estimated for OMSSA

isCorrectPrecursorMass

public java.lang.Boolean isCorrectPrecursorMass()

Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).

Returns:

a boolean indicating whether the precursor mass shall be corrected (TagDB setting)

setCorrectPrecursorMass

public void setCorrectPrecursorMass(java.lang.Boolean correctPrecursorMass)

Sets whether the precursor mass shall be corrected (TagDB setting).

Parameters:

correctPrecursorMass - a boolean indicating whether the precursor mass shall be corrected (TagDB setting)

getDiscardLowQualitySpectra

public java.lang.Boolean getDiscardLowQualitySpectra()

Returns a boolean indicating whether low quality spectra shall be discarded.

Returns:

a boolean indicating whether low quality spectra shall be discarded

setDiscardLowQualitySpectra

public void setDiscardLowQualitySpectra(java.lang.Boolean discardLowQualitySpectra)

Sets whether low quality spectra shall be discarded.

Parameters:

discardLowQualitySpectra - a boolean indicating whether low quality spectra shall be discarded

getFragmentationModel

public java.lang.String getFragmentationModel()

Returns the name of the fragmentation model.

Returns:

the name of the fragmentation model

setFragmentationModel

public void setFragmentationModel(java.lang.String fragmentationModel)

Sets the name of the fragmentation model.

Parameters:

fragmentationModel - the name of the fragmentation model

generateQuery

public java.lang.Boolean generateQuery()

Returns a boolean indicating whether a blast query shall be generated.

Returns:

a boolean indicating whether a blast query shall be generated

setGenerateQuery

public void setGenerateQuery(java.lang.Boolean generateQuery)

Sets a boolean indicating whether a blast query shall be generated.

Parameters:

generateQuery - a boolean indicating whether a blast query shall be generated

getPepNovoPtmMap

public java.util.Map<java.lang.String,java.lang.String> getPepNovoPtmMap()

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

Returns:

the PepNovo to utilities PTM map, null if not set

setPepNovoPtmMap

public void setPepNovoPtmMap(java.util.Map<java.lang.String,java.lang.String> pepNovoPtmMap)

Set the PepNovo to utilities PTM map.

Parameters:

pepNovoPtmMap - the pepNovoPtmMap to set

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 java.lang.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