com.compomics.util.experiment.identification

Class SearchParameters

java.lang.Object

com.compomics.util.experiment.identification.SearchParameters

All Implemented Interfaces:

java.io.Serializable

public class SearchParameters
extends java.lang.Object
implements java.io.Serializable

This class groups the parameters used for identification.

Author:

Marc Vaudel

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SearchParameters.MassAccuracyType Possible mass accuracy types.
static class	SearchParameters.PrecursorAccuracyType Deprecated. use MassAccuracyType

Constructor Summary

Constructors

Constructor and Description
SearchParameters() Constructor.

Method Summary

Methods

Modifier and Type	Method and Description
void	correctPrecursorMass(java.lang.Boolean correctPrecursorMass) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
boolean	equals(SearchParameters otherSearchParameters) Returns true of the search parameter objects have identical settings.
java.lang.Boolean	generateQuery() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
java.util.Set<java.lang.Integer>	getAlgorithms() Returns the algorithms for which specific parameters are stored.
java.util.HashMap<java.lang.Integer,IdentificationAlgorithmParameter>	getAlgorithmSpecificParameters() Returns the algorithm specific parameters in a map: algorithm as indexed in the Advocate class -> parameters.
java.lang.Boolean	getDiscardLowQualitySpectra() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
Enzyme	getEnzyme() Returns the enzyme used for digestion.
java.io.File	getFastaFile() Returns the sequence database file used for identification.
static java.lang.String[]	getForwardIons() Returns the list of forward ions.
java.util.HashMap<java.lang.String,no.uib.jsparklines.data.XYDataPoint>	getFractionMolecularWeightRanges() Returns the user provided molecular weight ranges for the fractions.
java.util.HashMap<java.lang.String,java.lang.Double>	getFractionMolecularWeights() Deprecated. use getFractionMolecularWeightRanges instead
SearchParameters.MassAccuracyType	getFragmentAccuracyType() Returns the fragment accuracy type.
java.lang.String	getFragmentationModel() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
java.lang.Double	getFragmentIonAccuracy() Returns the MS2 ion m/z tolerance.
java.lang.Integer	getHitListLength() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
java.lang.Integer	getHitListLengthDeNovo() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
IdentificationAlgorithmParameter	getIdentificationAlgorithmParameter(int algorithmID) Returns the algorithm specific parameters, null if not found.
static SearchParameters	getIdentificationParameters(java.io.File file) Loads the identification parameters from a serialized file.
static java.lang.String[]	getIons() Getter for the list of ion symbols used.
java.lang.Integer	getIonSearched1() Getter for the first kind of ion searched.
java.lang.Integer	getIonSearched2() Getter for the second kind of ion searched.
Charge	getMaxChargeSearched() Returns the maximal charge searched.
java.lang.Double	getMaxEValue() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
java.lang.Integer	getMaxPeptideLength() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
Charge	getMinChargeSearched() Returns the minimal charge searched.
Charge	getMinimalChargeForMultipleChargedFragments() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
java.lang.Integer	getMinPeptideLength() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
ModificationProfile	getModificationProfile() Returns the modification profile of the project.
java.lang.Integer	getnMissedCleavages() Returns the allowed number of missed cleavages.
java.io.File	getParametersFile() Returns the parameters file loaded.
java.util.Map<java.lang.String,java.lang.String>	getPepNovoPtmMap() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
java.lang.Double	getPrecursorAccuracy() Returns the precursor tolerance.
java.lang.Double	getPrecursorAccuracyDalton() Returns the precursor tolerance in Dalton (for de novo searches).
SearchParameters.MassAccuracyType	getPrecursorAccuracyType() Returns the precursor accuracy type.
static java.lang.String[]	getRewindIons() Returns the list of rewind ions.
java.lang.Boolean	isCorrectPrecursorMass() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
java.lang.Boolean	isEstimateCharge() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
java.lang.Boolean	isPrecursorAccuracyTypePpm() Returns true if the current precursor accuracy type is ppm.
java.lang.Boolean	isRemovePrecursor() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
java.lang.Boolean	isScalePrecursor() Deprecated. use the appropriated IdentificationAlgorithmParameters instead
static void	saveIdentificationParameters(SearchParameters identificationParameters, java.io.File file) Saves the identification parameters to a serialized file.
void	saveIdentificationParametersAsTextFile(java.io.File file) Saves the identification parameters as a human readable text file.
void	setDiscardLowQualitySpectra(java.lang.Boolean discardLowQualitySpectra) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setEnzyme(Enzyme enzyme) Sets the enzyme used for digestion.
void	setEstimateCharge(java.lang.Boolean estimateCharge) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setFastaFile(java.io.File fastaFile) Sets the sequence database file used for identification.
void	setFractionMolecularWeightRanges(java.util.HashMap<java.lang.String,no.uib.jsparklines.data.XYDataPoint> fractionMolecularWeightRanges) Set the user provided molecular weight ranges for the fractions.
void	setFractionMolecularWeights(java.util.HashMap<java.lang.String,java.lang.Double> fractionMolecularWeights) Deprecated. use setFractionMolecularWeightRanges instead
void	setFragmentAccuracyType(SearchParameters.MassAccuracyType fragmentAccuracyType) Sets the fragment accuracy type.
void	setFragmentationModel(java.lang.String fragmentationModel) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setFragmentIonAccuracy(java.lang.Double fragmentIonMZTolerance) Sets the fragment ion m/z tolerance.
void	setGenerateQuery(java.lang.Boolean generateQuery) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setHitListLength(java.lang.Integer hitListLength) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setHitListLengthDeNovo(java.lang.Integer hitListLengthDeNovo) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setIdentificationAlgorithmParameter(int algorithmID, IdentificationAlgorithmParameter identificationAlgorithmParameter) Adds identification algorithm specific paramters
void	setIonSearched1(java.lang.String ionSearched1) Setter for the first kind of ion searched, indexed by its single letter code, for example "a".
void	setIonSearched2(java.lang.String ionSearched2) Setter for the second kind of ion searched, indexed by its single letter code, for example "a".
void	setMaxChargeSearched(Charge maxChargeSearched) Sets the maximal charge searched.
void	setMaxEValue(java.lang.Double maxEValue) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setMaxPeptideLength(java.lang.Integer maxPeptideLength) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setMinChargeSearched(Charge minChargeSearched) Sets the minimal charge searched.
void	setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setMinPeptideLength(java.lang.Integer minPeptideLength) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setModificationProfile(ModificationProfile modificationProfile) Sets the modification profile of the project.
void	setnMissedCleavages(java.lang.Integer nMissedCleavages) Sets the allowed number of missed cleavages.
void	setParametersFile(java.io.File parametersFile) Sets the parameter file loaded.
void	setPepNovoPtmMap(java.util.Map<java.lang.String,java.lang.String> pepNovoPtmMap) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setPrecursorAccuracy(java.lang.Double precursorTolerance) Sets the precursor tolerance.
void	setPrecursorAccuracyDalton(java.lang.Double precursorToleranceDalton) Sets the precursor tolerance in Dalton (for de novo searches).
void	setPrecursorAccuracyType(SearchParameters.MassAccuracyType precursorAccuracyType) Sets the precursor accuracy type.
void	setRemovePrecursor(java.lang.Boolean removePrecursor) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
void	setScalePrecursor(java.lang.Boolean scalePrecursor) Deprecated. use the appropriated IdentificationAlgorithmParameters instead
java.lang.String	toString()
java.lang.String	toString(boolean html) Returns the search parameters as a string.

Methods inherited from class java.lang.Object

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

Constructor Detail

SearchParameters

public SearchParameters()

Constructor.

Method Detail

getModificationProfile

public ModificationProfile getModificationProfile()

Returns the modification profile of the project.

Returns:

the modification profile of the project

setModificationProfile

public void setModificationProfile(ModificationProfile modificationProfile)

Sets the modification profile of the project.

Parameters:

modificationProfile - The modification profile

getFragmentIonAccuracy

public java.lang.Double getFragmentIonAccuracy()

Returns the MS2 ion m/z tolerance.

Returns:

the MS2 ion m/z tolerance

setFragmentIonAccuracy

public void setFragmentIonAccuracy(java.lang.Double fragmentIonMZTolerance)

Sets the fragment ion m/z tolerance.

Parameters:

fragmentIonMZTolerance -

getEnzyme

public Enzyme getEnzyme()

Returns the enzyme used for digestion.

Returns:

the enzyme used for digestion

setEnzyme

public void setEnzyme(Enzyme enzyme)

Sets the enzyme used for digestion.

Parameters:

enzyme - the enzyme used for digestion

getParametersFile

public java.io.File getParametersFile()

Returns the parameters file loaded.

Returns:

the parameters file loaded

setParametersFile

public void setParametersFile(java.io.File parametersFile)

Sets the parameter file loaded.

Parameters:

parametersFile - the parameter file loaded

getFastaFile

public java.io.File getFastaFile()

Returns the sequence database file used for identification.

Returns:

the sequence database file used for identification

setFastaFile

public void setFastaFile(java.io.File fastaFile)

Sets the sequence database file used for identification.

Parameters:

fastaFile - the sequence database file used for identification

getnMissedCleavages

public java.lang.Integer getnMissedCleavages()

Returns the allowed number of missed cleavages.

Returns:

the allowed number of missed cleavages

setnMissedCleavages

public void setnMissedCleavages(java.lang.Integer nMissedCleavages)

Sets the allowed number of missed cleavages.

Parameters:

nMissedCleavages - the allowed number of missed cleavages

getIonSearched1

public java.lang.Integer getIonSearched1()

Getter for the first kind of ion searched.

Returns:

the first kind of ion searched as an integer (see static fields of the PeptideFragmentIon class)

setIonSearched1

public void setIonSearched1(java.lang.String ionSearched1)

Setter for the first kind of ion searched, indexed by its single letter code, for example "a".

Parameters:

ionSearched1 - the first kind of ion searched

getIonSearched2

public java.lang.Integer getIonSearched2()

Getter for the second kind of ion searched.

Returns:

the second kind of ion searched as an integer (see static fields of the PeptideFragmentIon class)

setIonSearched2

public void setIonSearched2(java.lang.String ionSearched2)

Setter for the second kind of ion searched, indexed by its single letter code, for example "a".

Parameters:

ionSearched2 - the second kind of ion searched

getIons

public static java.lang.String[] getIons()

Getter for the list of ion symbols used.

Returns:

the list of ion symbols used

getForwardIons

public static java.lang.String[] getForwardIons()

Returns the list of forward ions.

Returns:

the forwardIons

getRewindIons

public static java.lang.String[] getRewindIons()

Returns the list of rewind ions.

Returns:

the rewindIons

getPrecursorAccuracy

public java.lang.Double getPrecursorAccuracy()

Returns the precursor tolerance.

Returns:

the precursor tolerance

setPrecursorAccuracy

public void setPrecursorAccuracy(java.lang.Double precursorTolerance)

Sets the precursor tolerance.

Parameters:

precursorTolerance - the precursor tolerance

getPrecursorAccuracyDalton

public java.lang.Double getPrecursorAccuracyDalton()

Returns the precursor tolerance in Dalton (for de novo searches).

Returns:

the precursor tolerance

setPrecursorAccuracyDalton

public void setPrecursorAccuracyDalton(java.lang.Double precursorToleranceDalton)

Sets the precursor tolerance in Dalton (for de novo searches).

Parameters:

precursorToleranceDalton - the precursor tolerance

getPrecursorAccuracyType

public SearchParameters.MassAccuracyType getPrecursorAccuracyType()

Returns the precursor accuracy type.

Returns:

the precursor accuracy type

setPrecursorAccuracyType

public void setPrecursorAccuracyType(SearchParameters.MassAccuracyType precursorAccuracyType)

Sets the precursor accuracy type.

Parameters:

precursorAccuracyType - the precursor accuracy type

getFragmentAccuracyType

public SearchParameters.MassAccuracyType getFragmentAccuracyType()

Returns the fragment accuracy type.

Returns:

the fragment accuracy type

setFragmentAccuracyType

public void setFragmentAccuracyType(SearchParameters.MassAccuracyType fragmentAccuracyType)

Sets the fragment accuracy type.

Parameters:

fragmentAccuracyType - the fragment accuracy type

isPrecursorAccuracyTypePpm

public java.lang.Boolean isPrecursorAccuracyTypePpm()

Returns true if the current precursor accuracy type is ppm.

Returns:

true if the current precursor accuracy type is ppm

getFractionMolecularWeights

public java.util.HashMap<java.lang.String,java.lang.Double> getFractionMolecularWeights()

Deprecated. use getFractionMolecularWeightRanges instead

Returns the user provided molecular weights of the fractions. The key is the fraction file path.

Returns:

the user provided molecular weights of the fractions

setFractionMolecularWeights

public void setFractionMolecularWeights(java.util.HashMap<java.lang.String,java.lang.Double> fractionMolecularWeights)

Deprecated. use setFractionMolecularWeightRanges instead

Set the user provided molecular weights of the fractions. The key is the fraction file path.

Parameters:

fractionMolecularWeights - the fractionMolecularWeights to set

getFractionMolecularWeightRanges

public java.util.HashMap<java.lang.String,no.uib.jsparklines.data.XYDataPoint> getFractionMolecularWeightRanges()

Returns the user provided molecular weight ranges for the fractions. The key is the fraction file path.

Returns:

the user provided molecular weight ranges of the fractions

setFractionMolecularWeightRanges

public void setFractionMolecularWeightRanges(java.util.HashMap<java.lang.String,no.uib.jsparklines.data.XYDataPoint> fractionMolecularWeightRanges)

Set the user provided molecular weight ranges for the fractions. The key is the fraction file path.

Parameters:

fractionMolecularWeightRanges - the fractionMolecularWeightRanges to set

getMaxChargeSearched

public Charge getMaxChargeSearched()

Returns the maximal charge searched.

Returns:

the maximal charge searched

setMaxChargeSearched

public void setMaxChargeSearched(Charge maxChargeSearched)

Sets the maximal charge searched.

Parameters:

maxChargeSearched - the maximal charge searched

getMinChargeSearched

public Charge getMinChargeSearched()

Returns the minimal charge searched.

Returns:

the minimal charge searched

setMinChargeSearched

public void setMinChargeSearched(Charge minChargeSearched)

Sets the minimal charge searched.

Parameters:

minChargeSearched - the minimal charge searched

getMaxEValue

public java.lang.Double getMaxEValue()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Returns the maximal e-value searched for.

Returns:

the maximal e-value searched for

setMaxEValue

public void setMaxEValue(java.lang.Double maxEValue)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets the maximal e-value searched for.

Parameters:

maxEValue - the maximal e-value searched for

getHitListLength

public java.lang.Integer getHitListLength()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Returns the length of the hit list for OMSSA.

Returns:

the length of the hit list for OMSSA

setHitListLength

public void setHitListLength(java.lang.Integer hitListLength)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets the length of the hit list for OMSSA.

Parameters:

hitListLength - the length of the hit list for OMSSA

getHitListLengthDeNovo

public java.lang.Integer getHitListLengthDeNovo()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Returns the length of the hit list for PepNovo+.

Returns:

the length of the hit list for OMSSA

setHitListLengthDeNovo

public void setHitListLengthDeNovo(java.lang.Integer hitListLengthDeNovo)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets the length of the hit list for PepNovo.

Parameters:

hitListLengthDeNovo - the length of the hit list for PepNovo

getMinimalChargeForMultipleChargedFragments

public Charge getMinimalChargeForMultipleChargedFragments()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Returns the minimal precursor charge to account for multiply charged fragments in OMSSA.

Returns:

the minimal precursor charge to account for multiply charged fragments in OMSSA

setMinimalChargeForMultipleChargedFragments

public void setMinimalChargeForMultipleChargedFragments(Charge minimalChargeForMultipleChargedFragments)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets the minimal precursor charge to account for multiply charged fragments in OMSSA.

Parameters:

minimalChargeForMultipleChargedFragments - the minimal precursor charge to account for multiply charged fragments in OMSSA

getMaxPeptideLength

public java.lang.Integer getMaxPeptideLength()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Returns the maximal peptide length allowed.

Returns:

the maximal peptide length allowed

setMaxPeptideLength

public void setMaxPeptideLength(java.lang.Integer maxPeptideLength)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets the maximal peptide length allowed.

Parameters:

maxPeptideLength - the maximal peptide length allowed

getMinPeptideLength

public java.lang.Integer getMinPeptideLength()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets the minimal peptide length allowed.

Returns:

the minimal peptide length allowed

setMinPeptideLength

public void setMinPeptideLength(java.lang.Integer minPeptideLength)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets the minimal peptide length allowed.

Parameters:

minPeptideLength - the minimal peptide length allowed

isEstimateCharge

public java.lang.Boolean isEstimateCharge()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

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)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets whether the precursor charge shall be estimated for OMSSA.

Parameters:

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

isRemovePrecursor

public java.lang.Boolean isRemovePrecursor()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Indicates whether the precursor shall be removed for OMSSA.

Returns:

a boolean indicating whether the precursor shall be removed for OMSSA

setRemovePrecursor

public void setRemovePrecursor(java.lang.Boolean removePrecursor)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets whether the precursor shall be removed for OMSSA

Parameters:

removePrecursor - a boolean indicating whether the precursor shall be removed for OMSSA

isScalePrecursor

public java.lang.Boolean isScalePrecursor()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Indicates whether the precursor shall be scaled for OMSSA.

Returns:

a boolean indicating whether the precursor shall be scaled for OMSSA

setScalePrecursor

public void setScalePrecursor(java.lang.Boolean scalePrecursor)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets whether the precursor shall be scaled for OMSSA.

Parameters:

scalePrecursor - a boolean indicating whether the precursor shall be scaled for OMSSA

getAlgorithmSpecificParameters

public java.util.HashMap<java.lang.Integer,IdentificationAlgorithmParameter> getAlgorithmSpecificParameters()

Returns the algorithm specific parameters in a map: algorithm as indexed in the Advocate class -> parameters. null if not set.

Returns:

the algorithm specific parameters in a map

getIdentificationAlgorithmParameter

public IdentificationAlgorithmParameter getIdentificationAlgorithmParameter(int algorithmID)

Returns the algorithm specific parameters, null if not found.

Parameters:

algorithmID - the index of the search engine as indexed in the Advocate class

Returns:

the algorithm specific parameters

setIdentificationAlgorithmParameter

public void setIdentificationAlgorithmParameter(int algorithmID,
                                       IdentificationAlgorithmParameter identificationAlgorithmParameter)

Adds identification algorithm specific paramters

Parameters:

algorithmID - the algorithm id as indexed in the Advocate class

identificationAlgorithmParameter - the specific parameters

getAlgorithms

public java.util.Set<java.lang.Integer> getAlgorithms()

Returns the algorithms for which specific parameters are stored. Warning: this does not mean that the algorithm was actually used.

Returns:

the algorithms for which specific parameters are stored in a set of indexes as listed in the Advocate class

getIdentificationParameters

public static SearchParameters getIdentificationParameters(java.io.File file)
                                                    throws java.io.FileNotFoundException,
                                                           java.io.IOException,
                                                           java.lang.ClassNotFoundException

Loads the identification parameters from a serialized file.

Parameters:

file - the file

Returns:

the modification file

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.ClassNotFoundException

saveIdentificationParameters

public static void saveIdentificationParameters(SearchParameters identificationParameters,
                                java.io.File file)
                                         throws java.io.FileNotFoundException,
                                                java.io.IOException,
                                                java.lang.ClassNotFoundException

Saves the identification parameters to a serialized file.

Parameters:

identificationParameters -

file - the file

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.ClassNotFoundException

saveIdentificationParametersAsTextFile

public void saveIdentificationParametersAsTextFile(java.io.File file)
                                            throws java.io.FileNotFoundException,
                                                   java.io.IOException,
                                                   java.lang.ClassNotFoundException

Saves the identification parameters as a human readable text file.

Parameters:

file - the file

Throws:

java.io.FileNotFoundException

java.io.IOException

java.lang.ClassNotFoundException

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

toString

public java.lang.String toString(boolean html)

Returns the search parameters as a string.

Parameters:

html - use HTML formatting

Returns:

the search parameters as a string

equals

public boolean equals(SearchParameters otherSearchParameters)

Returns true of the search parameter objects have identical settings.

Parameters:

otherSearchParameters - the parameters to compare to

Returns:

true of the search parameter objects have identical settings

isCorrectPrecursorMass

public java.lang.Boolean isCorrectPrecursorMass()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

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)

correctPrecursorMass

public void correctPrecursorMass(java.lang.Boolean correctPrecursorMass)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

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()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

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)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

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()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Returns the name of the fragmentation model.

Returns:

the name of the fragmentation model

setFragmentationModel

public void setFragmentationModel(java.lang.String fragmentationModel)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Sets the name of the fragmentation model.

Parameters:

fragmentationModel - the name of the fragmentation model

generateQuery

public java.lang.Boolean generateQuery()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

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)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

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()

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

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)

Deprecated. use the appropriated IdentificationAlgorithmParameters instead

Set the PepNovo to utilities PTM map

Parameters:

pepNovoPtmMap - the pepNovoPtmMap to set