public class IdentificationParameters extends Object implements Serializable, MarshallableParameter
MarshallableParameter.Type
Constructor and Description |
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IdentificationParameters()
Creates empty identification parameters.
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IdentificationParameters(SearchParameters searchParameters)
Creates default identification parameters from the given search
parameters.
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IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationSettings annotationSettings,
SequenceMatchingPreferences sequenceMatchingPreferences,
GenePreferences genePreferences,
PsmScoringPreferences psmScoringPreferences,
PeptideAssumptionFilter peptideAssumptionFilter,
PTMScoringPreferences ptmScoringPreferences,
ProteinInferencePreferences proteinInferencePreferences,
IdMatchValidationPreferences idValidationPreferences,
FractionSettings fractionSettings)
Constructor.
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Modifier and Type | Method and Description |
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boolean |
equals(IdentificationParameters otherIdentificationParameters)
Returns true if the identification parameter objects have identical
settings.
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boolean |
equalsExceptValidationPreferences(IdentificationParameters otherIdentificationParameters)
Returns true if the identification parameter objects have identical
settings except for the validation preferences.
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AnnotationSettings |
getAnnotationPreferences()
Returns the annotation preferences used for identification.
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static double |
getDaTolerance(double ppmTolerance,
double refMass)
Returns the absolute tolerance in Dalton corresponding to the relative
tolerance in ppm at the given reference mass.
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Boolean |
getDefaultDescription()
Indicates whether the description is automatically generated.
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String |
getDescription()
Returns the description of the parameters.
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FractionSettings |
getFractionSettings()
Returns the fraction settings.
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GenePreferences |
getGenePreferences()
Returns the gene preferences.
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static IdentificationParameters |
getIdentificationParameters(File identificationParametersFile)
Loads the identification parameters from a file.
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IdMatchValidationPreferences |
getIdValidationPreferences()
Returns the identification matches validation preferences.
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String |
getName()
Returns the name of the parameters.
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PeptideAssumptionFilter |
getPeptideAssumptionFilter()
Returns the filter used when importing PSMs.
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static double |
getPpmTolerance(double daltonTolerance,
double refMass)
Returns the relative tolerance in ppm corresponding to the absolute
tolerance in Dalton at the given reference mass.
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ProteinInferencePreferences |
getProteinInferencePreferences()
Returns the protein inference preferences.
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PsmScoringPreferences |
getPsmScoringPreferences()
Returns the scoring preferences used when scoring PSMs.
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PTMScoringPreferences |
getPtmScoringPreferences()
Returns the PTM localization scoring preferences.
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SearchParameters |
getSearchParameters()
Returns the parameters used for the spectrum matching.
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SequenceMatchingPreferences |
getSequenceMatchingPreferences()
Returns the sequence matching preferences.
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MarshallableParameter.Type |
getType()
Returns the type of marshalled parameter from an unmarshalled object.
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static void |
saveIdentificationParameters(IdentificationParameters identificationParameters,
File identificationParametersFile)
Saves the identification parameters to a file.
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void |
setAnnotationSettings(AnnotationSettings annotationSettings)
Sets the annotation preferences used for identification.
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void |
setDescription(String description,
boolean automaticallyGenerated)
Sets the description of the parameters.
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void |
setFractionSettings(FractionSettings fractionSettings)
Sets the fraction settings.
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void |
setGenePreferences(GenePreferences genePreferences)
Sets the gene preferences.
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void |
setIdFilter(PeptideAssumptionFilter peptideAssumptionFilter)
Sets the filter used when importing PSMs.
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void |
setIdValidationPreferences(IdMatchValidationPreferences idValidationPreferences)
Sets the identification matches validation preferences.
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void |
setName(String name)
Sets the name of the parameters.
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void |
setParametersFromSearch(SearchParameters searchParameters)
Sets identification parameters based on given search parameters.
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void |
setProteinInferencePreferences(ProteinInferencePreferences proteinInferencePreferences)
Sets the protein inference preferences.
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void |
setPsmScoringPreferences(PsmScoringPreferences psmScoringPreferences)
Sets the scoring preferences used when scoring PSMs.
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void |
setPtmScoringPreferences(PTMScoringPreferences ptmScoringPreferences)
Sets the PTM localization scoring preferences.
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void |
setSearchParameters(SearchParameters searchParameters)
Sets the parameters used for the spectrum matching.
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void |
setSequenceMatchingPreferences(SequenceMatchingPreferences sequenceMatchingPreferences)
Sets the sequence matching preferences.
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void |
setType()
Sets the parameters type.
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public IdentificationParameters()
public IdentificationParameters(SearchParameters searchParameters)
searchParameters
- the search parameterspublic IdentificationParameters(String name, String description, SearchParameters searchParameters, AnnotationSettings annotationSettings, SequenceMatchingPreferences sequenceMatchingPreferences, GenePreferences genePreferences, PsmScoringPreferences psmScoringPreferences, PeptideAssumptionFilter peptideAssumptionFilter, PTMScoringPreferences ptmScoringPreferences, ProteinInferencePreferences proteinInferencePreferences, IdMatchValidationPreferences idValidationPreferences, FractionSettings fractionSettings)
name
- the name of the parametersdescription
- the descriptionsearchParameters
- the search parametersannotationSettings
- the annotation preferencessequenceMatchingPreferences
- the sequence matching preferencesgenePreferences
- the gene preferencespsmScoringPreferences
- the PSM scoring preferencespeptideAssumptionFilter
- the peptide assumption filtersptmScoringPreferences
- the PTM localization scoring preferencesproteinInferencePreferences
- the protein inference preferencesidValidationPreferences
- the matches validation preferencesfractionSettings
- the fraction settingspublic SearchParameters getSearchParameters()
public void setSearchParameters(SearchParameters searchParameters)
searchParameters
- the parameters used for the spectrum matchingpublic static double getPpmTolerance(double daltonTolerance, double refMass)
daltonTolerance
- the absolute tolerance in DaltonrefMass
- the reference mass in Daltonpublic static double getDaTolerance(double ppmTolerance, double refMass)
ppmTolerance
- the absolute tolerance in ppmrefMass
- the reference mass in Daltonpublic AnnotationSettings getAnnotationPreferences()
public void setAnnotationSettings(AnnotationSettings annotationSettings)
annotationSettings
- the annotation preferences used for
identificationpublic PeptideAssumptionFilter getPeptideAssumptionFilter()
public void setIdFilter(PeptideAssumptionFilter peptideAssumptionFilter)
peptideAssumptionFilter
- the filter used when importing PSMspublic PsmScoringPreferences getPsmScoringPreferences()
public void setPsmScoringPreferences(PsmScoringPreferences psmScoringPreferences)
psmScoringPreferences
- the scoring preferences used when scoring
PSMspublic PTMScoringPreferences getPtmScoringPreferences()
public void setPtmScoringPreferences(PTMScoringPreferences ptmScoringPreferences)
ptmScoringPreferences
- the PTM localization scoring preferencespublic SequenceMatchingPreferences getSequenceMatchingPreferences()
public void setSequenceMatchingPreferences(SequenceMatchingPreferences sequenceMatchingPreferences)
sequenceMatchingPreferences
- the sequence matching preferencespublic IdMatchValidationPreferences getIdValidationPreferences()
public void setIdValidationPreferences(IdMatchValidationPreferences idValidationPreferences)
idValidationPreferences
- the identification matches validation
preferencespublic ProteinInferencePreferences getProteinInferencePreferences()
public void setProteinInferencePreferences(ProteinInferencePreferences proteinInferencePreferences)
proteinInferencePreferences
- the protein inference preferencespublic GenePreferences getGenePreferences()
public void setGenePreferences(GenePreferences genePreferences)
genePreferences
- the gene preferencespublic FractionSettings getFractionSettings()
public void setFractionSettings(FractionSettings fractionSettings)
fractionSettings
- the fraction settingspublic static IdentificationParameters getIdentificationParameters(File identificationParametersFile) throws IOException, ClassNotFoundException
identificationParametersFile
- the fileIOException
- if an IOException occursClassNotFoundException
- if a ClassNotFoundException occurspublic static void saveIdentificationParameters(IdentificationParameters identificationParameters, File identificationParametersFile) throws IOException
identificationParameters
- the identification parametersidentificationParametersFile
- the fileIOException
- if an IOException occurspublic String getName()
public void setName(String name)
name
- the name of the parameterspublic String getDescription()
public Boolean getDefaultDescription()
public void setDescription(String description, boolean automaticallyGenerated)
description
- the description of the parametersautomaticallyGenerated
- boolean indicating whether the description
is automatically generatedpublic void setParametersFromSearch(SearchParameters searchParameters)
searchParameters
- the parameters used for the searchpublic void setType()
MarshallableParameter
setType
in interface MarshallableParameter
public MarshallableParameter.Type getType()
MarshallableParameter
getType
in interface MarshallableParameter
public boolean equals(IdentificationParameters otherIdentificationParameters)
otherIdentificationParameters
- the parameters to compare topublic boolean equalsExceptValidationPreferences(IdentificationParameters otherIdentificationParameters)
otherIdentificationParameters
- the parameters to compare toCopyright © 2016. All rights reserved.