public class IdentificationParameters extends ExperimentObject implements MarshallableParameter
MarshallableParameter.Type
Modifier and Type | Field and Description |
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static String |
CURRENT_VERSION
Currently supported version number.
|
String |
version
Version number.
|
NO_KEY
Constructor and Description |
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IdentificationParameters()
Creates empty identification parameters.
|
IdentificationParameters(SearchParameters searchParameters)
Creates default identification parameters from the given search
parameters.
|
IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationParameters annotationParameters,
SequenceMatchingParameters sequenceMatchingParameters,
PeptideVariantsParameters peptideVariantsParameters,
GeneParameters geneParameters,
PsmScoringParameters psmScoringParameters,
PeptideAssumptionFilter peptideAssumptionFilter,
ModificationLocalizationParameters ModificationLocalizationParameters,
ProteinInferenceParameters proteinInferenceParameters,
IdMatchValidationParameters idValidationParameters,
FractionParameters fractionParameters,
FastaParameters fastaParameters)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
boolean |
equals(IdentificationParameters otherIdentificationParameters)
Returns true if the identification parameter objects have identical
settings.
|
AnnotationParameters |
getAnnotationParameters()
Returns the annotation parameters used for identification.
|
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.
|
boolean |
getDefaultDescription()
Indicates whether the description is automatically generated.
|
String |
getDescription()
Returns the description of the parameters.
|
FastaParameters |
getFastaParameters()
Returns the FASTA processing parameters.
|
FractionParameters |
getFractionParameters()
Returns the fraction parameters.
|
GeneParameters |
getGeneParameters()
Returns the gene parameters.
|
static IdentificationParameters |
getIdentificationParameters(File identificationParametersFile)
Loads the identification parameters from a file.
|
IdMatchValidationParameters |
getIdValidationParameters()
Returns the identification matches validation parameters.
|
ModificationLocalizationParameters |
getModificationLocalizationParameters()
Returns the modification localization scoring parameters.
|
String |
getName()
Returns the name of the parameters.
|
PeptideAssumptionFilter |
getPeptideAssumptionFilter()
Returns the filter used when importing PSMs.
|
PeptideVariantsParameters |
getPeptideVariantsParameters()
Returns the peptide variant parameters.
|
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.
|
ProteinInferenceParameters |
getProteinInferenceParameters()
Returns the protein inference parameters.
|
PsmScoringParameters |
getPsmScoringParameters()
Returns the scoring parameters used when scoring PSMs.
|
SearchParameters |
getSearchParameters()
Returns the parameters used for the spectrum matching.
|
SequenceMatchingParameters |
getSequenceMatchingParameters()
Returns the sequence matching parameters.
|
MarshallableParameter.Type |
getType()
Returns the type of marshalled parameter from an unmarshalled object.
|
static void |
saveIdentificationParameters(IdentificationParameters identificationParameters,
File identificationParametersFile)
Saves the identification parameters to a file.
|
void |
setAnnotationParameters(AnnotationParameters annotationParameters)
Sets the annotation parameters used for identification.
|
void |
setDescription(String description,
boolean automaticallyGenerated)
Sets the description of the parameters.
|
void |
setFastaParameters(FastaParameters fastaParameters)
Sets the ASTA processing parameters.
|
void |
setFractionParameters(FractionParameters fractionParameters)
Sets the fraction parameters.
|
void |
setGeneParameters(GeneParameters geneParameters)
Sets the gene parameters.
|
void |
setIdValidationParameters(IdMatchValidationParameters idValidationParameters)
Sets the identification matches validation parameters.
|
void |
setModificationLocalizationParameters(ModificationLocalizationParameters modificationLocalizationParameters)
Sets the modification localization parameters.
|
void |
setName(String name)
Sets the name of the parameters.
|
void |
setParametersFromSearch(SearchParameters searchParameters)
Sets identification parameters based on given search parameters.
|
void |
setPeptideAssumptionFilter(PeptideAssumptionFilter peptideAssumptionFilter)
Sets the filter used when importing PSMs.
|
void |
setPeptideVariantsParameters(PeptideVariantsParameters peptideVariantsParameters)
Sets the peptide variant parameters.
|
void |
setProteinInferenceParameters(ProteinInferenceParameters proteinInferenceParameters)
Sets the protein inference parameters.
|
void |
setPsmScoringParameters(PsmScoringParameters psmScoringParameters)
Sets the scoring preferences used when scoring PSMs.
|
void |
setSearchParameters(SearchParameters searchParameters)
Sets the parameters used for the spectrum matching.
|
void |
setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)
Sets the sequence matching preferences.
|
void |
setType()
Sets the parameters type.
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static boolean |
supportedVersion(File identificationParametersFile)
Returns a boolean indicating whether the version of the parameters file
is supported.
|
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final String CURRENT_VERSION
public final String version
public IdentificationParameters()
public IdentificationParameters(SearchParameters searchParameters)
searchParameters
- the search parameterspublic IdentificationParameters(String name, String description, SearchParameters searchParameters, AnnotationParameters annotationParameters, SequenceMatchingParameters sequenceMatchingParameters, PeptideVariantsParameters peptideVariantsParameters, GeneParameters geneParameters, PsmScoringParameters psmScoringParameters, PeptideAssumptionFilter peptideAssumptionFilter, ModificationLocalizationParameters ModificationLocalizationParameters, ProteinInferenceParameters proteinInferenceParameters, IdMatchValidationParameters idValidationParameters, FractionParameters fractionParameters, FastaParameters fastaParameters)
name
- the name of the parametersdescription
- the descriptionsearchParameters
- the search parametersannotationParameters
- the annotation parameterssequenceMatchingParameters
- the sequence matching parameterspeptideVariantsParameters
- the peptide variant parametersgeneParameters
- the gene parameterspsmScoringParameters
- the PSM scoring parameterspeptideAssumptionFilter
- the peptide assumption filtersModificationLocalizationParameters
- the PTM localization scoring
parametersproteinInferenceParameters
- the protein inference parametersidValidationParameters
- the matches validation parametersfractionParameters
- the fraction parametersfastaParameters
- the FASTA parameterspublic 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 AnnotationParameters getAnnotationParameters()
public void setAnnotationParameters(AnnotationParameters annotationParameters)
annotationParameters
- the annotation parameters used for
identificationpublic PeptideAssumptionFilter getPeptideAssumptionFilter()
public void setPeptideAssumptionFilter(PeptideAssumptionFilter peptideAssumptionFilter)
peptideAssumptionFilter
- the filter used when importing PSMspublic PsmScoringParameters getPsmScoringParameters()
public void setPsmScoringParameters(PsmScoringParameters psmScoringParameters)
psmScoringParameters
- the scoring preferences used when scoring
PSMspublic ModificationLocalizationParameters getModificationLocalizationParameters()
public void setModificationLocalizationParameters(ModificationLocalizationParameters modificationLocalizationParameters)
modificationLocalizationParameters
- the modification localization
parameterspublic SequenceMatchingParameters getSequenceMatchingParameters()
public void setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)
sequenceMatchingParameters
- the sequence matching preferencespublic PeptideVariantsParameters getPeptideVariantsParameters()
public void setPeptideVariantsParameters(PeptideVariantsParameters peptideVariantsParameters)
peptideVariantsParameters
- the peptide variant parameterspublic IdMatchValidationParameters getIdValidationParameters()
public void setIdValidationParameters(IdMatchValidationParameters idValidationParameters)
idValidationParameters
- the identification matches validation
parameterspublic ProteinInferenceParameters getProteinInferenceParameters()
public void setProteinInferenceParameters(ProteinInferenceParameters proteinInferenceParameters)
proteinInferenceParameters
- the protein inference parameterspublic GeneParameters getGeneParameters()
public void setGeneParameters(GeneParameters geneParameters)
geneParameters
- the gene parameterspublic FractionParameters getFractionParameters()
public void setFractionParameters(FractionParameters fractionParameters)
fractionParameters
- the fraction parameterspublic FastaParameters getFastaParameters()
public void setFastaParameters(FastaParameters fastaParameters)
fastaParameters
- the FASTA processing parameterspublic static IdentificationParameters getIdentificationParameters(File identificationParametersFile) throws IOException
identificationParametersFile
- the fileIOException
- if an error occurs while reading the filepublic static boolean supportedVersion(File identificationParametersFile) throws IOException
identificationParametersFile
- the parameters fileIOException
- if an error occurs while reading the filepublic static void saveIdentificationParameters(IdentificationParameters identificationParameters, File identificationParametersFile) throws IOException
identificationParameters
- the identification parametersidentificationParametersFile
- the fileIOException
- if an error occurred while writing the filepublic 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 toCopyright © 2021. All rights reserved.