public class IdentificationParameters extends Object implements Serializable
Constructor and Description |
---|
IdentificationParameters() |
Modifier and Type | Method and Description |
---|---|
AnnotationSettings |
getAnnotationPreferences()
Returns the annotation preferences 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.
|
static IdentificationParameters |
getDefaultIdentificationParameters()
Creates blank parameters.
|
static IdentificationParameters |
getDefaultIdentificationParameters(SearchParameters searchParameters)
Returns default identification parameters based on given search
parameters.
|
GenePreferences |
getGenePreferences()
Returns the gene preferences.
|
IdMatchValidationPreferences |
getIdValidationPreferences()
Returns the identification matches validation preferences.
|
PeptideAssumptionFilter |
getPeptideAssumptionFilter()
Returns the filter used when importing PSMs.
|
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.
|
ProteinInferencePreferences |
getProteinInferencePreferences()
Returns the protein inference preferences.
|
PsmScoringPreferences |
getPsmScoringPreferences()
Returns the scoring preferences used when scoring PSMs.
|
PTMScoringPreferences |
getPtmScoringPreferences()
Returns the PTM localization scoring preferences.
|
SearchParameters |
getSearchParameters()
Returns the parameters used for the spectrum matching.
|
SequenceMatchingPreferences |
getSequenceMatchingPreferences()
Returns the sequence matching preferences.
|
void |
setAnnotationPreferences(AnnotationSettings annotationPreferences)
Sets the annotation preferences used for identification.
|
void |
setGenePreferences(GenePreferences genePreferences)
Sets the gene preferences.
|
void |
setIdFilter(PeptideAssumptionFilter peptideAssumptionFilter)
Sets the filter used when importing PSMs.
|
void |
setIdValidationPreferences(IdMatchValidationPreferences idValidationPreferences)
Sets the identification matches validation preferences.
|
void |
setParametersFromSearch(SearchParameters searchParameters)
Sets identification parameters based on given search parameters.
|
void |
setProteinInferencePreferences(ProteinInferencePreferences proteinInferencePreferences)
Sets the protein inference preferences.
|
void |
setPsmScoringPreferences(PsmScoringPreferences psmScoringPreferences)
Sets the scoring preferences used when scoring PSMs.
|
void |
setPtmScoringPreferences(PTMScoringPreferences ptmScoringPreferences)
Sets the PTM localization scoring preferences.
|
void |
setSearchParameters(SearchParameters searchParameters)
Sets the parameters used for the spectrum matching.
|
void |
setSequenceMatchingPreferences(SequenceMatchingPreferences sequenceMatchingPreferences)
Sets the sequence matching preferences.
|
public 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 setAnnotationPreferences(AnnotationSettings annotationPreferences)
annotationPreferences
- 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 static IdentificationParameters getDefaultIdentificationParameters()
public static IdentificationParameters getDefaultIdentificationParameters(SearchParameters searchParameters)
searchParameters
- the parameters used for the searchpublic void setParametersFromSearch(SearchParameters searchParameters)
searchParameters
- the parameters used for the searchCopyright © 2015. All rights reserved.