Class ProteinInferenceParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
- All Implemented Interfaces:
Serializable
public class ProteinInferenceParameters extends ExperimentObject
Generic class grouping the protein inference preferences.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description ProteinInferenceParameters()
Empty default constructor -
Method Summary
Modifier and Type Method Description boolean
equals(ProteinInferenceParameters otherProteinInferencePreferences)
Returns true if the objects have identical settings.double
getConfidenceThreshold()
Returns the confidence below which a peptide is considered absent.String
getShortDescription()
Returns a short description of the parameters.boolean
getSimplifyGroups()
Returns a boolean indicating whether the protein groups should be simplified.boolean
getSimplifyGroupsConfidence()
Returns a boolean indicating whether the protein groups should be simplified based on the peptide confidence.boolean
getSimplifyGroupsEnzymaticity()
Returns a boolean indicating whether the protein groups should be simplified based on the peptide enzymaticity.boolean
getSimplifyGroupsEvidence()
Returns a boolean indicating whether the protein groups should be simplified based on the Uniprot evidence level.boolean
getSimplifyGroupsVariants()
Returns a boolean indicating whether the protein groups should be simplified based on the peptide variant matching.boolean
isModificationRefinement()
Returns whether the protein mapping should be refined based on terminal and pattern modifications.void
setConfidenceThreshold(double confidenceThreshold)
Sets the confidence below which a peptide is considered absent.void
setModificationRefinement(boolean modificationRefinement)
Sets whether the protein mapping should be refined based on terminal and pattern modifications.void
setSimplifyGroups(boolean simplifyProteinGroups)
Sets whether the protein groups should be simplified based on the PeptideShaker confidence.void
setSimplifyGroupsConfidence(boolean simplifyGroupsConfidence)
Sets whether the protein groups should be simplified based on the peptide confidence level.void
setSimplifyGroupsEnzymaticity(boolean simplifyGroupsEnzymaticity)
Sets whether the protein groups should be simplified based on the peptide enzymaticity.void
setSimplifyGroupsEvidence(boolean simplifyGroupsEvidence)
Sets whether the protein groups should be simplified based on the Uniprot evidence level.void
setSimplifyGroupsVariants(boolean simplifyGroupsVariants)
Sets whether the protein groups should be simplified based on the peptide variant matching.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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ProteinInferenceParameters
public ProteinInferenceParameters()Empty default constructor
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Method Details
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getShortDescription
Returns a short description of the parameters.- Returns:
- a short description of the parameters
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equals
Returns true if the objects have identical settings.- Parameters:
otherProteinInferencePreferences
- the ProteinInferencePreferences to compare to- Returns:
- true if the objects have identical settings
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getSimplifyGroups
public boolean getSimplifyGroups()Returns a boolean indicating whether the protein groups should be simplified.- Returns:
- a boolean indicating whether the protein groups should be simplified
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setSimplifyGroups
public void setSimplifyGroups(boolean simplifyProteinGroups)Sets whether the protein groups should be simplified based on the PeptideShaker confidence.- Parameters:
simplifyProteinGroups
- whether the protein groups should be simplified
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getSimplifyGroupsEvidence
public boolean getSimplifyGroupsEvidence()Returns a boolean indicating whether the protein groups should be simplified based on the Uniprot evidence level.- Returns:
- a boolean indicating whether the protein groups should be simplified based on the Uniprot evidence level
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setSimplifyGroupsEvidence
public void setSimplifyGroupsEvidence(boolean simplifyGroupsEvidence)Sets whether the protein groups should be simplified based on the Uniprot evidence level.- Parameters:
simplifyGroupsEvidence
- whether the protein groups should be simplified based on the Uniprot evidence level
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getSimplifyGroupsConfidence
public boolean getSimplifyGroupsConfidence()Returns a boolean indicating whether the protein groups should be simplified based on the peptide confidence.- Returns:
- a boolean indicating whether the protein groups should be simplified based on the peptide confidence
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setSimplifyGroupsConfidence
public void setSimplifyGroupsConfidence(boolean simplifyGroupsConfidence)Sets whether the protein groups should be simplified based on the peptide confidence level.- Parameters:
simplifyGroupsConfidence
- whether the protein groups should be simplified based on the peptide confidence level
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getConfidenceThreshold
public double getConfidenceThreshold()Returns the confidence below which a peptide is considered absent.- Returns:
- the confidence below which a peptide is considered absent
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setConfidenceThreshold
public void setConfidenceThreshold(double confidenceThreshold)Sets the confidence below which a peptide is considered absent.- Parameters:
confidenceThreshold
- the confidence below which a peptide is considered absent
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getSimplifyGroupsEnzymaticity
public boolean getSimplifyGroupsEnzymaticity()Returns a boolean indicating whether the protein groups should be simplified based on the peptide enzymaticity.- Returns:
- a boolean indicating whether the protein groups should be simplified based on the peptide enzymaticity
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setSimplifyGroupsEnzymaticity
public void setSimplifyGroupsEnzymaticity(boolean simplifyGroupsEnzymaticity)Sets whether the protein groups should be simplified based on the peptide enzymaticity.- Parameters:
simplifyGroupsEnzymaticity
- whether the protein groups should be simplified based on the peptide enzymaticity
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getSimplifyGroupsVariants
public boolean getSimplifyGroupsVariants()Returns a boolean indicating whether the protein groups should be simplified based on the peptide variant matching.- Returns:
- a boolean indicating whether the protein groups should be simplified based on the peptide variant matching
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setSimplifyGroupsVariants
public void setSimplifyGroupsVariants(boolean simplifyGroupsVariants)Sets whether the protein groups should be simplified based on the peptide variant matching.- Parameters:
simplifyGroupsVariants
- whether the protein groups should be simplified based on the peptide variant matching
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isModificationRefinement
public boolean isModificationRefinement()Returns whether the protein mapping should be refined based on terminal and pattern modifications.- Returns:
- a boolean indicating whether the protein mapping should be refined based on terminal and pattern modifications
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setModificationRefinement
public void setModificationRefinement(boolean modificationRefinement)Sets whether the protein mapping should be refined based on terminal and pattern modifications.- Parameters:
modificationRefinement
- a boolean indicating whether the protein mapping should be refined based on terminal and pattern modifications
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