public class ProteinInferenceParameters extends ExperimentObject
NO_KEY
Constructor and Description |
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ProteinInferenceParameters()
Empty default constructor
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Modifier and Type | Method and Description |
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boolean |
equals(ProteinInferenceParameters otherProteinInferencePreferences)
Returns true if the objects have identical settings.
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double |
getConfidenceThreshold()
Returns the confidence below which a peptide is considered absent.
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String |
getShortDescription()
Returns a short description of the parameters.
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boolean |
getSimplifyGroups()
Returns a boolean indicating whether the protein groups should be
simplified.
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boolean |
getSimplifyGroupsConfidence()
Returns a boolean indicating whether the protein groups should be
simplified based on the peptide confidence.
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boolean |
getSimplifyGroupsEnzymaticity()
Returns a boolean indicating whether the protein groups should be
simplified based on the peptide enzymaticity.
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boolean |
getSimplifyGroupsEvidence()
Returns a boolean indicating whether the protein groups should be
simplified based on the Uniprot evidence level.
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boolean |
getSimplifyGroupsVariants()
Returns a boolean indicating whether the protein groups should be
simplified based on the peptide variant matching.
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boolean |
isModificationRefinement()
Returns whether the protein mapping should be refined based on terminal and pattern modifications.
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void |
setConfidenceThreshold(double confidenceThreshold)
Sets the confidence below which a peptide is considered absent.
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void |
setModificationRefinement(boolean modificationRefinement)
Sets whether the protein mapping should be refined based on terminal and pattern modifications.
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void |
setSimplifyGroups(boolean simplifyProteinGroups)
Sets whether the protein groups should be simplified based on the
PeptideShaker confidence.
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void |
setSimplifyGroupsConfidence(boolean simplifyGroupsConfidence)
Sets whether the protein groups should be simplified based on the peptide
confidence level.
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void |
setSimplifyGroupsEnzymaticity(boolean simplifyGroupsEnzymaticity)
Sets whether the protein groups should be simplified based on the peptide
enzymaticity.
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void |
setSimplifyGroupsEvidence(boolean simplifyGroupsEvidence)
Sets whether the protein groups should be simplified based on the Uniprot
evidence level.
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void |
setSimplifyGroupsVariants(boolean simplifyGroupsVariants)
Sets whether the protein groups should be simplified based on the peptide
variant matching.
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addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public ProteinInferenceParameters()
public String getShortDescription()
public boolean equals(ProteinInferenceParameters otherProteinInferencePreferences)
otherProteinInferencePreferences
- the ProteinInferencePreferences
to compare topublic boolean getSimplifyGroups()
public void setSimplifyGroups(boolean simplifyProteinGroups)
simplifyProteinGroups
- whether the protein groups should be
simplifiedpublic boolean getSimplifyGroupsEvidence()
public void setSimplifyGroupsEvidence(boolean simplifyGroupsEvidence)
simplifyGroupsEvidence
- whether the protein groups should be
simplified based on the Uniprot evidence levelpublic boolean getSimplifyGroupsConfidence()
public void setSimplifyGroupsConfidence(boolean simplifyGroupsConfidence)
simplifyGroupsConfidence
- whether the protein groups should be
simplified based on the peptide confidence levelpublic double getConfidenceThreshold()
public void setConfidenceThreshold(double confidenceThreshold)
confidenceThreshold
- the confidence below which a peptide is considered absentpublic boolean getSimplifyGroupsEnzymaticity()
public void setSimplifyGroupsEnzymaticity(boolean simplifyGroupsEnzymaticity)
simplifyGroupsEnzymaticity
- whether the protein groups should be
simplified based on the peptide enzymaticitypublic boolean getSimplifyGroupsVariants()
public void setSimplifyGroupsVariants(boolean simplifyGroupsVariants)
simplifyGroupsVariants
- whether the protein groups should be
simplified based on the peptide variant matchingpublic boolean isModificationRefinement()
public void setModificationRefinement(boolean modificationRefinement)
modificationRefinement
- a boolean indicating whether the protein mapping should be refined based on terminal and pattern modificationsCopyright © 2021. All rights reserved.