public class ProteinInferenceParameters extends Object implements Serializable
Constructor and Description |
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ProteinInferenceParameters() |
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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FastaParameters |
getFastaParameters()
Returns the parameters to use to parse the fasta file.
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File |
getProteinSequenceDatabase()
Returns the path to the database used.
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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 |
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 |
getSimplifyGroupsUncharacterized()
Returns a boolean indicating whether the protein groups consisting of
uncharacterized proteins.
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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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void |
setFastaParameters(FastaParameters fastaParameters)
Sets the parameters to use to parse the fasta file.
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void |
setProteinSequenceDatabase(File proteinSequenceDatabase)
Sets the path to the database used.
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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 |
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 |
setSimplifyGroupsUncharacterized(boolean simplifyGroupsUncharacterized)
Sets whether the protein groups consisting of uncharacterized proteins.
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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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public File getProteinSequenceDatabase()
public void setProteinSequenceDatabase(File proteinSequenceDatabase)
proteinSequenceDatabase
- the path to the database usedpublic 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 getSimplifyGroupsUncharacterized()
public void setSimplifyGroupsUncharacterized(boolean simplifyGroupsUncharacterized)
simplifyGroupsUncharacterized
- whether the protein groups
consisting of uncharacterized proteinspublic 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 FastaParameters getFastaParameters()
public void setFastaParameters(FastaParameters fastaParameters)
fastaParameters
- the parameters to use to parse the fasta fileCopyright © 2018. All rights reserved.