Class PepnovoParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.PepnovoParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class PepnovoParameters extends ExperimentObject implements IdentificationAlgorithmParameter
PepNovo specific parameters.
- Author:
- Marc Vaudel
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description PepnovoParameters()
Constructor. -
Method Summary
Modifier and Type Method Description boolean
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same parameters.Boolean
generateQuery()
Returns a boolean indicating whether a blast query shall be generated.Advocate
getAlgorithm()
Returns the identification algorithm.Boolean
getDiscardLowQualitySpectra()
Returns a boolean indicating whether low quality spectra shall be discarded.String
getFragmentationModel()
Returns the name of the fragmentation model.Integer
getHitListLength()
Returns the length of the hit list.Map<String,String>
getPepNovoPtmMap()
Returns the PepNovo to utilities PTM map.String
getUtilitiesPtmName(String pepnovoPtmName)
Returns the utilities PTM name corresponding to the given PepNovo PTM name.Boolean
isCorrectPrecursorMass()
Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).Boolean
isEstimateCharge()
Indicates whether the precursor charge shall be estimated for PepNovo.void
setCorrectPrecursorMass(Boolean correctPrecursorMass)
Sets whether the precursor mass shall be corrected (TagDB setting).void
setDiscardLowQualitySpectra(Boolean discardLowQualitySpectra)
Sets whether low quality spectra shall be discarded.void
setEstimateCharge(Boolean estimateCharge)
Sets whether the precursor charge shall be estimated for PepNovo.void
setFragmentationModel(String fragmentationModel)
Sets the name of the fragmentation model.void
setGenerateQuery(Boolean generateQuery)
Sets a boolean indicating whether a blast query shall be generated.void
setHitListLength(Integer hitListLength)
Sets the length of the hit list.void
setPepNovoPtmMap(Map<String,String> pepNovoPtmMap)
Set the PepNovo to utilities PTM map.String
toString(boolean html)
Returns the parameters as a string.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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PepnovoParameters
public PepnovoParameters()Constructor.
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Method Details
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getHitListLength
Returns the length of the hit list.- Returns:
- the length of the hit list
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setHitListLength
Sets the length of the hit list.- Parameters:
hitListLength
- the length of the hit list
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isEstimateCharge
Indicates whether the precursor charge shall be estimated for PepNovo.- Returns:
- a boolean indicating whether the precursor charge shall be estimated for PepNovo
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setEstimateCharge
Sets whether the precursor charge shall be estimated for PepNovo.- Parameters:
estimateCharge
- a boolean indicating whether the precursor charge shall be estimated for PepNovo
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isCorrectPrecursorMass
Returns a boolean indicating whether the precursor mass shall be corrected (TagDB setting).- Returns:
- a boolean indicating whether the precursor mass shall be corrected (TagDB setting)
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setCorrectPrecursorMass
Sets whether the precursor mass shall be corrected (TagDB setting).- Parameters:
correctPrecursorMass
- a boolean indicating whether the precursor mass shall be corrected (TagDB setting)
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getDiscardLowQualitySpectra
Returns a boolean indicating whether low quality spectra shall be discarded.- Returns:
- a boolean indicating whether low quality spectra shall be discarded
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setDiscardLowQualitySpectra
Sets whether low quality spectra shall be discarded.- Parameters:
discardLowQualitySpectra
- a boolean indicating whether low quality spectra shall be discarded
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getFragmentationModel
Returns the name of the fragmentation model.- Returns:
- the name of the fragmentation model
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setFragmentationModel
Sets the name of the fragmentation model.- Parameters:
fragmentationModel
- the name of the fragmentation model
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generateQuery
Returns a boolean indicating whether a blast query shall be generated.- Returns:
- a boolean indicating whether a blast query shall be generated
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setGenerateQuery
Sets a boolean indicating whether a blast query shall be generated.- Parameters:
generateQuery
- a boolean indicating whether a blast query shall be generated
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getPepNovoPtmMap
Returns the PepNovo to utilities PTM map. Null if not set.- Returns:
- the PepNovo to utilities PTM map, null if not set
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getUtilitiesPtmName
Returns the utilities PTM name corresponding to the given PepNovo PTM name. Null if not found.- Parameters:
pepnovoPtmName
- the PepNovo PTM name- Returns:
- the utilities PTM name
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setPepNovoPtmMap
Set the PepNovo to utilities PTM map.- Parameters:
pepNovoPtmMap
- the pepNovoPtmMap to set
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getAlgorithm
Description copied from interface:IdentificationAlgorithmParameter
Returns the identification algorithm.- Specified by:
getAlgorithm
in interfaceIdentificationAlgorithmParameter
- Returns:
- the identification algorithm
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equals
Description copied from interface:IdentificationAlgorithmParameter
Indicates whether another identificationAlgorithmParameter has the same parameters.- Specified by:
equals
in interfaceIdentificationAlgorithmParameter
- Parameters:
identificationAlgorithmParameter
- the other identificationAlgorithmParameter- Returns:
- true if the algorithm and parameters are the same
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toString
Description copied from interface:IdentificationAlgorithmParameter
Returns the parameters as a string.- Specified by:
toString
in interfaceIdentificationAlgorithmParameter
- Parameters:
html
- use HTML formatting- Returns:
- the parameters as a string
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