Class MyriMatchParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class MyriMatchParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The MyriMatch specific parameters.
- Author:
- Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description MyriMatchParameters()
Constructor. -
Method Summary
Modifier and Type Method Description static String
enzymeMapping(DigestionParameters digestionPreferences)
Tries to map the utilities enzyme in the digestion preferences to the enzymes supported by MyriMatch.boolean
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same parameters.Advocate
getAlgorithm()
Returns the identification algorithm.Integer
getClassSizeMultiplier()
Returns the intensity class size multiplier.boolean
getComputeXCorr()
Returns true if a Sequest-like cross correlation score will be calculated for the top ranking hits in each spectrum’s result set.String
getFragmentationRule()
Returns the fragmentation rule.Integer
getMaxDynamicMods()
Returns the maximum number of variable modifications.Integer
getMaxPeakCount()
Returns the max peak count.Integer
getMaxPeptideLength()
Returns the maximal peptide length allowed.Double
getMaxPrecursorMass()
Returns the maxPrecursorMass precursor mass.Integer
getMinPeptideLength()
Sets the minimal peptide length allowed.Double
getMinPrecursorMass()
Returns the minimum precursor mass.Integer
getMinTerminiCleavages()
Returns the minimum number of termini cleavages.Integer
getNumberOfBatches()
Set the number of batches per node to strive for when using the MPI-based parallelization features.Integer
getNumberOfSpectrumMatches()
Returns the maximum number of spectrum matches.Integer
getNumIntensityClasses()
Returns the number of intensity classes.String
getOutputFormat()
Returns the output format.Double
getTicCutoffPercentage()
Returns the TicCutoffPercentage.boolean
getUseSmartPlusThreeModel()
Returns true if the UseSmartPlusThreeModel is to be used.void
setClassSizeMultiplier(Integer classSizeMultiplier)
Set the intensity class size multiplier.void
setComputeXCorr(boolean computeXCorr)
Sets if a Sequest-like cross correlation score will be calculated for the top ranking hits in each spectrum’s result set.void
setFragmentationRule(String fragmentationRule)
Set the fragmentation rule.void
setMaxDynamicMods(Integer maxDynamicMods)
Set the maximum number of variable modifications.void
setMaxPeakCount(Integer maxPeakCount)
Set the max peak count.void
setMaxPeptideLength(Integer maxPeptideLength)
Sets the maximal peptide length allowed.void
setMaxPrecursorMass(Double maxPrecursorMass)
Sets the maximum precursor mass.void
setMinPeptideLength(Integer minPeptideLength)
Sets the minimal peptide length allowed.void
setMinPrecursorMass(Double minPrecursorMass)
Sets the minimum precursor mass.void
setMinTerminiCleavages(Integer minTerminiCleavages)
Set the minimum number of termini cleavages.void
setNumberOfBatches(Integer numberOfBatches)
Set the number of batches per node to strive for when using the MPI-based parallelization features.void
setNumberOfSpectrumMatches(Integer numberOfSpectrumMarches)
Set the maximum number of spectrum matches.void
setNumIntensityClasses(Integer numIntensityClasses)
Set the number of intensity classes.void
setOutputFormat(String outputFormat)
Set the output format.void
setTicCutoffPercentage(Double ticCutoffPercentage)
Set the TicCutoffPercentage.void
setUseSmartPlusThreeModel(boolean useSmartPlusThreeModel)
Sets if the UseSmartPlusThreeModel is to be used.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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MyriMatchParameters
public MyriMatchParameters()Constructor.
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Method Details
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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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getMaxPeptideLength
Returns the maximal peptide length allowed.- Returns:
- the maximal peptide length allowed
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setMaxPeptideLength
Sets the maximal peptide length allowed.- Parameters:
maxPeptideLength
- the maximal peptide length allowed
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getMinPeptideLength
Sets the minimal peptide length allowed.- Returns:
- the minimal peptide length allowed
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setMinPeptideLength
Sets the minimal peptide length allowed.- Parameters:
minPeptideLength
- the minimal peptide length allowed
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getNumberOfSpectrumMatches
Returns the maximum number of spectrum matches.- Returns:
- the numberOfSpectrumMarches
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setNumberOfSpectrumMatches
Set the maximum number of spectrum matches.- Parameters:
numberOfSpectrumMarches
- the numberOfSpectrumMarches to set
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getTicCutoffPercentage
Returns the TicCutoffPercentage.- Returns:
- the ticCutoffPercentage
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setTicCutoffPercentage
Set the TicCutoffPercentage.- Parameters:
ticCutoffPercentage
- the ticCutoffPercentage to set
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getMaxDynamicMods
Returns the maximum number of variable modifications.- Returns:
- the maxDynamicMods
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setMaxDynamicMods
Set the maximum number of variable modifications.- Parameters:
maxDynamicMods
- the maxDynamicMods to set
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getMinTerminiCleavages
Returns the minimum number of termini cleavages.- Returns:
- the maxDynamicMods
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setMinTerminiCleavages
Set the minimum number of termini cleavages.- Parameters:
minTerminiCleavages
- the minTerminiCleavages to set
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getMinPrecursorMass
Returns the minimum precursor mass.- Returns:
- the minimum precursor mass
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setMinPrecursorMass
Sets the minimum precursor mass.- Parameters:
minPrecursorMass
- the minPrecursorMass to set
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getMaxPrecursorMass
Returns the maxPrecursorMass precursor mass.- Returns:
- the maximum precursor mass
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setMaxPrecursorMass
Sets the maximum precursor mass.- Parameters:
maxPrecursorMass
- the maximum to set
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getUseSmartPlusThreeModel
public boolean getUseSmartPlusThreeModel()Returns true if the UseSmartPlusThreeModel is to be used.- Returns:
- true if the UseSmartPlusThreeModel is to be used
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setUseSmartPlusThreeModel
public void setUseSmartPlusThreeModel(boolean useSmartPlusThreeModel)Sets if the UseSmartPlusThreeModel is to be used.- Parameters:
useSmartPlusThreeModel
- if the UseSmartPlusThreeModel is to be used
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getComputeXCorr
public boolean getComputeXCorr()Returns true if a Sequest-like cross correlation score will be calculated for the top ranking hits in each spectrum’s result set.- Returns:
- true if the Sequest-like cross correlation score is to be calculated
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setComputeXCorr
public void setComputeXCorr(boolean computeXCorr)Sets if a Sequest-like cross correlation score will be calculated for the top ranking hits in each spectrum’s result set.- Parameters:
computeXCorr
- if the Sequest-like cross correlation score is to be calculated
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getNumIntensityClasses
Returns the number of intensity classes.- Returns:
- the number of intensity classes
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setNumIntensityClasses
Set the number of intensity classes.- Parameters:
numIntensityClasses
- he number of intensity classes
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getClassSizeMultiplier
Returns the intensity class size multiplier.- Returns:
- the intensity class size multiplier
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setClassSizeMultiplier
Set the intensity class size multiplier.- Parameters:
classSizeMultiplier
- the intensity class size multiplier
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getNumberOfBatches
Set the number of batches per node to strive for when using the MPI-based parallelization features.- Returns:
- the number of batches per node
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setNumberOfBatches
Set the number of batches per node to strive for when using the MPI-based parallelization features.- Parameters:
numberOfBatches
- the number of batches per node
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getFragmentationRule
Returns the fragmentation rule.- Returns:
- the fragmentation rule
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setFragmentationRule
Set the fragmentation rule.- Parameters:
fragmentationRule
- the fragmentation rule
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getMaxPeakCount
Returns the max peak count.- Returns:
- the max peak count
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setMaxPeakCount
Set the max peak count.- Parameters:
maxPeakCount
- the max peak count
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getOutputFormat
Returns the output format.- Returns:
- the outputFormat
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setOutputFormat
Set the output format.- Parameters:
outputFormat
- the outputFormat to set
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enzymeMapping
Tries to map the utilities enzyme in the digestion preferences to the enzymes supported by MyriMatch.- Parameters:
digestionPreferences
- the digestion preferences- Returns:
- the MyriMatch enzyme as a string, or null of no mapping is found
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