public class MyriMatchParameters extends Object implements IdentificationAlgorithmParameter
Constructor and Description |
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MyriMatchParameters()
Constructor.
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Modifier and Type | Method and Description |
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static String |
enzymeMapping(Enzyme enzyme)
Tries to map the utilities enzyme to the enzymes supported by MyriMatch.
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boolean |
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same
parameters.
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Advocate |
getAlgorithm()
Returns the identification algorithm.
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Integer |
getClassSizeMultiplier()
Returns the intensity class size multiplier.
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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.
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String |
getFragmentationRule()
Returns the fragmentation rule.
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Integer |
getMaxDynamicMods()
Returns the maximum number of variable modifications.
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Integer |
getMaxPeakCount()
Returns the max peak count.
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Integer |
getMaxPeptideLength()
Returns the maximal peptide length allowed.
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Double |
getMaxPrecursorMass()
Returns the maxPrecursorMass precursor mass.
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Integer |
getMinPeptideLength()
Sets the minimal peptide length allowed.
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Double |
getMinPrecursorMass()
Returns the minimum precursor mass.
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Integer |
getMinTerminiCleavages()
Returns the minimum number of termini cleavages.
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Integer |
getNumberOfBatches()
Set the number of batches per node to strive for when using the MPI-based
parallelization features.
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Integer |
getNumberOfSpectrumMatches()
Returns the maximum number of spectrum matches.
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Integer |
getNumIntensityClasses()
Returns the number of intensity classes.
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String |
getOutputFormat()
Returns the output format.
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Double |
getTicCutoffPercentage()
Returns the TicCutoffPercentage.
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boolean |
getUseSmartPlusThreeModel()
Returns true if the UseSmartPlusThreeModel is to be used.
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void |
setClassSizeMultiplier(Integer classSizeMultiplier)
Set the intensity class size multiplier.
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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.
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void |
setFragmentationRule(String fragmentationRule)
Set the fragmentation rule.
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void |
setMaxDynamicMods(Integer maxDynamicMods)
Set the maximum number of variable modifications.
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void |
setMaxPeakCount(Integer maxPeakCount)
Set the max peak count.
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void |
setMaxPeptideLength(Integer maxPeptideLength)
Sets the maximal peptide length allowed.
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void |
setMaxPrecursorMass(Double maxPrecursorMass)
Sets the maximum precursor mass.
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void |
setMinPeptideLength(Integer minPeptideLength)
Sets the minimal peptide length allowed.
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void |
setMinPrecursorMass(Double minPrecursorMass)
Sets the minimum precursor mass.
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void |
setMinTerminiCleavages(Integer minTerminiCleavages)
Set the minimum number of termini cleavages.
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void |
setNumberOfBatches(Integer numberOfBatches)
Set the number of batches per node to strive for when using the MPI-based
parallelization features.
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void |
setNumberOfSpectrumMatches(Integer numberOfSpectrumMarches)
Set the maximum number of spectrum matches.
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void |
setNumIntensityClasses(Integer numIntensityClasses)
Set the number of intensity classes.
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void |
setOutputFormat(String outputFormat)
Set the output format.
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void |
setTicCutoffPercentage(Double ticCutoffPercentage)
Set the TicCutoffPercentage.
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void |
setUseSmartPlusThreeModel(boolean useSmartPlusThreeModel)
Sets if the UseSmartPlusThreeModel is to be used.
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String |
toString(boolean html)
Returns the parameters as a string.
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public Advocate getAlgorithm()
IdentificationAlgorithmParameter
getAlgorithm
in interface IdentificationAlgorithmParameter
public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
IdentificationAlgorithmParameter
equals
in interface IdentificationAlgorithmParameter
identificationAlgorithmParameter
- the other
identificationAlgorithmParameterpublic String toString(boolean html)
IdentificationAlgorithmParameter
toString
in interface IdentificationAlgorithmParameter
html
- use HTML formattingpublic Integer getMaxPeptideLength()
public void setMaxPeptideLength(Integer maxPeptideLength)
maxPeptideLength
- the maximal peptide length allowedpublic Integer getMinPeptideLength()
public void setMinPeptideLength(Integer minPeptideLength)
minPeptideLength
- the minimal peptide length allowedpublic Integer getNumberOfSpectrumMatches()
public void setNumberOfSpectrumMatches(Integer numberOfSpectrumMarches)
numberOfSpectrumMarches
- the numberOfSpectrumMarches to setpublic Double getTicCutoffPercentage()
public void setTicCutoffPercentage(Double ticCutoffPercentage)
ticCutoffPercentage
- the ticCutoffPercentage to setpublic Integer getMaxDynamicMods()
public void setMaxDynamicMods(Integer maxDynamicMods)
maxDynamicMods
- the maxDynamicMods to setpublic Integer getMinTerminiCleavages()
public void setMinTerminiCleavages(Integer minTerminiCleavages)
minTerminiCleavages
- the minTerminiCleavages to setpublic Double getMinPrecursorMass()
public void setMinPrecursorMass(Double minPrecursorMass)
minPrecursorMass
- the minPrecursorMass to setpublic Double getMaxPrecursorMass()
public void setMaxPrecursorMass(Double maxPrecursorMass)
maxPrecursorMass
- the maximum to setpublic boolean getUseSmartPlusThreeModel()
public void setUseSmartPlusThreeModel(boolean useSmartPlusThreeModel)
useSmartPlusThreeModel
- if the UseSmartPlusThreeModel is to be usedpublic boolean getComputeXCorr()
public void setComputeXCorr(boolean computeXCorr)
computeXCorr
- if the Sequest-like cross correlation score is to be
calculatedpublic Integer getNumIntensityClasses()
public void setNumIntensityClasses(Integer numIntensityClasses)
numIntensityClasses
- he number of intensity classespublic Integer getClassSizeMultiplier()
public void setClassSizeMultiplier(Integer classSizeMultiplier)
classSizeMultiplier
- the intensity class size multiplierpublic Integer getNumberOfBatches()
public void setNumberOfBatches(Integer numberOfBatches)
numberOfBatches
- the number of batches per nodepublic String getFragmentationRule()
public void setFragmentationRule(String fragmentationRule)
fragmentationRule
- the fragmentation rulepublic Integer getMaxPeakCount()
public void setMaxPeakCount(Integer maxPeakCount)
maxPeakCount
- the max peak countpublic String getOutputFormat()
public void setOutputFormat(String outputFormat)
outputFormat
- the outputFormat to setCopyright © 2016. All rights reserved.