public class DirecTagParameters extends Object implements Serializable, IdentificationAlgorithmParameter
Constructor and Description |
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DirecTagParameters()
Constructor.
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Modifier and Type | Method and Description |
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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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double |
getComplementMzTolerance()
Returns the complement m/z tolerance.
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double |
getComplementScoreWeight()
Returns the complement score weight.
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int |
getDeisotopingMode()
Returns the deisotoping flag value.
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double |
getIntensityScoreWeight()
Returns the intensity score weight.
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double |
getIsotopeMzTolerance()
Returns the deisotoping m/z tolerance.
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int |
getMaxDynamicMods()
Returns the maximum number of dynamic mods.
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int |
getMaxPeakCount()
Returns the maximum peak count.
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double |
getMaxPrecursorAdjustment()
Returns the maximum precursor adjustment.
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int |
getMaxTagCount()
Returns the maximum number of tags per spectrum to be generated.
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double |
getMinPrecursorAdjustment()
Returns the minimum precursor adjustment.
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double |
getMzFidelityScoreWeight()
Returns the mzFidelity score weight.
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int |
getNumChargeStates()
Returns the number of charge states.
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int |
getNumIntensityClasses()
Returns the number of intensity classes.
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String |
getOutputSuffix()
Returns the output tags suffix.
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double |
getPrecursorAdjustmentStep()
Returns the precursor adjustment step.
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int |
getTagLength()
Returns the tag length.
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double |
getTicCutoffPercentage()
Returns the TIC cutoff in percent.
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String |
getUtilitiesPtmName(int index)
Returns the name of the PTM indexed by the given index.
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boolean |
isAdjustPrecursorMass()
Returns if the precursor mass is to be adjusted.
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boolean |
isDuplicateSpectra()
Indicates whether to use duplicate spectra option.
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boolean |
isUseChargeStateFromMS()
Indicates whether the charge state from the spectrum should be used.
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void |
setAdjustPrecursorMass(boolean adjustPrecursorMass)
Set if the precursor mass is to be adjusted.
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void |
setComplementMzTolerance(double complementMzTolerance)
Sets the complement m/z tolerance.
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void |
setComplementScoreWeight(double complementScoreWeight)
Set the complement score weight.
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void |
setDeisotopingMode(int deisotopingMode)
Sets the deisotoping flag value.
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void |
setDuplicateSpectra(boolean duplicateSpectra)
Sets whether to use duplicate spectra option.
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void |
setIntensityScoreWeight(double intensityScoreWeight)
Set the intensity score weight.
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void |
setIsotopeMzTolerance(double isotopeMzTolerance)
Sets the deisotoping m/z tolerance.
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void |
setMaxDynamicMods(int maxDynamicMods)
Sets the maximum number of dynamic mods.
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void |
setMaxPeakCount(int maxPeakCount)
Set the maximum peak count.
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void |
setMaxPrecursorAdjustment(double maxPrecursorAdjustment)
Set the maximum precursor adjustment.
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void |
setMaxTagCount(int maxTagCount)
Sets the maximum number of tags per spectrum to be generated.
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void |
setMinPrecursorAdjustment(double minPrecursorAdjustment)
Set the minimum precursor adjustment.
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void |
setMzFidelityScoreWeight(double mzFidelityScoreWeight)
Set the mzFidelity score weight.
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void |
setNumChargeStates(int numChargeStates)
Sets the number of charge states.
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void |
setNumIntensityClasses(int numIntensityClasses)
Sets the number of intensity classes.
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void |
setOutputSuffix(String outputSuffix)
Sets the output tags suffix.
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void |
setPrecursorAdjustmentStep(double PrecursorAdjustmentStep)
Set the precursor adjustment step.
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void |
setPtms(ArrayList<String> variablePtms)
Sets the variable PTMs searched.
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void |
setTagLength(int tagLength)
Sets the tag length.
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void |
setTicCutoffPercentage(double ticCutoffPercentage)
Set the TIC cutoff in percent.
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void |
setUseChargeStateFromMS(boolean useChargeStateFromMS)
Sets whether the charge state from the spectrum should be used.
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String |
toString(boolean html)
Returns the parameters as a string.
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public int getNumChargeStates()
public void setNumChargeStates(int numChargeStates)
numChargeStates
- the number of charge statespublic String getOutputSuffix()
public void setOutputSuffix(String outputSuffix)
outputSuffix
- the output tags suffix.public boolean isUseChargeStateFromMS()
public void setUseChargeStateFromMS(boolean useChargeStateFromMS)
useChargeStateFromMS
- boolean indicating whether the charge states
from the spectrum should be usedpublic boolean isDuplicateSpectra()
public void setDuplicateSpectra(boolean duplicateSpectra)
duplicateSpectra
- boolean indicating whether to use duplicate
spectra optionpublic int getDeisotopingMode()
public void setDeisotopingMode(int deisotopingMode)
deisotopingMode
- deisotoping flag valuepublic double getIsotopeMzTolerance()
public void setIsotopeMzTolerance(double isotopeMzTolerance)
isotopeMzTolerance
- deisotoping m/z tolerancepublic double getComplementMzTolerance()
public void setComplementMzTolerance(double complementMzTolerance)
complementMzTolerance
- the complement m/z tolerancepublic int getTagLength()
public void setTagLength(int tagLength)
tagLength
- the tag lengthpublic int getMaxDynamicMods()
public void setMaxDynamicMods(int maxDynamicMods)
maxDynamicMods
- the maximum number of dynamic modspublic int getMaxTagCount()
public void setMaxTagCount(int maxTagCount)
maxTagCount
- the maximum number of tags per spectrum to be
generatedpublic double getIntensityScoreWeight()
public void setIntensityScoreWeight(double intensityScoreWeight)
intensityScoreWeight
- the intensity score weightpublic double getMzFidelityScoreWeight()
public void setMzFidelityScoreWeight(double mzFidelityScoreWeight)
mzFidelityScoreWeight
- the mzFidelity score weightpublic double getComplementScoreWeight()
public void setComplementScoreWeight(double complementScoreWeight)
complementScoreWeight
- the complement score weightpublic double getTicCutoffPercentage()
public void setTicCutoffPercentage(double ticCutoffPercentage)
ticCutoffPercentage
- the ticCutoffPercentage to setpublic int getMaxPeakCount()
public void setMaxPeakCount(int maxPeakCount)
maxPeakCount
- the maxPeakCount to setpublic int getNumIntensityClasses()
public void setNumIntensityClasses(int numIntensityClasses)
numIntensityClasses
- the numIntensityClasses to setpublic boolean isAdjustPrecursorMass()
public void setAdjustPrecursorMass(boolean adjustPrecursorMass)
adjustPrecursorMass
- the adjustPrecursorMass to setpublic double getMinPrecursorAdjustment()
public void setMinPrecursorAdjustment(double minPrecursorAdjustment)
minPrecursorAdjustment
- the minPrecursorAdjustment to setpublic double getMaxPrecursorAdjustment()
public void setMaxPrecursorAdjustment(double maxPrecursorAdjustment)
maxPrecursorAdjustment
- the maxPrecursorAdjustment to setpublic double getPrecursorAdjustmentStep()
public void setPrecursorAdjustmentStep(double PrecursorAdjustmentStep)
PrecursorAdjustmentStep
- the precursorAdjustmentStep to setpublic void setPtms(ArrayList<String> variablePtms)
variablePtms
- list of the names of the searched variable PTMspublic String getUtilitiesPtmName(int index)
index
- the index of the PTM of interestpublic 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 formattingCopyright © 2016. All rights reserved.