Class DirecTagParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.DirecTagParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class DirecTagParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The DirecTag specific parameters.
- Author:
- Thilo Muth, Harald Barsnes
- See Also:
- Serialized Form
-
Field Summary
-
Constructor Summary
Constructors Constructor Description DirecTagParameters()
Constructor. -
Method Summary
Modifier and Type Method Description boolean
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same parameters.Advocate
getAlgorithm()
Returns the identification algorithm.double
getComplementMzTolerance()
Returns the complement m/z tolerance.double
getComplementScoreWeight()
Returns the complement score weight.int
getDeisotopingMode()
Returns the deisotoping flag value.double
getIntensityScoreWeight()
Returns the intensity score weight.double
getIsotopeMzTolerance()
Returns the deisotoping m/z tolerance.int
getMaxDynamicMods()
Returns the maximum number of dynamic mods.int
getMaxPeakCount()
Returns the maximum peak count.double
getMaxPrecursorAdjustment()
Returns the maximum precursor adjustment.int
getMaxTagCount()
Returns the maximum number of tags per spectrum to be generated.double
getMinPrecursorAdjustment()
Returns the minimum precursor adjustment.double
getMzFidelityScoreWeight()
Returns the mzFidelity score weight.int
getNumChargeStates()
Returns the number of charge states.int
getNumIntensityClasses()
Returns the number of intensity classes.String
getOutputSuffix()
Returns the output tags suffix.double
getPrecursorAdjustmentStep()
Returns the precursor adjustment step.int
getTagLength()
Returns the tag length.double
getTicCutoffPercentage()
Returns the TIC cutoff in percent.String
getUtilitiesModificationName(int index)
Returns the name of the modification indexed by the given index.boolean
isAdjustPrecursorMass()
Returns if the precursor mass is to be adjusted.boolean
isDuplicateSpectra()
Indicates whether to use duplicate spectra option.boolean
isUseChargeStateFromMS()
Indicates whether the charge state from the spectrum should be used.void
setAdjustPrecursorMass(boolean adjustPrecursorMass)
Set if the precursor mass is to be adjusted.void
setComplementMzTolerance(double complementMzTolerance)
Sets the complement m/z tolerance.void
setComplementScoreWeight(double complementScoreWeight)
Set the complement score weight.void
setDeisotopingMode(int deisotopingMode)
Sets the deisotoping flag value.void
setDuplicateSpectra(boolean duplicateSpectra)
Sets whether to use duplicate spectra option.void
setIntensityScoreWeight(double intensityScoreWeight)
Set the intensity score weight.void
setIsotopeMzTolerance(double isotopeMzTolerance)
Sets the deisotoping m/z tolerance.void
setMaxDynamicMods(int maxDynamicMods)
Sets the maximum number of dynamic mods.void
setMaxPeakCount(int maxPeakCount)
Set the maximum peak count.void
setMaxPrecursorAdjustment(double maxPrecursorAdjustment)
Set the maximum precursor adjustment.void
setMaxTagCount(int maxTagCount)
Sets the maximum number of tags per spectrum to be generated.void
setMinPrecursorAdjustment(double minPrecursorAdjustment)
Set the minimum precursor adjustment.void
setModifications(ArrayList<String> variableModifications)
Sets the variable modifications searched.void
setMzFidelityScoreWeight(double mzFidelityScoreWeight)
Set the mzFidelity score weight.void
setNumChargeStates(int numChargeStates)
Sets the number of charge states.void
setNumIntensityClasses(int numIntensityClasses)
Sets the number of intensity classes.void
setOutputSuffix(String outputSuffix)
Sets the output tags suffix.void
setPrecursorAdjustmentStep(double PrecursorAdjustmentStep)
Set the precursor adjustment step.void
setTagLength(int tagLength)
Sets the tag length.void
setTicCutoffPercentage(double ticCutoffPercentage)
Set the TIC cutoff in percent.void
setUseChargeStateFromMS(boolean useChargeStateFromMS)
Sets whether the charge state from the spectrum should 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
-
Constructor Details
-
DirecTagParameters
public DirecTagParameters()Constructor.
-
-
Method Details
-
getNumChargeStates
public int getNumChargeStates()Returns the number of charge states.- Returns:
- numChargeStates the number of charge states
-
setNumChargeStates
public void setNumChargeStates(int numChargeStates)Sets the number of charge states.- Parameters:
numChargeStates
- the number of charge states
-
getOutputSuffix
Returns the output tags suffix.- Returns:
- the output tags suffix.
-
setOutputSuffix
Sets the output tags suffix.- Parameters:
outputSuffix
- the output tags suffix.
-
isUseChargeStateFromMS
public boolean isUseChargeStateFromMS()Indicates whether the charge state from the spectrum should be used.- Returns:
- boolean indicating whether the charge states from the spectrum should be used
-
setUseChargeStateFromMS
public void setUseChargeStateFromMS(boolean useChargeStateFromMS)Sets whether the charge state from the spectrum should be used.- Parameters:
useChargeStateFromMS
- boolean indicating whether the charge states from the spectrum should be used
-
isDuplicateSpectra
public boolean isDuplicateSpectra()Indicates whether to use duplicate spectra option.- Returns:
- boolean indicating whether to use duplicate spectra option
-
setDuplicateSpectra
public void setDuplicateSpectra(boolean duplicateSpectra)Sets whether to use duplicate spectra option.- Parameters:
duplicateSpectra
- boolean indicating whether to use duplicate spectra option
-
getDeisotopingMode
public int getDeisotopingMode()Returns the deisotoping flag value.- Returns:
- deisotoping flag value
-
setDeisotopingMode
public void setDeisotopingMode(int deisotopingMode)Sets the deisotoping flag value.- Parameters:
deisotopingMode
- deisotoping flag value
-
getIsotopeMzTolerance
public double getIsotopeMzTolerance()Returns the deisotoping m/z tolerance.- Returns:
- deisotoping m/z tolerance
-
setIsotopeMzTolerance
public void setIsotopeMzTolerance(double isotopeMzTolerance)Sets the deisotoping m/z tolerance.- Parameters:
isotopeMzTolerance
- deisotoping m/z tolerance
-
getComplementMzTolerance
public double getComplementMzTolerance()Returns the complement m/z tolerance.- Returns:
- the complement m/z tolerance
-
setComplementMzTolerance
public void setComplementMzTolerance(double complementMzTolerance)Sets the complement m/z tolerance.- Parameters:
complementMzTolerance
- the complement m/z tolerance
-
getTagLength
public int getTagLength()Returns the tag length.- Returns:
- the tag length
-
setTagLength
public void setTagLength(int tagLength)Sets the tag length.- Parameters:
tagLength
- the tag length
-
getMaxDynamicMods
public int getMaxDynamicMods()Returns the maximum number of dynamic mods.- Returns:
- the maximum number of dynamic mods
-
setMaxDynamicMods
public void setMaxDynamicMods(int maxDynamicMods)Sets the maximum number of dynamic mods.- Parameters:
maxDynamicMods
- the maximum number of dynamic mods
-
getMaxTagCount
public int getMaxTagCount()Returns the maximum number of tags per spectrum to be generated.- Returns:
- the maximum number of tags per spectrum to be generated
-
setMaxTagCount
public void setMaxTagCount(int maxTagCount)Sets the maximum number of tags per spectrum to be generated.- Parameters:
maxTagCount
- the maximum number of tags per spectrum to be generated
-
getIntensityScoreWeight
public double getIntensityScoreWeight()Returns the intensity score weight.- Returns:
- the intensity score weight
-
setIntensityScoreWeight
public void setIntensityScoreWeight(double intensityScoreWeight)Set the intensity score weight.- Parameters:
intensityScoreWeight
- the intensity score weight
-
getMzFidelityScoreWeight
public double getMzFidelityScoreWeight()Returns the mzFidelity score weight.- Returns:
- the mzFidelity score weight
-
setMzFidelityScoreWeight
public void setMzFidelityScoreWeight(double mzFidelityScoreWeight)Set the mzFidelity score weight.- Parameters:
mzFidelityScoreWeight
- the mzFidelity score weight
-
getComplementScoreWeight
public double getComplementScoreWeight()Returns the complement score weight.- Returns:
- the complement score weight
-
setComplementScoreWeight
public void setComplementScoreWeight(double complementScoreWeight)Set the complement score weight.- Parameters:
complementScoreWeight
- the complement score weight
-
getTicCutoffPercentage
public double getTicCutoffPercentage()Returns the TIC cutoff in percent. Default is 85%.- Returns:
- the ticCutoffPercentage
-
setTicCutoffPercentage
public void setTicCutoffPercentage(double ticCutoffPercentage)Set the TIC cutoff in percent. Default is 85%.- Parameters:
ticCutoffPercentage
- the ticCutoffPercentage to set
-
getMaxPeakCount
public int getMaxPeakCount()Returns the maximum peak count.- Returns:
- the maxPeakCount
-
setMaxPeakCount
public void setMaxPeakCount(int maxPeakCount)Set the maximum peak count.- Parameters:
maxPeakCount
- the maxPeakCount to set
-
getNumIntensityClasses
public int getNumIntensityClasses()Returns the number of intensity classes.- Returns:
- the numIntensityClasses
-
setNumIntensityClasses
public void setNumIntensityClasses(int numIntensityClasses)Sets the number of intensity classes.- Parameters:
numIntensityClasses
- the numIntensityClasses to set
-
isAdjustPrecursorMass
public boolean isAdjustPrecursorMass()Returns if the precursor mass is to be adjusted.- Returns:
- the adjustPrecursorMass
-
setAdjustPrecursorMass
public void setAdjustPrecursorMass(boolean adjustPrecursorMass)Set if the precursor mass is to be adjusted.- Parameters:
adjustPrecursorMass
- the adjustPrecursorMass to set
-
getMinPrecursorAdjustment
public double getMinPrecursorAdjustment()Returns the minimum precursor adjustment.- Returns:
- the minPrecursorAdjustment
-
setMinPrecursorAdjustment
public void setMinPrecursorAdjustment(double minPrecursorAdjustment)Set the minimum precursor adjustment.- Parameters:
minPrecursorAdjustment
- the minPrecursorAdjustment to set
-
getMaxPrecursorAdjustment
public double getMaxPrecursorAdjustment()Returns the maximum precursor adjustment.- Returns:
- the maxPrecursorAdjustment
-
setMaxPrecursorAdjustment
public void setMaxPrecursorAdjustment(double maxPrecursorAdjustment)Set the maximum precursor adjustment.- Parameters:
maxPrecursorAdjustment
- the maxPrecursorAdjustment to set
-
getPrecursorAdjustmentStep
public double getPrecursorAdjustmentStep()Returns the precursor adjustment step.- Returns:
- the precursorAdjustmentStep
-
setPrecursorAdjustmentStep
public void setPrecursorAdjustmentStep(double PrecursorAdjustmentStep)Set the precursor adjustment step.- Parameters:
PrecursorAdjustmentStep
- the precursorAdjustmentStep to set
-
setModifications
Sets the variable modifications searched. The order is the one used by DirecTag and the name is the utilities one.- Parameters:
variableModifications
- list of the names of the searched variable modifications
-
getUtilitiesModificationName
Returns the name of the modification indexed by the given index.- Parameters:
index
- the index of the modification of interest- Returns:
- the name of the modification of interest
-
getAlgorithm
Description copied from interface:IdentificationAlgorithmParameter
Returns the identification algorithm.- Specified by:
getAlgorithm
in interfaceIdentificationAlgorithmParameter
- Returns:
- the identification algorithm
-
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
-
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
-