CometParameters (computational omics utilities 4.5.7 API)

java.lang.Object
- com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters

All Implemented Interfaces:

IdentificationAlgorithmParameter, Serializable
```
public class CometParameters
extends Object
implements IdentificationAlgorithmParameter
```
The Comet specific parameters.

Author:

Harald Barsnes

See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class CometParameters.CometOutputFormat
The available output formats.

Nested Classes
Modifier and Type	Class and Description
`static class`	`CometParameters.CometOutputFormat` The available output formats.

Constructor Summary

Constructors
Constructor and Description

CometParameters()
Constructor.

Constructors
Constructor and Description
`CometParameters()` Constructor.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`boolean`	`equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)` Indicates whether another identificationAlgorithmParameter has the same parameters.
`Advocate`	`getAlgorithm()` Returns the identification algorithm.
`Integer`	`getBatchSize()` Returns the batch size.
`Integer`	`getEnzymeType()` Returns the enzyme type.
`Double`	`getFragmentBinOffset()` Returns the fragment ion bin offset.
`Integer`	`getIsotopeCorrection()` Returns the isotope correction setting.
`Double`	`getLowerClearMzRange()` Returns the lower mass value for the clear mz range.
`Integer`	`getMaxFragmentCharge()` Returns the maximum fragment ion charge.
`Double`	`getMaxPrecursorMass()` Returns the maximum precursor mass.
`Integer`	`getMaxVariableMods()` Returns the maximum number of variable modifications per peptide.
`Double`	`getMinPeakIntensity()` Returns the minimum peak intensity.
`Integer`	`getMinPeaks()` Returns the minimum number of peaks.
`Double`	`getMinPrecursorMass()` Returns the minimum precursor mass.
`Integer`	`getNumberOfSpectrumMatches()` Returns the maximum number of spectrum matches.
`boolean`	`getPrintExpectScore()` Returns true if the export score is to be printed.
`Boolean`	`getRemoveMethionine()` Returns true if n-term methionine is to be removed.
`Integer`	`getRemovePrecursor()` Returns if the precursor is to be removed.
`Double`	`getRemovePrecursorTolerance()` Returns the precursor removal tolerance.
`boolean`	`getRequireVariableMods()` Returns true if at least one variable modification is required per peptide.
`CometParameters.CometOutputFormat`	`getSelectedOutputFormat()` Returns the selected output format.
`Boolean`	`getTheoreticalFragmentIonsSumOnly()` Returns true if the theoretical fragment ions are calculated on the sum in the bin alone.
`Double`	`getUpperClearMzRange()` Returns the upper mass value for the clear mz range.
`Boolean`	`getUseSparseMatrix()` Deprecated. from Comet release 2015.02 all searches use this internal data representation by default
`void`	`setBatchSize(Integer batchSize)` Set the batch size.
`void`	`setEnzymeType(Integer enzymeType)` Set the enzyme type.
`void`	`setFragmentBinOffset(Double fragmentBinOffset)` Set the fragment ion bin offset.
`void`	`setIsotopeCorrection(Integer isotopeCorrection)` Set the isotope correction setting.
`void`	`setLowerClearMzRange(Double lowerClearMzRange)` Set the lower mass value for the clear mz range.
`void`	`setMaxFragmentCharge(Integer maxFragmentCharge)` Set the maximum fragment ion charge.
`void`	`setMaxPrecursorMass(Double maxPrecursorMass)` Set the maximum precursor mass.
`void`	`setMaxVariableMods(Integer maxVariableMods)` Set the maximum number of variable modifications per peptide.
`void`	`setMinPeakIntensity(Double minPeakIntensity)` Set the minimum peak intensity.
`void`	`setMinPeaks(Integer minPeaks)` Set the minimum number of peaks.
`void`	`setMinPrecursorMass(Double minPrecursorMass)` Set the minimum precursor mass.
`void`	`setNumberOfSpectrumMatches(Integer numberOfSpectrumMarches)` Set the maximum number of spectrum matches.
`void`	`setPrintExpectScore(boolean printExpectScore)` Set if the export score is to be printed.
`void`	`setRemoveMethionine(Boolean removeMethionine)` Sets if n-term methionine is to be removed.
`void`	`setRemovePrecursor(Integer removePrecursor)` Set if the precursor is to be removed.
`void`	`setRemovePrecursorTolerance(Double removePrecursorTolerance)` Set the precursor removal tolerance.
`void`	`setRequireVariableMods(Boolean requireVariableMods)` Set if at least one variable modification is required per peptide.
`void`	`setSelectedOutputFormat(CometParameters.CometOutputFormat selectedOutputFormat)` Sets the output format.
`void`	`setTheoreticalFragmentIonsSumOnly(Boolean theoreticalFragmentIonsSumOnly)` Set if the theoretical fragment ions are calculated on the sum in the bin alone.
`void`	`setUpperClearMzRange(Double upperClearMzRange)` Set the upper mass value for the clear mz range.
`void`	`setUseSparseMatrix(Boolean useSparseMatrix)` Deprecated. from Comet release 2015.02 all searches use this internal data representation by default
`String`	`toString(boolean html)` Returns the parameters as a string.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CometParameters
```
public CometParameters()
```
    Constructor.
- Method Detail
  - getAlgorithm
```
public Advocate getAlgorithm()
```
    Description copied from interface: IdentificationAlgorithmParameter
    
    Returns the identification algorithm.
    
    Specified by:
    
    getAlgorithm in interface IdentificationAlgorithmParameter
    
    Returns:
    
    the identification algorithm
  - equals
```
public boolean equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
```
    Description copied from interface: IdentificationAlgorithmParameter
    
    Indicates whether another identificationAlgorithmParameter has the same parameters.
    
    Specified by:
    
    equals in interface IdentificationAlgorithmParameter
    
    Parameters:
    
    identificationAlgorithmParameter - the other identificationAlgorithmParameter
    
    Returns:
    
    true if the algorithm and parameters are the same
  - toString
```
public String toString(boolean html)
```
    Description copied from interface: IdentificationAlgorithmParameter
    
    Returns the parameters as a string.
    
    Specified by:
    
    toString in interface IdentificationAlgorithmParameter
    
    Parameters:
    
    html - use HTML formatting
    
    Returns:
    
    the parameters as a string
  - getNumberOfSpectrumMatches
```
public Integer getNumberOfSpectrumMatches()
```
    Returns the maximum number of spectrum matches.
    
    Returns:
    
    the numberOfSpectrumMarches
  - setNumberOfSpectrumMatches
```
public void setNumberOfSpectrumMatches(Integer numberOfSpectrumMarches)
```
    Set the maximum number of spectrum matches.
    
    Parameters:
    
    numberOfSpectrumMarches - the numberOfSpectrumMarches to set
  - getMaxVariableMods
```
public Integer getMaxVariableMods()
```
    Returns the maximum number of variable modifications per peptide.
    
    Returns:
    
    the maxVariableMods
  - setMaxVariableMods
```
public void setMaxVariableMods(Integer maxVariableMods)
```
    Set the maximum number of variable modifications per peptide.
    
    Parameters:
    
    maxVariableMods - the maxVariableMods to set
  - getMinPeaks
```
public Integer getMinPeaks()
```
    Returns the minimum number of peaks.
    
    Returns:
    
    the minPeaks
  - setMinPeaks
```
public void setMinPeaks(Integer minPeaks)
```
    Set the minimum number of peaks.
    
    Parameters:
    
    minPeaks - the minPeaks to set
  - getMinPeakIntensity
```
public Double getMinPeakIntensity()
```
    Returns the minimum peak intensity.
    
    Returns:
    
    the minPeakIntensity
  - setMinPeakIntensity
```
public void setMinPeakIntensity(Double minPeakIntensity)
```
    Set the minimum peak intensity.
    
    Parameters:
    
    minPeakIntensity - the minPeakIntensity to set
  - getRemovePrecursor
```
public Integer getRemovePrecursor()
```
    Returns if the precursor is to be removed.
    
    Returns:
    
    the removePrecursor
  - setRemovePrecursor
```
public void setRemovePrecursor(Integer removePrecursor)
```
    Set if the precursor is to be removed.
    
    Parameters:
    
    removePrecursor - the removePrecursor to set
  - getRemovePrecursorTolerance
```
public Double getRemovePrecursorTolerance()
```
    Returns the precursor removal tolerance.
    
    Returns:
    
    the removePrecursorTolerance
  - setRemovePrecursorTolerance
```
public void setRemovePrecursorTolerance(Double removePrecursorTolerance)
```
    Set the precursor removal tolerance.
    
    Parameters:
    
    removePrecursorTolerance - the removePrecursorTolerance to set
  - getLowerClearMzRange
```
public Double getLowerClearMzRange()
```
    Returns the lower mass value for the clear mz range.
    
    Returns:
    
    the lowerClearMzRange
  - setLowerClearMzRange
```
public void setLowerClearMzRange(Double lowerClearMzRange)
```
    Set the lower mass value for the clear mz range.
    
    Parameters:
    
    lowerClearMzRange - the lowerClearMzRange to set
  - getUpperClearMzRange
```
public Double getUpperClearMzRange()
```
    Returns the upper mass value for the clear mz range.
    
    Returns:
    
    the upperClearMzRange
  - setUpperClearMzRange
```
public void setUpperClearMzRange(Double upperClearMzRange)
```
    Set the upper mass value for the clear mz range.
    
    Parameters:
    
    upperClearMzRange - the upperClearMzRange to set
  - getEnzymeType
```
public Integer getEnzymeType()
```
    Returns the enzyme type.
    
    Returns:
    
    the enzymeType
  - setEnzymeType
```
public void setEnzymeType(Integer enzymeType)
```
    Set the enzyme type.
    
    Parameters:
    
    enzymeType - the enzymeType to set
  - getIsotopeCorrection
```
public Integer getIsotopeCorrection()
```
    Returns the isotope correction setting.
    
    Returns:
    
    the isotopeCorrection
  - setIsotopeCorrection
```
public void setIsotopeCorrection(Integer isotopeCorrection)
```
    Set the isotope correction setting.
    
    Parameters:
    
    isotopeCorrection - the isotopeCorrection to set
  - getMinPrecursorMass
```
public Double getMinPrecursorMass()
```
    Returns the minimum precursor mass.
    
    Returns:
    
    the minPrecursorMass
  - setMinPrecursorMass
```
public void setMinPrecursorMass(Double minPrecursorMass)
```
    Set the minimum precursor mass.
    
    Parameters:
    
    minPrecursorMass - the minPrecursorMass to set
  - getMaxPrecursorMass
```
public Double getMaxPrecursorMass()
```
    Returns the maximum precursor mass.
    
    Returns:
    
    the maxPrecursorMass
  - setMaxPrecursorMass
```
public void setMaxPrecursorMass(Double maxPrecursorMass)
```
    Set the maximum precursor mass.
    
    Parameters:
    
    maxPrecursorMass - the maxPrecursorMass to set
  - getMaxFragmentCharge
```
public Integer getMaxFragmentCharge()
```
    Returns the maximum fragment ion charge.
    
    Returns:
    
    the maxFragmentCharge
  - setMaxFragmentCharge
```
public void setMaxFragmentCharge(Integer maxFragmentCharge)
```
    Set the maximum fragment ion charge.
    
    Parameters:
    
    maxFragmentCharge - the maxFragmentCharge to set
  - getRemoveMethionine
```
public Boolean getRemoveMethionine()
```
    Returns true if n-term methionine is to be removed.
    
    Returns:
    
    the removeMethionine
  - setRemoveMethionine
```
public void setRemoveMethionine(Boolean removeMethionine)
```
    Sets if n-term methionine is to be removed.
    
    Parameters:
    
    removeMethionine - the removeMethionine to set
  - getBatchSize
```
public Integer getBatchSize()
```
    Returns the batch size.
    
    Returns:
    
    the batchSize
  - setBatchSize
```
public void setBatchSize(Integer batchSize)
```
    Set the batch size.
    
    Parameters:
    
    batchSize - the batchSize to set
  - getTheoreticalFragmentIonsSumOnly
```
public Boolean getTheoreticalFragmentIonsSumOnly()
```
    Returns true if the theoretical fragment ions are calculated on the sum in the bin alone. False means that flanking bins are used as well.
    
    Returns:
    
    the theoreticalFragmentIonsSumOnly
  - setTheoreticalFragmentIonsSumOnly
```
public void setTheoreticalFragmentIonsSumOnly(Boolean theoreticalFragmentIonsSumOnly)
```
    Set if the theoretical fragment ions are calculated on the sum in the bin alone. False means that flanking bins are used as well.
    
    Parameters:
    
    theoreticalFragmentIonsSumOnly - the theoreticalFragmentIonsSumOnly to set
  - getFragmentBinOffset
```
public Double getFragmentBinOffset()
```
    Returns the fragment ion bin offset.
    
    Returns:
    
    the fragmentBinOffset
  - setFragmentBinOffset
```
public void setFragmentBinOffset(Double fragmentBinOffset)
```
    Set the fragment ion bin offset.
    
    Parameters:
    
    fragmentBinOffset - the fragmentBinOffset to set
  - getUseSparseMatrix
```
public Boolean getUseSparseMatrix()
```
    Deprecated. from Comet release 2015.02 all searches use this internal data representation by default
    
    Returns true if a sparse matrix is to be used.
    
    Returns:
    
    the useSparseMatrix
  - setUseSparseMatrix
```
public void setUseSparseMatrix(Boolean useSparseMatrix)
```
    Deprecated. from Comet release 2015.02 all searches use this internal data representation by default
    
    Set if a sparse matrix is to be used.
    
    Parameters:
    
    useSparseMatrix - the useSparseMatrix to set
  - getRequireVariableMods
```
public boolean getRequireVariableMods()
```
    Returns true if at least one variable modification is required per peptide.
    
    Returns:
    
    the requireVariableMods
  - setRequireVariableMods
```
public void setRequireVariableMods(Boolean requireVariableMods)
```
    Set if at least one variable modification is required per peptide.
    
    Parameters:
    
    requireVariableMods - the requireVariableMods to set
  - getPrintExpectScore
```
public boolean getPrintExpectScore()
```
    Returns true if the export score is to be printed.
    
    Returns:
    
    true if the export score is to be printed
  - setPrintExpectScore
```
public void setPrintExpectScore(boolean printExpectScore)
```
    Set if the export score is to be printed.
    
    Parameters:
    
    printExpectScore - the printExpectScore to set
  - getSelectedOutputFormat
```
public CometParameters.CometOutputFormat getSelectedOutputFormat()
```
    Returns the selected output format.
    
    Returns:
    
    the selected output format
  - setSelectedOutputFormat
```
public void setSelectedOutputFormat(CometParameters.CometOutputFormat selectedOutputFormat)
```
    Sets the output format.
    
    Parameters:
    
    selectedOutputFormat - the output format

Class CometParameters

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

CometParameters

Method Detail

getAlgorithm

equals

toString

getNumberOfSpectrumMatches

setNumberOfSpectrumMatches

getMaxVariableMods

setMaxVariableMods

getMinPeaks

setMinPeaks

getMinPeakIntensity

setMinPeakIntensity

getRemovePrecursor

setRemovePrecursor

getRemovePrecursorTolerance

setRemovePrecursorTolerance

getLowerClearMzRange

setLowerClearMzRange

getUpperClearMzRange

setUpperClearMzRange

getEnzymeType

setEnzymeType

getIsotopeCorrection

setIsotopeCorrection

getMinPrecursorMass

setMinPrecursorMass

getMaxPrecursorMass

setMaxPrecursorMass

getMaxFragmentCharge

setMaxFragmentCharge

getRemoveMethionine

setRemoveMethionine

getBatchSize

setBatchSize

getTheoreticalFragmentIonsSumOnly

setTheoreticalFragmentIonsSumOnly

getFragmentBinOffset

setFragmentBinOffset

getUseSparseMatrix

setUseSparseMatrix

getRequireVariableMods

setRequireVariableMods

getPrintExpectScore

setPrintExpectScore

getSelectedOutputFormat

setSelectedOutputFormat