Class AndromedaParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.AndromedaParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class AndromedaParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The Andromeda specific parameters.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
AndromedaParameters.AndromedaDecoyMode
The available decoy modes. -
Field Summary
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Constructor Summary
Constructors Constructor Description AndromedaParameters()
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.AndromedaParameters.AndromedaDecoyMode
getDecoyMode()
Returns the decoy mode.FragmentationMethod
getFragmentationMethod()
Returns the fragmentation method used.int
getMaxCombinations()
Returns the maximal number of combinations.int
getMaxNumberOfModifications()
Returns the maximal number of modifications.int
getMaxPeptideLengthNoEnzyme()
Returns the maximal peptide length to use when searching with no enzyme.double
getMaxPeptideMass()
Returns the maximal peptide mass.int
getMinPeptideLengthNoEnzyme()
Returns the minimal peptide length to use when searching with no enzyme.String
getModificationName(int ptmIndex)
Returns the name of the modification indexed by the given index.int
getNumberOfCandidates()
Returns the number of candidates.Integer
getPtmIndex(String modificationName)
Returns the index of a given modification, null if not found.HashMap<Integer,String>
getPtmIndexes()
Returns the PTM indexes as a map.int
getTopPeaks()
Returns the top peaks number.int
getTopPeaksWindow()
Returns the top peaks window size.boolean
hasModificationIndexes()
Indicates whether the modification profile has PTM indexes.boolean
isDependentLosses()
Returns whether neutral losses should be sequence dependent.boolean
isEmpiricalCorrection()
Indicates whether empirical correction should be used.boolean
isEqualIL()
Indicates whether I and L should be considered indistinguishable.boolean
isFragmentAll()
Indicates whether the fragment all option should be used.boolean
isHigherCharge()
Indicates whether higher charge should be considered.boolean
isIncludeAmmonia()
Returns a boolean indicating whether ammonia losses should be accounted for.boolean
isIncludeWater()
Returns a boolean indicating whether water losses should be accounted for.void
setDecoyMode(AndromedaParameters.AndromedaDecoyMode decoyMode)
Set the decoy mode.void
setDependentLosses(boolean dependentLosses)
Sets whether neutral losses should be sequence dependent.void
setEmpiricalCorrection(boolean empiricalCorrection)
Sets whether empirical correction should be used.void
setEqualIL(boolean equalIL)
Sets whether I and L should be considered indistinguishable.void
setFragmentAll(boolean fragmentAll)
Sets whether the fragment all option should be used.void
setFragmentationMethod(FragmentationMethod fragmentationMethod)
Sets the fragmentation method used.void
setHigherCharge(boolean higherCharge)
Sets whether higher charge should be considered.void
setIncludeAmmonia(boolean includeAmmonia)
Sets whether ammonia losses should be accounted for.void
setIncludeWater(boolean includeWater)
Sets whether water losses should be accounted for.void
setMaxCombinations(int maxCombinations)
Sets the maximal number of combinations.void
setMaxNumberOfModifications(int maxNumberOfModifications)
Sets the maximal number of modifications.void
setMaxPeptideLengthNoEnzyme(int maxPeptideLengthNoEnzyme)
Sets the maximal peptide length to use when searching with no enzyme.void
setMaxPeptideMass(Double maxPeptideMass)
Sets the maximal peptide mass.void
setMinPeptideLengthNoEnzyme(int minPeptideLengthNoEnzyme)
Sets the minimal peptide length to use when searching with no enzyme.void
setNumberOfCandidates(int numberOfCandidates)
Sets the number of candidates.void
setPtmIndex(String modificationName, int ptmIndex)
Sets the index for a given modification.void
setTopPeaks(int topPeaks)
Sets the top peaks number.void
setTopPeaksWindow(int topPeaksWindow)
Sets the top peaks window size.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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AndromedaParameters
public AndromedaParameters()Constructor.
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Method Details
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getMaxPeptideMass
public double getMaxPeptideMass()Returns the maximal peptide mass.- Returns:
- the maximal peptide mass
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setMaxPeptideMass
Sets the maximal peptide mass.- Parameters:
maxPeptideMass
- the maximal peptide mass
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getMaxCombinations
public int getMaxCombinations()Returns the maximal number of combinations.- Returns:
- the maximal number of combinations
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setMaxCombinations
public void setMaxCombinations(int maxCombinations)Sets the maximal number of combinations.- Parameters:
maxCombinations
- the maximal number of combinations
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getTopPeaks
public int getTopPeaks()Returns the top peaks number.- Returns:
- the top peaks number
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setTopPeaks
public void setTopPeaks(int topPeaks)Sets the top peaks number.- Parameters:
topPeaks
- the top peaks number
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getTopPeaksWindow
public int getTopPeaksWindow()Returns the top peaks window size.- Returns:
- the top peaks window size
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setTopPeaksWindow
public void setTopPeaksWindow(int topPeaksWindow)Sets the top peaks window size.- Parameters:
topPeaksWindow
- the top peaks window size
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isIncludeWater
public boolean isIncludeWater()Returns a boolean indicating whether water losses should be accounted for.- Returns:
- a boolean indicating whether water losses should be accounted for
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setIncludeWater
public void setIncludeWater(boolean includeWater)Sets whether water losses should be accounted for.- Parameters:
includeWater
- a boolean indicating whether water losses should be accounted for
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isIncludeAmmonia
public boolean isIncludeAmmonia()Returns a boolean indicating whether ammonia losses should be accounted for.- Returns:
- a boolean indicating whether ammonia losses should be accounted for
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setIncludeAmmonia
public void setIncludeAmmonia(boolean includeAmmonia)Sets whether ammonia losses should be accounted for.- Parameters:
includeAmmonia
- a boolean indicating whether ammonia losses should be accounted for
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isDependentLosses
public boolean isDependentLosses()Returns whether neutral losses should be sequence dependent.- Returns:
- a boolean indicating whether neutral losses should be sequence dependent
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setDependentLosses
public void setDependentLosses(boolean dependentLosses)Sets whether neutral losses should be sequence dependent.- Parameters:
dependentLosses
- a boolean indicating whether neutral losses should be sequence dependent
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isFragmentAll
public boolean isFragmentAll()Indicates whether the fragment all option should be used.- Returns:
- a boolean indicating whether the fragment all option should be used
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setFragmentAll
public void setFragmentAll(boolean fragmentAll)Sets whether the fragment all option should be used.- Parameters:
fragmentAll
- a boolean indicating whether the fragment all option should be used
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isEmpiricalCorrection
public boolean isEmpiricalCorrection()Indicates whether empirical correction should be used.- Returns:
- a boolean indicating whether empirical correction should be used
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setEmpiricalCorrection
public void setEmpiricalCorrection(boolean empiricalCorrection)Sets whether empirical correction should be used.- Parameters:
empiricalCorrection
- a boolean indicating whether empirical correction should be used
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isHigherCharge
public boolean isHigherCharge()Indicates whether higher charge should be considered.- Returns:
- a boolean indicating whether higher charge should be considered
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setHigherCharge
public void setHigherCharge(boolean higherCharge)Sets whether higher charge should be considered.- Parameters:
higherCharge
- a boolean indicating whether higher charge should be considered
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getFragmentationMethod
Returns the fragmentation method used.- Returns:
- the fragmentation method used
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setFragmentationMethod
Sets the fragmentation method used.- Parameters:
fragmentationMethod
- the fragmentation method used
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getMaxNumberOfModifications
public int getMaxNumberOfModifications()Returns the maximal number of modifications.- Returns:
- the maximal number of modifications
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setMaxNumberOfModifications
public void setMaxNumberOfModifications(int maxNumberOfModifications)Sets the maximal number of modifications.- Parameters:
maxNumberOfModifications
- the maximal number of modifications
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getMinPeptideLengthNoEnzyme
public int getMinPeptideLengthNoEnzyme()Returns the minimal peptide length to use when searching with no enzyme.- Returns:
- the minimal peptide length to use when searching with no enzyme
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setMinPeptideLengthNoEnzyme
public void setMinPeptideLengthNoEnzyme(int minPeptideLengthNoEnzyme)Sets the minimal peptide length to use when searching with no enzyme.- Parameters:
minPeptideLengthNoEnzyme
- the minimal peptide length to use when searching with no enzyme
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getMaxPeptideLengthNoEnzyme
public int getMaxPeptideLengthNoEnzyme()Returns the maximal peptide length to use when searching with no enzyme.- Returns:
- the maximal peptide length to use when searching with no enzyme
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setMaxPeptideLengthNoEnzyme
public void setMaxPeptideLengthNoEnzyme(int maxPeptideLengthNoEnzyme)Sets the maximal peptide length to use when searching with no enzyme.- Parameters:
maxPeptideLengthNoEnzyme
- the maximal peptide length to use when searching with no enzyme
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isEqualIL
public boolean isEqualIL()Indicates whether I and L should be considered indistinguishable.- Returns:
- a boolean indicating whether I and L should be considered indistinguishable
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setEqualIL
public void setEqualIL(boolean equalIL)Sets whether I and L should be considered indistinguishable.- Parameters:
equalIL
- a boolean indicating whether I and L should be considered indistinguishable
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getDecoyMode
Returns the decoy mode.- Returns:
- the decoy mode.
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setDecoyMode
Set the decoy mode.- Parameters:
decoyMode
- the decoy mode
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getNumberOfCandidates
public int getNumberOfCandidates()Returns the number of candidates.- Returns:
- the number of candidates
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setPtmIndex
Sets the index for a given modification. If another modification was already given with the same index the previous setting will be silently overwritten.- Parameters:
modificationName
- the name of the modificationptmIndex
- the index of the modification
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getModificationName
Returns the name of the modification indexed by the given index. Null if not found.- Parameters:
ptmIndex
- the index of the modification to look for- Returns:
- the name of the modification indexed by the given index
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hasModificationIndexes
public boolean hasModificationIndexes()Indicates whether the modification profile has PTM indexes.- Returns:
- true if an PTM indexes map is set
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getPtmIndex
Returns the index of a given modification, null if not found.- Parameters:
modificationName
- the name of the modification- Returns:
- the corresponding index
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getPtmIndexes
Returns the PTM indexes as a map.- Returns:
- the PTM indexes
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setNumberOfCandidates
public void setNumberOfCandidates(int numberOfCandidates)Sets the number of candidates.- Parameters:
numberOfCandidates
- the number of candidates
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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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