Class PNovoParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.PNovoParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class PNovoParameters extends ExperimentObject implements IdentificationAlgorithmParameter
pNovo specific parameters.
- Author:
- Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description PNovoParameters()
Constructor. -
Method Summary
Modifier and Type Method Description boolean
equals(IdentificationAlgorithmParameter identificationAlgorithmParameter)
Indicates whether another identificationAlgorithmParameter has the same parameters.String
getActicationType()
Returns the activation type.Advocate
getAlgorithm()
Returns the identification algorithm.int
getLowerPrecursorMass()
Returns the lower precursor mass.int
getNumberOfPeptides()
Returns the number of peptides to report per spectrum.HashMap<Character,String>
getPNovoPtmMap()
Returns the pNovo to utilities PTM map.HashMap<Character,Character>
getPNovoPtmResiduesMap()
Returns the pNovo to original amino acids residue map.Character
getPtmResidue(Character pNovoPtmCharacter)
Returns the original amino acids residue corresponding to the given pNovo PTM character.int
getUpperPrecursorMass()
Returns the upper precursor mass.String
getUtilitiesPtmName(Character pNovoPtmCharacter)
Returns the utilities PTM name corresponding to the given pNovo PTM character.void
setActicationType(String acticationType)
Sets the activation type.void
setLowerPrecursorMass(int lowerPrecursorMass)
Set the lower precursor mass.void
setNumberOfPeptides(int numberOfPeptides)
Set the number of peptides to report per spectrum.void
setPNovoPtmMap(HashMap<Character,String> pNovoPtmMap)
Set the pNovo to utilities PTM map.void
setPNovoPtmResiduesMap(HashMap<Character,Character> pNovoResidueMap)
Set the pNovo to original amino acids residue map.void
setUpperPrecursorMass(int upperPrecursorMass)
Set the upper precursor mass.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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PNovoParameters
public PNovoParameters()Constructor.
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Method Details
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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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getNumberOfPeptides
public int getNumberOfPeptides()Returns the number of peptides to report per spectrum.- Returns:
- the number of peptides to report per spectrum
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setNumberOfPeptides
public void setNumberOfPeptides(int numberOfPeptides)Set the number of peptides to report per spectrum.- Parameters:
numberOfPeptides
- the number of peptides to report per spectrum
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getLowerPrecursorMass
public int getLowerPrecursorMass()Returns the lower precursor mass.- Returns:
- the lowerPrecursorMass
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setLowerPrecursorMass
public void setLowerPrecursorMass(int lowerPrecursorMass)Set the lower precursor mass.- Parameters:
lowerPrecursorMass
- the lowerPrecursorMass to set
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getUpperPrecursorMass
public int getUpperPrecursorMass()Returns the upper precursor mass.- Returns:
- the upperPrecursorMass
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setUpperPrecursorMass
public void setUpperPrecursorMass(int upperPrecursorMass)Set the upper precursor mass.- Parameters:
upperPrecursorMass
- the upperPrecursorMass to set
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getActicationType
Returns the activation type.- Returns:
- the acticationType
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setActicationType
Sets the activation type.- Parameters:
acticationType
- the acticationType to set
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getPNovoPtmMap
Returns the pNovo to utilities PTM map. Null if not set.- Returns:
- the pNovo to utilities PTM map, null if not set
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getUtilitiesPtmName
Returns the utilities PTM name corresponding to the given pNovo PTM character. Null if not found.- Parameters:
pNovoPtmCharacter
- the pNovo PTM character- Returns:
- the utilities PTM name
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setPNovoPtmMap
Set the pNovo to utilities PTM map.- Parameters:
pNovoPtmMap
- the pNovoPtmMap to set
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getPNovoPtmResiduesMap
Returns the pNovo to original amino acids residue map. Null if not set.- Returns:
- the pNovo to original amino acids residue map, null if not set
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getPtmResidue
Returns the original amino acids residue corresponding to the given pNovo PTM character. Null if not found.- Parameters:
pNovoPtmCharacter
- the pNovo PTM character- Returns:
- the original amino acids residue
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setPNovoPtmResiduesMap
Set the pNovo to original amino acids residue map.- Parameters:
pNovoResidueMap
- the pNovoResidueMap to set
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