public class PepnovoParameters extends Object implements IdentificationAlgorithmParameter
Constructor and Description |
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PepnovoParameters()
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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Boolean |
generateQuery()
Returns a boolean indicating whether a blast query shall be generated.
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Advocate |
getAlgorithm()
Returns the identification algorithm.
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Boolean |
getDiscardLowQualitySpectra()
Returns a boolean indicating whether low quality spectra shall be
discarded.
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String |
getFragmentationModel()
Returns the name of the fragmentation model.
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Integer |
getHitListLength()
Returns the length of the hit list.
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Map<String,String> |
getPepNovoPtmMap()
Returns the PepNovo to utilities PTM map.
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String |
getUtilitiesPtmName(String pepnovoPtmName)
Returns the utilities PTM name corresponding to the given PepNovo PTM
name.
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Boolean |
isCorrectPrecursorMass()
Returns a boolean indicating whether the precursor mass shall be
corrected (TagDB setting).
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Boolean |
isEstimateCharge()
Indicates whether the precursor charge shall be estimated for PepNovo.
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void |
setCorrectPrecursorMass(Boolean correctPrecursorMass)
Sets whether the precursor mass shall be corrected (TagDB setting).
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void |
setDiscardLowQualitySpectra(Boolean discardLowQualitySpectra)
Sets whether low quality spectra shall be discarded.
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void |
setEstimateCharge(Boolean estimateCharge)
Sets whether the precursor charge shall be estimated for PepNovo.
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void |
setFragmentationModel(String fragmentationModel)
Sets the name of the fragmentation model.
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void |
setGenerateQuery(Boolean generateQuery)
Sets a boolean indicating whether a blast query shall be generated.
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void |
setHitListLength(Integer hitListLength)
Sets the length of the hit list.
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void |
setPepNovoPtmMap(Map<String,String> pepNovoPtmMap)
Set the PepNovo to utilities PTM map.
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String |
toString(boolean html)
Returns the parameters as a string.
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public Integer getHitListLength()
public void setHitListLength(Integer hitListLength)
hitListLength
- the length of the hit listpublic Boolean isEstimateCharge()
public void setEstimateCharge(Boolean estimateCharge)
estimateCharge
- a boolean indicating whether the precursor charge
shall be estimated for PepNovopublic Boolean isCorrectPrecursorMass()
public void setCorrectPrecursorMass(Boolean correctPrecursorMass)
correctPrecursorMass
- a boolean indicating whether the precursor
mass shall be corrected (TagDB setting)public Boolean getDiscardLowQualitySpectra()
public void setDiscardLowQualitySpectra(Boolean discardLowQualitySpectra)
discardLowQualitySpectra
- a boolean indicating whether low quality
spectra shall be discardedpublic String getFragmentationModel()
public void setFragmentationModel(String fragmentationModel)
fragmentationModel
- the name of the fragmentation modelpublic Boolean generateQuery()
public void setGenerateQuery(Boolean generateQuery)
generateQuery
- a boolean indicating whether a blast query shall be
generatedpublic Map<String,String> getPepNovoPtmMap()
public String getUtilitiesPtmName(String pepnovoPtmName)
pepnovoPtmName
- the PepNovo PTM namepublic void setPepNovoPtmMap(Map<String,String> pepNovoPtmMap)
pepNovoPtmMap
- the pepNovoPtmMap to setpublic 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.