public class PNovoParameters extends Object implements IdentificationAlgorithmParameter
Constructor and Description |
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PNovoParameters()
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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String |
getActicationType()
Returns the activation type.
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Advocate |
getAlgorithm()
Returns the identification algorithm.
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int |
getLowerPrecursorMass()
Returns the lower precursor mass.
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int |
getNumberOfPeptides()
Returns the number of peptides to report per spectrum.
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HashMap<Character,String> |
getPNovoPtmMap()
Returns the pNovo to utilities PTM map.
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HashMap<Character,Character> |
getPNovoPtmResiduesMap()
Returns the pNovo to original amino acids residue map.
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Character |
getPtmResidue(Character pNovoPtmCharacter)
Returns the original amino acids residue corresponding to the given pNovo
PTM character.
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int |
getUpperPrecursorMass()
Returns the upper precursor mass.
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String |
getUtilitiesPtmName(Character pNovoPtmCharacter)
Returns the utilities PTM name corresponding to the given pNovo PTM
character.
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void |
setActicationType(String acticationType)
Sets the activation type.
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void |
setLowerPrecursorMass(int lowerPrecursorMass)
Set the lower precursor mass.
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void |
setNumberOfPeptides(int numberOfPeptides)
Set the number of peptides to report per spectrum.
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void |
setPNovoPtmMap(HashMap<Character,String> pNovoPtmMap)
Set the pNovo to utilities PTM map.
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void |
setPNovoPtmResiduesMap(HashMap<Character,Character> pNovoResidueMap)
Set the pNovo to original amino acids residue map.
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void |
setUpperPrecursorMass(int upperPrecursorMass)
Set the upper precursor mass.
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String |
toString(boolean html)
Returns the parameters as a string.
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public 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 formattingpublic int getNumberOfPeptides()
public void setNumberOfPeptides(int numberOfPeptides)
numberOfPeptides
- the number of peptides to report per spectrumpublic int getLowerPrecursorMass()
public void setLowerPrecursorMass(int lowerPrecursorMass)
lowerPrecursorMass
- the lowerPrecursorMass to setpublic int getUpperPrecursorMass()
public void setUpperPrecursorMass(int upperPrecursorMass)
upperPrecursorMass
- the upperPrecursorMass to setpublic String getActicationType()
public void setActicationType(String acticationType)
acticationType
- the acticationType to setpublic HashMap<Character,String> getPNovoPtmMap()
public String getUtilitiesPtmName(Character pNovoPtmCharacter)
pNovoPtmCharacter
- the pNovo PTM characterpublic void setPNovoPtmMap(HashMap<Character,String> pNovoPtmMap)
pNovoPtmMap
- the pNovoPtmMap to setpublic HashMap<Character,Character> getPNovoPtmResiduesMap()
public Character getPtmResidue(Character pNovoPtmCharacter)
pNovoPtmCharacter
- the pNovo PTM characterCopyright © 2016. All rights reserved.