public class AndromedaParameters extends Object implements IdentificationAlgorithmParameter
Constructor and Description |
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AndromedaParameters()
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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Advocate |
getAlgorithm()
Returns the identification algorithm.
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FragmentationMethod |
getFragmentationMethod()
Returns the fragmentation method used.
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int |
getMaxCombinations()
Returns the maximal number of combinations.
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int |
getMaxNumberOfModifications()
Returns the maximal number of modifications.
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int |
getMaxPeptideLengthNoEnzyme()
Returns the maximal peptide length to use when searching with no enzyme.
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double |
getMaxPeptideMass()
Returns the maximal peptide mass.
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int |
getMinPeptideLengthNoEnzyme()
Returns the minimal peptide length to use when searching with no enzyme.
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String |
getModificationName(int ptmIndex)
Returns the name of the modification indexed by the given index.
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int |
getNumberOfCandidates()
Returns the number of candidates.
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Integer |
getPtmIndex(String modificationName)
Returns the index of a given modification, null if not found.
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HashMap<Integer,String> |
getPtmIndexes()
Returns the PTM indexes as a map.
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int |
getTopPeaks()
Returns the top peaks number.
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int |
getTopPeaksWindow()
Returns the top peaks window size.
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boolean |
hasPtmIndexes()
Indicates whether the modification profile has PTM indexes.
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boolean |
isDependentLosses()
Returns whether neutral losses should be sequence dependent.
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boolean |
isEmpiricalCorrection()
Indicates whether empirical correction should be used.
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boolean |
isEqualIL()
Indicates whether I and L should be considered indistinguishable.
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boolean |
isFragmentAll()
Indicates whether the fragment all option should be used.
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boolean |
isHigherCharge()
Indicates whether higher charge should be considered.
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boolean |
isIncludeAmmonia()
Returns a boolean indicating whether ammonia losses should be accounted
for.
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boolean |
isIncludeWater()
Returns a boolean indicating whether water losses should be accounted
for.
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void |
setDependentLosses(boolean dependentLosses)
Sets whether neutral losses should be sequence dependent.
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void |
setEmpiricalCorrection(boolean empiricalCorrection)
Sets whether empirical correction should be used.
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void |
setEqualIL(boolean equalIL)
Sets whether I and L should be considered indistinguishable.
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void |
setFragmentAll(boolean fragmentAll)
Sets whether the fragment all option should be used.
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void |
setFragmentationMethod(FragmentationMethod fragmentationMethod)
Sets the fragmentation method used.
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void |
setHigherCharge(boolean higherCharge)
Sets whether higher charge should be considered.
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void |
setIncludeAmmonia(boolean includeAmmonia)
Sets whether ammonia losses should be accounted for.
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void |
setIncludeWater(boolean includeWater)
Sets whether water losses should be accounted for.
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void |
setMaxCombinations(int maxCombinations)
Sets the maximal number of combinations.
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void |
setMaxNumberOfModifications(int maxNumberOfModifications)
Sets the maximal number of modifications.
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void |
setMaxPeptideLengthNoEnzyme(int maxPeptideLengthNoEnzyme)
Sets the maximal peptide length to use when searching with no enzyme.
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void |
setMaxPeptideMass(Double maxPeptideMass)
Sets the maximal peptide mass.
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void |
setMinPeptideLengthNoEnzyme(int minPeptideLengthNoEnzyme)
Sets the minimal peptide length to use when searching with no enzyme.
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void |
setNumberOfCandidates(int numberOfCandidates)
Sets the number of candidates.
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void |
setPtmIndex(String modificationName,
int ptmIndex)
Sets the index for a given modification.
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void |
setTopPeaks(int topPeaks)
Sets the top peaks number.
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void |
setTopPeaksWindow(int topPeaksWindow)
Sets the top peaks window size.
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String |
toString(boolean html)
Returns the parameters as a string.
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public double getMaxPeptideMass()
public void setMaxPeptideMass(Double maxPeptideMass)
maxPeptideMass
- the maximal peptide masspublic int getMaxCombinations()
public void setMaxCombinations(int maxCombinations)
maxCombinations
- the maximal number of combinationspublic int getTopPeaks()
public void setTopPeaks(int topPeaks)
topPeaks
- the top peaks numberpublic int getTopPeaksWindow()
public void setTopPeaksWindow(int topPeaksWindow)
topPeaksWindow
- the top peaks window sizepublic boolean isIncludeWater()
public void setIncludeWater(boolean includeWater)
includeWater
- a boolean indicating whether water losses should be
accounted forpublic boolean isIncludeAmmonia()
public void setIncludeAmmonia(boolean includeAmmonia)
includeAmmonia
- a boolean indicating whether ammonia losses should
be accounted forpublic boolean isDependentLosses()
public void setDependentLosses(boolean dependentLosses)
dependentLosses
- a boolean indicating whether neutral losses should
be sequence dependentpublic boolean isFragmentAll()
public void setFragmentAll(boolean fragmentAll)
fragmentAll
- a boolean indicating whether the fragment all option
should be usedpublic boolean isEmpiricalCorrection()
public void setEmpiricalCorrection(boolean empiricalCorrection)
empiricalCorrection
- a boolean indicating whether empirical
correction should be usedpublic boolean isHigherCharge()
public void setHigherCharge(boolean higherCharge)
higherCharge
- a boolean indicating whether higher charge should be
consideredpublic FragmentationMethod getFragmentationMethod()
public void setFragmentationMethod(FragmentationMethod fragmentationMethod)
fragmentationMethod
- the fragmentation method usedpublic int getMaxNumberOfModifications()
public void setMaxNumberOfModifications(int maxNumberOfModifications)
maxNumberOfModifications
- the maximal number of modificationspublic int getMinPeptideLengthNoEnzyme()
public void setMinPeptideLengthNoEnzyme(int minPeptideLengthNoEnzyme)
minPeptideLengthNoEnzyme
- the minimal peptide length to use when
searching with no enzymepublic int getMaxPeptideLengthNoEnzyme()
public void setMaxPeptideLengthNoEnzyme(int maxPeptideLengthNoEnzyme)
maxPeptideLengthNoEnzyme
- the maximal peptide length to use when
searching with no enzymepublic boolean isEqualIL()
public void setEqualIL(boolean equalIL)
equalIL
- a boolean indicating whether I and L should be considered
indistinguishablepublic int getNumberOfCandidates()
public void setPtmIndex(String modificationName, int ptmIndex)
modificationName
- the name of the modificationptmIndex
- the index of the modificationpublic String getModificationName(int ptmIndex)
ptmIndex
- the index of the modification to look forpublic boolean hasPtmIndexes()
public Integer getPtmIndex(String modificationName)
modificationName
- the name of the modificationpublic HashMap<Integer,String> getPtmIndexes()
public void setNumberOfCandidates(int numberOfCandidates)
numberOfCandidates
- the number of candidatespublic 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.