public class MsAmandaParameters extends ExperimentObject implements IdentificationAlgorithmParameter
Modifier and Type | Field and Description |
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static int |
MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH
The maximum allowed length of the FASTA file name.
|
NO_KEY
Constructor and Description |
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MsAmandaParameters()
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.
|
boolean |
generateDecoy()
Returns whether a decoy database shall be created and searched against.
|
Advocate |
getAlgorithm()
Returns the identification algorithm.
|
String |
getInstrumentID()
Return the instrument ID.
|
Integer |
getMaxLoadedProteins()
Returns the maximum number of proteins loaded into memory.
|
Integer |
getMaxLoadedSpectra()
Returns the maximum number of spectra loaded into memory.
|
Integer |
getMaxModifications()
Returns the maximum number of modifications per peptide.
|
Integer |
getMaxModificationSites()
Returns the maximum number of modifications sites per modification per
peptide.
|
Integer |
getMaxNeutralLosses()
Returns the maximum number of water and ammonia losses per peptide.
|
Integer |
getMaxNeutralLossesPerModification()
Returns the maximum number identical modification specific losses per
peptide.
|
Integer |
getMaxPeptideLength()
Returns the maximum peptide length.
|
Integer |
getMaxRank()
Returns the maximum rank.
|
Integer |
getMaxVariableModifications()
Returns the maximum number of variable modifications per peptide.
|
Integer |
getMinPeptideLength()
Returns the minimum peptide length.
|
String |
getOutputFormat()
Returns the output format.
|
boolean |
isLowMemoryMode()
Deprecated.
use getMaxLoadedProteins and getMaxLoadedSpectra instead
|
boolean |
isMonoIsotopic()
Returns whether monoisotopic mass values shall be used (in contrast to
average mass values).
|
boolean |
isPerformDeisotoping()
Returns whether deisotoping is to be performed.
|
boolean |
reportBothBestHitsForTD()
Returns true if target and decoy are ranked separately, false if shared
rank.
|
void |
setGenerateDecoyDatabase(boolean generateDecoy)
Set whether a decoy database shall be created and searched against.
|
void |
setInstrumentID(String instrumentID)
Set the instrument ID.
|
void |
setLowMemoryMode(boolean lowMemoryMode)
Deprecated.
use setMaxLoadedProteins and setMaxLoadedSpectra instead
|
void |
setMaxLoadedProteins(Integer maxLoadedProteins)
Set the maximum number of proteins loaded into memory.
|
void |
setMaxLoadedSpectra(Integer maxLoadedSpectra)
Set the maximum number of spectra loaded into memory.
|
void |
setMaxModifications(Integer maxModifications)
Set the maximum number of modifications per peptide.
|
void |
setMaxModificationSites(Integer maxModificationSites)
Set the maximum number of modifications sites per modification per
peptide.
|
void |
setMaxNeutralLosses(Integer maxNeutralLosses)
Set the maximum number of water and ammonia losses per peptide.
|
void |
setMaxNeutralLossesPerModification(Integer maxNeutralLossesPerModification)
Set the maximum number identical modification specific losses per
peptide.
|
void |
setMaxPeptideLength(Integer maxPeptideLength)
Set the maximum peptide length.
|
void |
setMaxRank(Integer maxRank)
Set the maximum rank.
|
void |
setMaxVariableModifications(Integer maxVariableModifications)
Set the maximum number of variable modifications per peptide.
|
void |
setMinPeptideLength(Integer minPeptideLength)
Set the minimum peptide length.
|
void |
setMonoIsotopic(boolean monoisotopic)
Set whether monoisotopic mass values shall be used (in contrast to
average mass values).
|
void |
setOutputFormat(String outputFormat)
Set the output format.
|
void |
setPerformDeisotoping(boolean performDeisotoping)
Sets if deisotoping is to be performed.
|
void |
setReportBothBestHitsForTD(boolean reportBothBestHitsForTD)
Set if target and decoy are ranked separately or shared.
|
String |
toString(boolean html)
Returns the parameters as a string.
|
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
public static final int MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH
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 boolean generateDecoy()
public void setGenerateDecoyDatabase(boolean generateDecoy)
generateDecoy
- the generateDecoy to setpublic boolean isMonoIsotopic()
public void setMonoIsotopic(boolean monoisotopic)
monoisotopic
- the monoisotopic to setpublic String getInstrumentID()
public void setInstrumentID(String instrumentID)
instrumentID
- the instrument ID to setpublic Integer getMaxRank()
public void setMaxRank(Integer maxRank)
maxRank
- the maxRank to setpublic boolean isLowMemoryMode()
public void setLowMemoryMode(boolean lowMemoryMode)
lowMemoryMode
- the low memory mode to setpublic boolean isPerformDeisotoping()
public void setPerformDeisotoping(boolean performDeisotoping)
performDeisotoping
- the performDeisotoping to setpublic Integer getMaxModifications()
public void setMaxModifications(Integer maxModifications)
maxModifications
- the maximum number of modificationspublic Integer getMaxVariableModifications()
public void setMaxVariableModifications(Integer maxVariableModifications)
maxVariableModifications
- the maximum number of variable
modificationspublic Integer getMaxModificationSites()
public void setMaxModificationSites(Integer maxModificationSites)
maxModificationSites
- the maximum number of modifications sites per
modification per peptidepublic Integer getMaxNeutralLosses()
public void setMaxNeutralLosses(Integer maxNeutralLosses)
maxNeutralLosses
- the maximum number of water and ammonia losses
per peptidepublic Integer getMaxNeutralLossesPerModification()
public void setMaxNeutralLossesPerModification(Integer maxNeutralLossesPerModification)
maxNeutralLossesPerModification
- the maximum number identical
modification specific losses per peptidepublic Integer getMinPeptideLength()
public void setMinPeptideLength(Integer minPeptideLength)
minPeptideLength
- the minimum peptide lengthpublic Integer getMaxPeptideLength()
public void setMaxPeptideLength(Integer maxPeptideLength)
maxPeptideLength
- the maximum peptide lengthpublic Integer getMaxLoadedProteins()
public void setMaxLoadedProteins(Integer maxLoadedProteins)
maxLoadedProteins
- the maximum number of proteins loaded into
memorypublic Integer getMaxLoadedSpectra()
public void setMaxLoadedSpectra(Integer maxLoadedSpectra)
maxLoadedSpectra
- the maximum number of spectra loaded into memorypublic String getOutputFormat()
public void setOutputFormat(String outputFormat)
outputFormat
- the outputFormat to setpublic boolean reportBothBestHitsForTD()
public void setReportBothBestHitsForTD(boolean reportBothBestHitsForTD)
reportBothBestHitsForTD
- the reportBothBestHitsForTD to setCopyright © 2021. All rights reserved.