Class MsAmandaParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters
- All Implemented Interfaces:
IdentificationAlgorithmParameter
,Serializable
public class MsAmandaParameters extends ExperimentObject implements IdentificationAlgorithmParameter
The MS Amanda specific parameters.
- Author:
- Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
Fields Modifier and Type Field Description static int
MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH
The maximum allowed length of the FASTA file name. -
Constructor Summary
Constructors Constructor Description MsAmandaParameters()
Constructor. -
Method Summary
Modifier and Type Method Description 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 insteadboolean
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 insteadvoid
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.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Field Details
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MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTH
public static final int MAX_MS_AMANDA_FASTA_FILE_NAME_LENGTHThe maximum allowed length of the FASTA file name.- See Also:
- Constant Field Values
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Constructor Details
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MsAmandaParameters
public MsAmandaParameters()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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generateDecoy
public boolean generateDecoy()Returns whether a decoy database shall be created and searched against.- Returns:
- true if a decoy database shall be created and searched against
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setGenerateDecoyDatabase
public void setGenerateDecoyDatabase(boolean generateDecoy)Set whether a decoy database shall be created and searched against.- Parameters:
generateDecoy
- the generateDecoy to set
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isMonoIsotopic
public boolean isMonoIsotopic()Returns whether monoisotopic mass values shall be used (in contrast to average mass values).- Returns:
- true if mass values shall be used (in contrast to average mass values)
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setMonoIsotopic
public void setMonoIsotopic(boolean monoisotopic)Set whether monoisotopic mass values shall be used (in contrast to average mass values).- Parameters:
monoisotopic
- the monoisotopic to set
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getInstrumentID
Return the instrument ID.- Returns:
- the instrument ID
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setInstrumentID
Set the instrument ID.- Parameters:
instrumentID
- the instrument ID to set
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getMaxRank
Returns the maximum rank.- Returns:
- the max rank
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setMaxRank
Set the maximum rank.- Parameters:
maxRank
- the maxRank to set
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isLowMemoryMode
public boolean isLowMemoryMode()Deprecated.use getMaxLoadedProteins and getMaxLoadedSpectra insteadReturns whether the low memory mode is used.- Returns:
- true if in low memory mode
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setLowMemoryMode
public void setLowMemoryMode(boolean lowMemoryMode)Deprecated.use setMaxLoadedProteins and setMaxLoadedSpectra insteadSet whether the low memory mode is used.- Parameters:
lowMemoryMode
- the low memory mode to set
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isPerformDeisotoping
public boolean isPerformDeisotoping()Returns whether deisotoping is to be performed.- Returns:
- true if deisotoping is to be performed
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setPerformDeisotoping
public void setPerformDeisotoping(boolean performDeisotoping)Sets if deisotoping is to be performed.- Parameters:
performDeisotoping
- the performDeisotoping to set
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getMaxModifications
Returns the maximum number of modifications per peptide.- Returns:
- the maximum number of modifications
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setMaxModifications
Set the maximum number of modifications per peptide.- Parameters:
maxModifications
- the maximum number of modifications
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getMaxVariableModifications
Returns the maximum number of variable modifications per peptide.- Returns:
- the maximum number of variable modifications
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setMaxVariableModifications
Set the maximum number of variable modifications per peptide.- Parameters:
maxVariableModifications
- the maximum number of variable modifications
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getMaxModificationSites
Returns the maximum number of modifications sites per modification per peptide.- Returns:
- the maximum number of modifications sites per modification per peptide
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setMaxModificationSites
Set the maximum number of modifications sites per modification per peptide.- Parameters:
maxModificationSites
- the maximum number of modifications sites per modification per peptide
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getMaxNeutralLosses
Returns the maximum number of water and ammonia losses per peptide.- Returns:
- the maximum number of water and ammonia losses per peptide
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setMaxNeutralLosses
Set the maximum number of water and ammonia losses per peptide.- Parameters:
maxNeutralLosses
- the maximum number of water and ammonia losses per peptide
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getMaxNeutralLossesPerModification
Returns the maximum number identical modification specific losses per peptide.- Returns:
- the the maximum number identical modification specific losses per peptide
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setMaxNeutralLossesPerModification
Set the maximum number identical modification specific losses per peptide.- Parameters:
maxNeutralLossesPerModification
- the maximum number identical modification specific losses per peptide
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getMinPeptideLength
Returns the minimum peptide length.- Returns:
- the the minimum peptide length
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setMinPeptideLength
Set the minimum peptide length.- Parameters:
minPeptideLength
- the minimum peptide length
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getMaxPeptideLength
Returns the maximum peptide length.- Returns:
- the the maximum peptide length
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setMaxPeptideLength
Set the maximum peptide length.- Parameters:
maxPeptideLength
- the maximum peptide length
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getMaxLoadedProteins
Returns the maximum number of proteins loaded into memory.- Returns:
- the maximum number of proteins loaded into memory
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setMaxLoadedProteins
Set the maximum number of proteins loaded into memory.- Parameters:
maxLoadedProteins
- the maximum number of proteins loaded into memory
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getMaxLoadedSpectra
Returns the maximum number of spectra loaded into memory.- Returns:
- the maximum number of spectra loaded into memory
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setMaxLoadedSpectra
Set the maximum number of spectra loaded into memory.- Parameters:
maxLoadedSpectra
- the maximum number of spectra loaded into memory
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getOutputFormat
Returns the output format.- Returns:
- the outputFormat
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setOutputFormat
Set the output format.- Parameters:
outputFormat
- the outputFormat to set
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reportBothBestHitsForTD
public boolean reportBothBestHitsForTD()Returns true if target and decoy are ranked separately, false if shared rank.- Returns:
- true if target and decoy are ranked separately, false if shared rank
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setReportBothBestHitsForTD
public void setReportBothBestHitsForTD(boolean reportBothBestHitsForTD)Set if target and decoy are ranked separately or shared.- Parameters:
reportBothBestHitsForTD
- the reportBothBestHitsForTD to set
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