public class TideParameters extends Object implements IdentificationAlgorithmParameter
Constructor and Description |
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TideParameters()
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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Boolean |
getClipNtermMethionine()
Returns if the starting methionine peptides will be included both with
and without the starting M.
|
Boolean |
getComputeExactPValues()
Returns true if the exact p-values are to be computed.
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Boolean |
getComputeSpScore()
Returns true of the SP score is to be computed.
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Boolean |
getConcatenatTargetDecoy()
Returns true if the target and decoy results are to be concatenated.
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String |
getDecoyFormat()
Returns the decoy format.
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Integer |
getDecoySeed()
Returns the decoy seed.
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String |
getDigestionType()
Returns the enzyme digestion type.
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String |
getFastIndexFolderName()
Returns the name of the FASTA index folder.
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String |
getKeepTerminalAminoAcids()
Returns the option for keeping the terminal amino acids when generating
the decoys.
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Integer |
getMaxPeptideLength()
Returns the maximal peptide length allowed.
|
Double |
getMaxPrecursorMass()
Returns the maxPrecursorMass precursor mass.
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Double |
getMaxSpectrumMz()
Returns the max spectrum m/z to search for.
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Integer |
getMaxVariablePtmsPerPeptide()
Returns the maximum number of variable modifications allowed on a single
peptide.
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Integer |
getMaxVariablePtmsPerTypePerPeptide()
Returns the maximum number of variable modifications of each modification
type allowed on a single peptide.
|
Integer |
getMinPeptideLength()
Sets the minimal peptide length allowed.
|
Double |
getMinPrecursorMass()
Returns the minimum precursor mass.
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Double |
getMinSpectrumMz()
Return the min spectrum m/z to search for.
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Integer |
getMinSpectrumPeaks()
Returns the min number of peaks in a spectrum.
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Boolean |
getMonoisotopicPrecursor()
Returns true if the precursor mass is monoisotopic, false if average.
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Double |
getMzBinOffset()
Returns the m/z bin offset.
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Double |
getMzBinWidth()
Returns the m/z bin width.
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Boolean |
getMzidOutput()
Returns true if the mzid output is to be created.
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Integer |
getNumberOfSpectrumMatches()
Returns the number of PSMs to report per spectrum.
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String |
getOutputFolderName()
Returns the name of the output folder.
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Boolean |
getPepXmlOutput()
Returns true if the pepxml output is to be created.
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Boolean |
getPinOutput()
Returns true if the Percolator output is to be created.
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Boolean |
getPrintPeptides()
Returns true of a list of the peptides should be printed to the output
folder.
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Integer |
getPrintProgressIndicatorSize()
Returns the progress indicator size.
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Boolean |
getRemovePrecursor()
Returns true of the precursor peak is to be removed.
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Double |
getRemovePrecursorTolerance()
Returns the tolerance with which to remove the precursor peak.
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Boolean |
getRemoveTempFolders()
Returns true if the output and index folders are to be removed when the
search has completed.
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String |
getSpectrumCharges()
Returns the spectrum charges to search for.
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Boolean |
getSqtOutput()
Returns true if the sqt output is to be created.
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String |
getStoreSpectraFileName()
Returns the name of the file where the binary spectra are to be stored.
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Boolean |
getTextOutput()
Returns true if the text output is to be created.
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Boolean |
getUseFlankingPeaks()
Returns true if flanking peaks are to be used.
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Boolean |
getUseNeutralLossPeaks()
Returns true if the neutral loss peaks are to be used.
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Integer |
getVerbosity()
Returns the verbosity type of progress output.
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void |
setClipNtermMethionine(Boolean clipNtermMethionine)
Set if the starting methionine peptides will be included both with and
without the starting M.
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void |
setComputeExactPValues(Boolean computeExactPValues)
Set if the exact p-values are to be computed.
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void |
setComputeSpScore(Boolean computeSpScore)
Set if the SP score is to be computed.
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void |
setConcatenatTargetDecoy(Boolean concatenate)
Set if the target and decoy results are to be concatenated.
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void |
setDecoyFormat(String decoyFormat)
Set the decoy format.
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void |
setDecoySeed(Integer decoySeed)
Set the decoy seed.
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void |
setDigestionType(String digestionType)
Set the enzyme digestion type.
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void |
setFastIndexFolderName(String fastIndexFolderName)
Set the name of the FASTA index folder.
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void |
setKeepTerminalAminoAcids(String keepTerminalAminoAcids)
Set the option for keeping the terminal amino acids when generating the
decoys
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void |
setMaxPeptideLength(Integer maxPeptideLength)
Sets the maximal peptide length allowed.
|
void |
setMaxPrecursorMass(Double maxPrecursorMass)
Sets the maximum precursor mass.
|
void |
setMaxSpectrumMz(Double maxSpectrumMz)
Set the max spectrum m/z to search for.
|
void |
setMaxVariablePtmsPerPeptide(Integer maxVariablePtmsPerPeptide)
Set the maximum number of variable modifications of allowed on a single
peptide.
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void |
setMaxVariablePtmsPerTypePerPeptide(Integer maxVariablePtmsPerTypePerPeptide)
Set the maximum number of variable modifications of each modification
type allowed on a single peptide.
|
void |
setMinPeptideLength(Integer minPeptideLength)
Sets the minimal peptide length allowed.
|
void |
setMinPrecursorMass(Double minPrecursorMass)
Sets the minimum precursor mass.
|
void |
setMinSpectrumMz(Double minSpectrumMz)
Set the min spectrum m/z to search for.
|
void |
setMinSpectrumPeaks(Integer minSpectrumPeaks)
Set the min number of peaks in a spectrum.
|
void |
setMonoisotopicPrecursor(Boolean monoisotopicPrecursor)
Set if the precursor mass is monoisotopic.
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void |
setMzBinOffset(Double mzBinOffset)
Set the m/z bin offset.
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void |
setMzBinWidth(Double mzBinWidth)
Set the m/z bin width.
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void |
setMzidOutput(Boolean mzidOutput)
Set if the mzid output is to be created.
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void |
setNumberOfSpectrumMatches(Integer numberOfSpectrumMatches)
Set the number of PSMs to report per spectrum.
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void |
setOutputFolderName(String outputFolderName)
Set the name of the output folder.
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void |
setPepXmlOutput(Boolean pepXmlOutput)
Set if the pepxml output is to be created.
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void |
setPinOutput(Boolean pinOutput)
Set if the Percolator output is to be created.
|
void |
setPrintPeptides(Boolean printPeptides)
Set if a list of the peptides should be printed to the output folder.
|
void |
setPrintProgressIndicatorSize(Integer printProgressIndicatorSize)
Set the progress indicator size.
|
void |
setRemovePrecursor(Boolean removePrecursor)
Set if the precursor peak is to be removed.
|
void |
setRemovePrecursorTolerance(Double removePrecursorTolerance)
Set the tolerance with which to remove the precursor peak.
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void |
setRemoveTempFolders(Boolean removeTempFolders)
Set if the output and index folders are to be removed when the search has
completed.
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void |
setSpectrumCharges(String spectrumCharges)
Set the spectrum charges to search for.
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void |
setSqtOutput(Boolean sqtOutput)
Set if the sqt output is to be created.
|
void |
setStoreSpectraFileName(String storeSpectraFileName)
Set the name of the file where the binary spectra are to be stored.
|
void |
setTextOutput(Boolean textOutput)
Set if the text output is to be created.
|
void |
setUseFlankingPeaks(Boolean useFlankingPeaks)
Set if flanking peaks are to be used.
|
void |
setUseNeutralLossPeaks(Boolean useNeutralLossPeaks)
Set if the neutral loss peaks are to be used.
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void |
setVerbosity(Integer verbosity)
Set the verbosity type of progress output.
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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 Integer getMaxVariablePtmsPerPeptide()
public void setMaxVariablePtmsPerPeptide(Integer maxVariablePtmsPerPeptide)
maxVariablePtmsPerPeptide
- the maxVariablePtmsPerPeptide to setpublic Integer getMaxVariablePtmsPerTypePerPeptide()
public void setMaxVariablePtmsPerTypePerPeptide(Integer maxVariablePtmsPerTypePerPeptide)
maxVariablePtmsPerTypePerPeptide
- the
maxVariablePtmsPerTypePerPeptide to setpublic Integer getMaxPeptideLength()
public void setMaxPeptideLength(Integer maxPeptideLength)
maxPeptideLength
- the maximal peptide length allowedpublic Integer getMinPeptideLength()
public void setMinPeptideLength(Integer minPeptideLength)
minPeptideLength
- the minimal peptide length allowedpublic Double getMinPrecursorMass()
public void setMinPrecursorMass(Double minPrecursorMass)
minPrecursorMass
- the minPrecursorMass to setpublic Double getMaxPrecursorMass()
public void setMaxPrecursorMass(Double maxPrecursorMass)
maxPrecursorMass
- the maximum to setpublic String getDecoyFormat()
public void setDecoyFormat(String decoyFormat)
decoyFormat
- the decoyFormat to setpublic String getKeepTerminalAminoAcids()
public void setKeepTerminalAminoAcids(String keepTerminalAminoAcids)
keepTerminalAminoAcids
- the keepTerminalAminoAcids to setpublic Integer getDecoySeed()
public void setDecoySeed(Integer decoySeed)
decoySeed
- the decoySeed to setpublic String getOutputFolderName()
public void setOutputFolderName(String outputFolderName)
outputFolderName
- the outputFolderName to setpublic Boolean getPrintPeptides()
public void setPrintPeptides(Boolean printPeptides)
printPeptides
- the printPeptides to setpublic Integer getVerbosity()
public void setVerbosity(Integer verbosity)
verbosity
- the verbosity to setpublic Boolean getMonoisotopicPrecursor()
public void setMonoisotopicPrecursor(Boolean monoisotopicPrecursor)
monoisotopicPrecursor
- the monoisotopicPrecursor to setpublic Boolean getClipNtermMethionine()
public void setClipNtermMethionine(Boolean clipNtermMethionine)
clipNtermMethionine
- the clipNtermMethionine to setpublic String getDigestionType()
public void setDigestionType(String digestionType)
digestionType
- the digestionType to setpublic Boolean getComputeSpScore()
public void setComputeSpScore(Boolean computeSpScore)
computeSpScore
- the computeSpScore to setpublic Integer getNumberOfSpectrumMatches()
public void setNumberOfSpectrumMatches(Integer numberOfSpectrumMatches)
numberOfSpectrumMatches
- the numberOfSpectrumMatches to setpublic Boolean getComputeExactPValues()
public void setComputeExactPValues(Boolean computeExactPValues)
computeExactPValues
- the computeExactPValues to setpublic Double getMinSpectrumMz()
public void setMinSpectrumMz(Double minSpectrumMz)
minSpectrumMz
- the minSpectrumMz to setpublic Double getMaxSpectrumMz()
public void setMaxSpectrumMz(Double maxSpectrumMz)
maxSpectrumMz
- the maxSpectrumMz to setpublic Integer getMinSpectrumPeaks()
public void setMinSpectrumPeaks(Integer minSpectrumPeaks)
minSpectrumPeaks
- the minSpectrumPeaks to setpublic String getSpectrumCharges()
public void setSpectrumCharges(String spectrumCharges)
spectrumCharges
- the spectrumCharges to setpublic Boolean getRemovePrecursor()
public void setRemovePrecursor(Boolean removePrecursor)
removePrecursor
- the removePrecursor to setpublic Double getRemovePrecursorTolerance()
public void setRemovePrecursorTolerance(Double removePrecursorTolerance)
removePrecursorTolerance
- the removePrecursorTolerance to setpublic Integer getPrintProgressIndicatorSize()
public void setPrintProgressIndicatorSize(Integer printProgressIndicatorSize)
printProgressIndicatorSize
- the printProgressIndicatorSize to setpublic Boolean getUseFlankingPeaks()
public void setUseFlankingPeaks(Boolean useFlankingPeaks)
useFlankingPeaks
- the useFlankingPeaks to setpublic Boolean getUseNeutralLossPeaks()
public void setUseNeutralLossPeaks(Boolean useNeutralLossPeaks)
useNeutralLossPeaks
- the useNeutralLossPeaks to setpublic Double getMzBinWidth()
public void setMzBinWidth(Double mzBinWidth)
mzBinWidth
- the mzBinWidth to setpublic Double getMzBinOffset()
public void setMzBinOffset(Double mzBinOffset)
mzBinOffset
- the mzBinOffset to setpublic Boolean getConcatenatTargetDecoy()
public void setConcatenatTargetDecoy(Boolean concatenate)
concatenate
- the concatenateTargetDecoy to setpublic String getStoreSpectraFileName()
public void setStoreSpectraFileName(String storeSpectraFileName)
storeSpectraFileName
- the storeSpectraFileName to setpublic Boolean getTextOutput()
public void setTextOutput(Boolean textOutput)
textOutput
- the textOutput to setpublic Boolean getSqtOutput()
public void setSqtOutput(Boolean sqtOutput)
sqtOutput
- the sqtOutput to setpublic Boolean getPepXmlOutput()
public void setPepXmlOutput(Boolean pepXmlOutput)
pepXmlOutput
- the pepXmlOutput to setpublic Boolean getMzidOutput()
public void setMzidOutput(Boolean mzidOutput)
mzidOutput
- the mzidOutput to setpublic Boolean getPinOutput()
public void setPinOutput(Boolean pinOutput)
pinOutput
- the pinOutput to setpublic String getFastIndexFolderName()
public void setFastIndexFolderName(String fastIndexFolderName)
fastIndexFolderName
- the fastIndexFolderName to setpublic Boolean getRemoveTempFolders()
public void setRemoveTempFolders(Boolean removeTempFolders)
removeTempFolders
- the removeTempFolders to setCopyright © 2016. All rights reserved.