Package com.compomics.util.parameters
Class UtilitiesUserParameters
java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.UtilitiesUserParameters
- All Implemented Interfaces:
Serializable
public class UtilitiesUserParameters extends ExperimentObject
Utilities user parameters can be used to store user parameters.
- Author:
- Marc Vaudel, Harald Barsnes
- See Also:
- Serialized Form
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Field Summary
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Constructor Summary
Constructors Constructor Description UtilitiesUserParameters()
Constructor. -
Method Summary
Modifier and Type Method Description boolean
checkDuplicateTitles()
Returns if the spectra should be checked for duplicate titles or not.boolean
checkMgfSize()
Returns if the mgf should be checked for size.boolean
checkPeakPicking()
Returns if the spectra should be checked for peak picking or not.File
getDbFolder()
Returns the last used database folder.File
getDbSummaryFolder()
Returns the folder where FASTA files summary statistics are stored.String
getDeNovoGuiPath()
Returns the path to the DeNovoGUI installation.ArrayList<String>
getDisplayedTips()
Returns the list of displayed tips.String
getJavaHome()
Returns the Java Home folder.LastSelectedFolder
getLastSelectedFolder()
Returns the last selected folder.String
getLocalPrideFolder()
Returns the local PRIDE folder.int
getMaxSpectrumChargeRange()
Returns the maximum charge added when the charge is missing for a given spectrum.Integer
getMemoryParameter()
Returns the upper memory limit in MB.double
getMgfMaxSize()
Returns the max mgf file size before splitting.int
getMgfNSpectra()
Get the max number of spectra in an mgf file.int
getMinSpectrumChargeRange()
Returns the minimum charge added when the charge is missing for a given spectrum.File
getOutputFolder()
Returns the last used output folder.Color
getPeptideSelected()
Returns the color for a selected peptide.String
getPeptideShakerPath()
Returns the path to the PeptideShaker installation.String
getProteoWizardPath()
Returns the path to ProteoWizard.ArrayList<String>
getReadTweets()
Returns the list of read tweets.double
getRefMass()
Returns the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.String
getRelimsPath()
Returns the path to the Relims installation.String
getReporterPath()
Returns the path to the Reporter installation.OutputParameters
getSearchGuiOutputParameters()
Returns the selected SearchGUI output option.String
getSearchGuiPath()
Returns the path to the SearchGUI installation.boolean
getSortPsmsOnRt()
Returns true if the PSMs are sorted on retention time, false sorts on PSM score.Color
getSparklineColor()
Getter for the sparkline color.Color
getSparklineColorDoubtful()
Returns the color for a doubtful sparkline bar chart plots.Color
getSparklineColorFalsePositives()
Returns the color for false positives in sparkline bar chart plots.Color
getSparklineColorNonValidated()
Getter for the non-validated sparkline color.Color
getSparklineColorNotFound()
Returns the color for a not found sparkline bar chart plots.Color
getSparklineColorPossible()
Returns the color for a possible sparkline bar chart plots.Color
getSpectrumAnnotatedMirroredPeakColor()
Returns the color to use for the annotated mirrored peaks.Color
getSpectrumAnnotatedPeakColor()
Returns the color to use for the annotated peaks.float
getSpectrumAnnotatedPeakWidth()
Returns the width of the annotated peaks.Color
getSpectrumBackgroundPeakColor()
Returns the color to use for the background peaks.float
getSpectrumBackgroundPeakWidth()
Returns the width of the background peaks.File
getSpectrumFolder()
Returns the last used spectrum folder.static String
getUserParametersFile()
Returns the user preferences file to be used.static String
getUserParametersFolder()
Returns the user preferences file to be used.boolean
isAutoUpdate()
Indicates whether the tools should use the auto update function.boolean
isCheckSpectrumCharges()
Returns whether the spectra are to be checked for missing charges.boolean
isGzip()
Indicates whether identification files should be gzipped.boolean
isIncludeDateInOutputName()
Indicates whether the date should be included in the SearchGUI output name.static UtilitiesUserParameters
loadUserParameters()
Loads the user parameters.boolean
outputData()
Indicates whether data should be copied along with the identification files in the SearchGUI output.boolean
renameXTandemFile()
Returns true if the X! Tandem file should be renamed.static void
saveUserParameters(UtilitiesUserParameters userParameters)
Convenience method saving the user parameters.void
setAutoUpdate(Boolean autoUpdate)
Sets whether the tools should use the auto update function.void
setCheckDuplicateTitles(boolean checkDuplicateTitles)
Set if the spectra should be checked for duplicate titles or not.void
setCheckMgfSize(boolean checkMgfSize)
Set if the mgf should be checked for size.void
setCheckPeakPicking(boolean checkPeakPicking)
Set if the spectra should be checked for peak picking or not.void
setCheckSpectrumCharges(boolean checkSpectrumCharges)
Set if the spectra are to be checked for missing charges.void
setDbFolder(File dbFolder)
Sets the last used database folder.void
setDeNovoGuiPath(String deNovoGuiPath)
Set the path to the DeNovoGUI installation.void
setDisplayedTips(ArrayList<String> displayedTips)
Set the list of displayed tips.void
setGzip(boolean gzip)
Sets whether identification files should be gzipped.void
setIncludeDateInOutputName(boolean includeDateInOutputName)
Sets whether the date should be included in the SearchGUI output name.void
setJavaHome(String javaHome)
Set the Java Home folder.void
setLastSelectedFolder(LastSelectedFolder lastSelectedFolder)
Sets the last selected folder.void
setLocalPrideFolder(String localPrideFolder)
Set the local PRIDE folder.void
setMaxSpectrumChargeRange(int maxSpectrumChargeRange)
Set the maximum charge added when the charge is missing for a given spectrum.void
setMemoryParameter(int memoryParameter)
Sets the upper memory limit.void
setMgfMaxSize(double mgfMaxSize)
Set the max mgf file size before splitting.void
setMgfNSpectra(int mgfNSpectra)
Set the max number of spectra in an mgf file.void
setMinSpectrumChargeRange(int minSpectrumChargeRange)
Set the minimum charge added when the charge is missing for a given spectrum.void
setOutputData(boolean outputData)
Sets whether data should be copied along with the identification files in the SearchGUI output.void
setOutputFolder(File outputFolder)
Sets the last used output folder.void
setPeptideShakerPath(String peptideShakerPath)
Set the path to the PeptideShaker installation.void
setProteoWizardPath(String proteoWizardPath)
Set the path to ProteoWizard.void
setReadTweets(ArrayList<String> readTweets)
Set the list of read tweets.void
setRefMass(double refMass)
Sets the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.void
setRelimsPath(String relimsPath)
Set the path to the Relims installation.void
setRenameXTandemFile(boolean renameXTandemFile)
Set if the X! Tandem file should be renamed.void
setReporterPath(String reporterPath)
Set the path to the PeptideShaker installation.void
setSearchGuiOutputParameters(OutputParameters outputOption)
Sets how SearchGUI output files should be organized.void
setSearchGuiPath(String searchGuiPath)
Set the path to the SearchGUI installation.void
setSortPsmsOnRt(Boolean sortPsmsOnRt)
Set if the PSMs are sorted on retention time, false sorts on PSM score.void
setSparklineColor(Color sparklineColorValidated)
Setter for the sparkline color.void
setSparklineColorDoubtful(Color sparklineColorDoubtful)
Setter for the doubtful sparkline color.void
setSparklineColorFalsePositives(Color sparklineColorFalsePositive)
Setter for the false positives sparkline color.void
setSparklineColorNonValidated(Color sparklineColorNonValidated)
Setter for the non-validated sparkline color.void
setSparklineColorNotFound(Color sparklineColorNotFound)
Setter for the not found sparkline color.void
setSparklineColorPossible(Color sparklineColorPossible)
Setter for the possible sparkline color.void
setSpectrumAnnotatedMirroredPeakColor(Color spectrumAnnotatedMirroredPeakColor)
Set the color to use for the annotated mirrored peaks.void
setSpectrumAnnotatedPeakColor(Color spectrumAnnotatedPeakColor)
Set the color to use for the annotated peaks.void
setSpectrumAnnotatedPeakWidth(float spectrumAnnotatedPeakWidth)
Set the width of the annotated peaks.void
setSpectrumBackgroundPeakColor(Color spectrumBackgroundPeakColor)
Set the color to use for the background peaks.void
setSpectrumBackgroundPeakWidth(float spectrumBackgroundPeakWidth)
Set the width of the background peaks.void
setSpectrumFolder(File spectrumFolder)
Sets the last used spectrum folder.static void
setUserParametersFolder(String userParametersFolder)
Sets the user preferences file to be used.Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject
addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams
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Constructor Details
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UtilitiesUserParameters
public UtilitiesUserParameters()Constructor.
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Method Details
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getSparklineColor
Getter for the sparkline color.- Returns:
- the sparkline color
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setSparklineColor
Setter for the sparkline color.- Parameters:
sparklineColorValidated
- the sparkline color
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getSparklineColorNonValidated
Getter for the non-validated sparkline color.- Returns:
- the non-validated sparkline color
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getPeptideSelected
Returns the color for a selected peptide.- Returns:
- the color for a selected peptide
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getSparklineColorNotFound
Returns the color for a not found sparkline bar chart plots.- Returns:
- the color for a not found sparkline bar chart plots
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setSparklineColorNotFound
Setter for the not found sparkline color.- Parameters:
sparklineColorNotFound
- the not found sparkline color
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setSparklineColorNonValidated
Setter for the non-validated sparkline color.- Parameters:
sparklineColorNonValidated
- the non-validated sparkline color
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getSparklineColorPossible
Returns the color for a possible sparkline bar chart plots.- Returns:
- the color for a possible sparkline bar chart plots
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setSparklineColorPossible
Setter for the possible sparkline color.- Parameters:
sparklineColorPossible
- the possible sparkline color
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getSparklineColorDoubtful
Returns the color for a doubtful sparkline bar chart plots.- Returns:
- the color for a doubtful sparkline bar chart plots
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setSparklineColorDoubtful
Setter for the doubtful sparkline color.- Parameters:
sparklineColorDoubtful
- the doubtful sparkline color
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getSparklineColorFalsePositives
Returns the color for false positives in sparkline bar chart plots.- Returns:
- the color for a false positives in sparkline bar chart plots
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setSparklineColorFalsePositives
Setter for the false positives sparkline color.- Parameters:
sparklineColorFalsePositive
- the false positives sparkline color
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getMemoryParameter
Returns the upper memory limit in MB.- Returns:
- the upper memory limit
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setMemoryParameter
public void setMemoryParameter(int memoryParameter)Sets the upper memory limit.- Parameters:
memoryParameter
- the preferred upper memory limit
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getJavaHome
Returns the Java Home folder.- Returns:
- the Java Home folder
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setJavaHome
Set the Java Home folder.- Parameters:
javaHome
- the new Java Home
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getSpectrumAnnotatedPeakColor
Returns the color to use for the annotated peaks.- Returns:
- the spectrumAnnotatedPeakColor
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setSpectrumAnnotatedPeakColor
Set the color to use for the annotated peaks.- Parameters:
spectrumAnnotatedPeakColor
- the spectrumAnnotatedPeakColor to set
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getSpectrumAnnotatedMirroredPeakColor
Returns the color to use for the annotated mirrored peaks.- Returns:
- the spectrumAnnotatedMirroredPeakColor
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setSpectrumAnnotatedMirroredPeakColor
Set the color to use for the annotated mirrored peaks.- Parameters:
spectrumAnnotatedMirroredPeakColor
- the spectrumAnnotatedMirroredPeakColor to set
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getSpectrumBackgroundPeakColor
Returns the color to use for the background peaks.- Returns:
- the spectrumBackgroundPeakColor
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setSpectrumBackgroundPeakColor
Set the color to use for the background peaks.- Parameters:
spectrumBackgroundPeakColor
- the spectrumBackgroundPeakColor to set
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getSpectrumAnnotatedPeakWidth
public float getSpectrumAnnotatedPeakWidth()Returns the width of the annotated peaks.- Returns:
- the spectrumAnnotatedPeakWidth
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setSpectrumAnnotatedPeakWidth
public void setSpectrumAnnotatedPeakWidth(float spectrumAnnotatedPeakWidth)Set the width of the annotated peaks.- Parameters:
spectrumAnnotatedPeakWidth
- the spectrumAnnotatedPeakWidth to set
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getSpectrumBackgroundPeakWidth
public float getSpectrumBackgroundPeakWidth()Returns the width of the background peaks.- Returns:
- the spectrumBackgroundPeakWidth
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setSpectrumBackgroundPeakWidth
public void setSpectrumBackgroundPeakWidth(float spectrumBackgroundPeakWidth)Set the width of the background peaks.- Parameters:
spectrumBackgroundPeakWidth
- the spectrumBackgroundPeakWidth to set
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getSearchGuiPath
Returns the path to the SearchGUI installation.- Returns:
- the path to the SearchGUI installation
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setSearchGuiPath
Set the path to the SearchGUI installation.- Parameters:
searchGuiPath
- the path to the SearchGUI installation
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getDeNovoGuiPath
Returns the path to the DeNovoGUI installation.- Returns:
- the path to the DeNovoGUI installation
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setDeNovoGuiPath
Set the path to the DeNovoGUI installation.- Parameters:
deNovoGuiPath
- the path to the DeNovoGUI installation
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getProteoWizardPath
Returns the path to ProteoWizard.- Returns:
- the path to ProteoWizard
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setProteoWizardPath
Set the path to ProteoWizard.- Parameters:
proteoWizardPath
- the path to ProteoWizard
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getRelimsPath
Returns the path to the Relims installation.- Returns:
- the path to the Relims installation
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setRelimsPath
Set the path to the Relims installation.- Parameters:
relimsPath
- the path to the * installation
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getPeptideShakerPath
Returns the path to the PeptideShaker installation.- Returns:
- the path to the PeptideShaker installation
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setPeptideShakerPath
Set the path to the PeptideShaker installation.- Parameters:
peptideShakerPath
- the path to the PeptideShaker installation
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getReporterPath
Returns the path to the Reporter installation.- Returns:
- the path to the Reporter installation
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setReporterPath
Set the path to the PeptideShaker installation.- Parameters:
reporterPath
- the path to the PeptideShaker installation
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saveUserParameters
Convenience method saving the user parameters. Exceptions are ignored silently and written to the stack trace.- Parameters:
userParameters
- the user preferences
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loadUserParameters
Loads the user parameters. If an error is encountered, parameters are set back to default.- Returns:
- returns the utilities user preferences
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getLocalPrideFolder
Returns the local PRIDE folder.- Returns:
- the localPrideFolder
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setLocalPrideFolder
Set the local PRIDE folder.- Parameters:
localPrideFolder
- the localPrideFolder to set
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getDbFolder
Returns the last used database folder. Null if not set.- Returns:
- the last used database folder
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setDbFolder
Sets the last used database folder.- Parameters:
dbFolder
- the last used database folder
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getSpectrumFolder
Returns the last used spectrum folder. Null if not set.- Returns:
- the last used spectrum folder
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setSpectrumFolder
Sets the last used spectrum folder.- Parameters:
spectrumFolder
- the last used spectrum folder
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getOutputFolder
Returns the last used output folder. Null if not set.- Returns:
- the last used output folder
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setOutputFolder
Sets the last used output folder.- Parameters:
outputFolder
- the last used output folder
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getReadTweets
Returns the list of read tweets.- Returns:
- the list of read tweets
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setReadTweets
Set the list of read tweets.- Parameters:
readTweets
- the readTweets to set
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getDisplayedTips
Returns the list of displayed tips.- Returns:
- the displayed tips
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setDisplayedTips
Set the list of displayed tips.- Parameters:
displayedTips
- the displayedTips to set
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getUserParametersFile
Returns the user preferences file to be used.- Returns:
- the user preferences file
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getUserParametersFolder
Returns the user preferences file to be used.- Returns:
- the user preferences file
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setUserParametersFolder
Sets the user preferences file to be used.- Parameters:
userParametersFolder
- the user preferences file to be used
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isAutoUpdate
public boolean isAutoUpdate()Indicates whether the tools should use the auto update function.- Returns:
- whether the tools should use the auto update function
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setAutoUpdate
Sets whether the tools should use the auto update function.- Parameters:
autoUpdate
- whether the tools should use the auto update function
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getLastSelectedFolder
Returns the last selected folder.- Returns:
- the last selected folder
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setLastSelectedFolder
Sets the last selected folder.- Parameters:
lastSelectedFolder
- the last selected folder
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getSortPsmsOnRt
public boolean getSortPsmsOnRt()Returns true if the PSMs are sorted on retention time, false sorts on PSM score.- Returns:
- the sortPsmsOnRt
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setSortPsmsOnRt
Set if the PSMs are sorted on retention time, false sorts on PSM score.- Parameters:
sortPsmsOnRt
- the sortPsmsOnRt to set
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checkPeakPicking
public boolean checkPeakPicking()Returns if the spectra should be checked for peak picking or not.- Returns:
- true if the spectra should be checked for peak picking
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setCheckPeakPicking
public void setCheckPeakPicking(boolean checkPeakPicking)Set if the spectra should be checked for peak picking or not.- Parameters:
checkPeakPicking
- the checkPeakPicking to set
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checkDuplicateTitles
public boolean checkDuplicateTitles()Returns if the spectra should be checked for duplicate titles or not.- Returns:
- true if the spectra should be checked for duplicate titles
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setCheckDuplicateTitles
public void setCheckDuplicateTitles(boolean checkDuplicateTitles)Set if the spectra should be checked for duplicate titles or not.- Parameters:
checkDuplicateTitles
- the checkDuplicateTitles to set
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checkMgfSize
public boolean checkMgfSize()Returns if the mgf should be checked for size.- Returns:
- true if the mgf should be checked for size
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setCheckMgfSize
public void setCheckMgfSize(boolean checkMgfSize)Set if the mgf should be checked for size.- Parameters:
checkMgfSize
- the mgf should be checked for size
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getMgfMaxSize
public double getMgfMaxSize()Returns the max mgf file size before splitting.- Returns:
- the mgfMaxSize
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setMgfMaxSize
public void setMgfMaxSize(double mgfMaxSize)Set the max mgf file size before splitting.- Parameters:
mgfMaxSize
- the mgfMaxSize to set
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getMgfNSpectra
public int getMgfNSpectra()Get the max number of spectra in an mgf file.- Returns:
- the mgfNSpectra
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setMgfNSpectra
public void setMgfNSpectra(int mgfNSpectra)Set the max number of spectra in an mgf file.- Parameters:
mgfNSpectra
- the mgfNSpectra to set
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getRefMass
public double getRefMass()Returns the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.- Returns:
- the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton
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setRefMass
public void setRefMass(double refMass)Sets the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.- Parameters:
refMass
- the reference mass for the conversion of the fragment ion tolerance from ppm to Dalton
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setSearchGuiOutputParameters
Sets how SearchGUI output files should be organized.- Parameters:
outputOption
- the SearchGUI output option
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getSearchGuiOutputParameters
Returns the selected SearchGUI output option.- Returns:
- the selected SearchGUI output option
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isGzip
public boolean isGzip()Indicates whether identification files should be gzipped.- Returns:
- A boolean indicating whether identification files should be gzipped.
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setGzip
public void setGzip(boolean gzip)Sets whether identification files should be gzipped.- Parameters:
gzip
- A boolean indicating whether identification files should be gzipped.
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outputData
public boolean outputData()Indicates whether data should be copied along with the identification files in the SearchGUI output.- Returns:
- a boolean indicating whether data should be copied along with the identification files in the SearchGUI output
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setOutputData
public void setOutputData(boolean outputData)Sets whether data should be copied along with the identification files in the SearchGUI output.- Parameters:
outputData
- whether data should be copied along with the identification files in the SearchGUI output
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isIncludeDateInOutputName
public boolean isIncludeDateInOutputName()Indicates whether the date should be included in the SearchGUI output name.- Returns:
- a boolean indicating whether the date should be included in the SearchGUI output name
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setIncludeDateInOutputName
public void setIncludeDateInOutputName(boolean includeDateInOutputName)Sets whether the date should be included in the SearchGUI output name.- Parameters:
includeDateInOutputName
- whether the date should be included in the SearchGUI output name
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renameXTandemFile
public boolean renameXTandemFile()Returns true if the X! Tandem file should be renamed.- Returns:
- true if the X! Tandem file should be renamed
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setRenameXTandemFile
public void setRenameXTandemFile(boolean renameXTandemFile)Set if the X! Tandem file should be renamed.- Parameters:
renameXTandemFile
- rename file?
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isCheckSpectrumCharges
public boolean isCheckSpectrumCharges()Returns whether the spectra are to be checked for missing charges.- Returns:
- true, if the spectra are to be checked for missing charges
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setCheckSpectrumCharges
public void setCheckSpectrumCharges(boolean checkSpectrumCharges)Set if the spectra are to be checked for missing charges.- Parameters:
checkSpectrumCharges
- the checkSpectrumCharges to set
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getMinSpectrumChargeRange
public int getMinSpectrumChargeRange()Returns the minimum charge added when the charge is missing for a given spectrum.- Returns:
- the minimum charge added when the charge is missing for a given spectrum
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setMinSpectrumChargeRange
public void setMinSpectrumChargeRange(int minSpectrumChargeRange)Set the minimum charge added when the charge is missing for a given spectrum.- Parameters:
minSpectrumChargeRange
- the minSpectrumChargeRange to set
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getMaxSpectrumChargeRange
public int getMaxSpectrumChargeRange()Returns the maximum charge added when the charge is missing for a given spectrum.- Returns:
- the maximum charge added when the charge is missing for a given spectrum
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setMaxSpectrumChargeRange
public void setMaxSpectrumChargeRange(int maxSpectrumChargeRange)Set the maximum charge added when the charge is missing for a given spectrum.- Parameters:
maxSpectrumChargeRange
- the maxSpectrumChargeRange to set
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getDbSummaryFolder
Returns the folder where FASTA files summary statistics are stored.- Returns:
- the folder where FASTA files summary statistics are stored
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