Skip navigation links
A B C D E F G H I J K L M N O P Q R S T U V W Z _ 

S

sameName(Package) - Method in class peridot.script.r.Package
 
save() - Static method in class peridot.Archiver.PeridotConfig
 
saveAtStr - Static variable in class peridot.CLI.AnalysisFileParser
 
saveFolder - Variable in class peridot.CLI.AnalysisFileParser
 
saveObjectAsBin(File, Object) - Static method in class peridot.Archiver.Persistence
Save an Object as a binary file
saveResults() - Method in class peridot.script.RModule
 
saveResultsAt(File) - Static method in class peridot.Operations
 
saveResultsAt(String) - Method in class peridot.script.RModule
 
savingFlag - Variable in class peridot.script.ScriptExec
 
script - Variable in class peridot.script.r.PackageInstaller
 
Script - Class in peridot.script.r
 
Script(File) - Constructor for class peridot.script.r.Script
 
Script(File, String[], boolean) - Constructor for class peridot.script.r.Script
 
script - Variable in class peridot.script.ScriptExec
 
scriptContent - Variable in class peridot.script.RModule
 
scriptDetails(String) - Static method in class peridot.CLI.PeridotCmd
 
ScriptExec - Class in peridot.script
 
ScriptExec(RModule, Output, Task, Interpreter) - Constructor for class peridot.script.ScriptExec
 
scriptExecs - Variable in class peridot.script.Task
 
scriptFile - Variable in class peridot.script.r.Script
 
scriptFile - Variable in class peridot.script.RModule
 
scriptName - Variable in class peridot.script.RModule
 
scriptOutputs - Variable in class peridot.script.Task
 
ScriptRunnable - Class in peridot.script
 
ScriptRunnable(ScriptExec) - Constructor for class peridot.script.ScriptRunnable
 
scriptsStatusWatcher - Variable in class peridot.script.Task
 
scriptsToExec - Variable in class peridot.CLI.AnalysisFile
 
scriptThread - Variable in class peridot.script.ScriptExec
 
separator - Variable in class peridot.Archiver.Spreadsheet.Info
Cell separator char
separatorChar - Variable in class peridot.CLI.AnalysisFileParser
 
sepStr - Static variable in class peridot.CLI.AnalysisFileParser
 
setConditionOf(String, String) - Method in class peridot.AnalysisData
 
setConditions(SortedMap<IndexedString, String>) - Method in class peridot.AnalysisData
 
setConditionsFile(File) - Method in class peridot.AnalysisData
 
setCountReadsFile(File) - Method in class peridot.AnalysisData
 
setDefault(int) - Static method in class peridot.script.r.Interpreter
 
setDefaultInterpreter() - Static method in class peridot.CLI.PeridotCmd
 
setExpression() - Method in class peridot.CLI.AnalysisFileParser
 
setFirstCellPresent(boolean) - Method in class peridot.Archiver.Spreadsheet.Info
 
setHeaderOnFirstLine(boolean) - Method in class peridot.Archiver.Spreadsheet.Info
 
setIndex(int) - Method in class peridot.IndexedString
 
setInfo(Spreadsheet.Info) - Method in class peridot.Archiver.Spreadsheet
 
setInfo(String) - Method in class peridot.script.RModule
 
setLabelsOnFirstCol(boolean) - Method in class peridot.Archiver.Spreadsheet.Info
 
setModules() - Method in class peridot.CLI.AnalysisFileParser
 
setResultAsMandatory(String) - Method in class peridot.script.RModule
 
setSeparator(String) - Method in class peridot.Archiver.Spreadsheet
 
setText(String) - Method in class peridot.Output
 
setTimeout(Runnable, int) - Static method in class peridot.Global
Run's a Runnable after a certain time delay.
speciesName - Variable in class peridot.Organism
 
specification - Static variable in class peridot.CLI.Commands.RUN
 
specificParams - Variable in class peridot.CLI.AnalysisFile
 
specificParams - Variable in class peridot.CLI.AnalysisFileParser
 
specificParams - Variable in class peridot.script.Task
 
specifyOperation - Static variable in class peridot.CLI.Commands.RUN
 
spliceBySpacesAndTabs(String) - Static method in class peridot.Global
 
split(String, String) - Static method in class peridot.Global
Splits a line with tabulation.
Spreadsheet - Class in peridot.Archiver
Collection of utilities to handle spreadsheet-like files, .csv or .tsv.
Spreadsheet(File) - Constructor for class peridot.Archiver.Spreadsheet
 
Spreadsheet(File, Spreadsheet.Info) - Constructor for class peridot.Archiver.Spreadsheet
 
Spreadsheet.Info - Class in peridot.Archiver
Meta-information about a spreadsheet file.
start(AnalysisFile) - Static method in class peridot.Operations
 
start(Set<String>, AnalysisParameters, Map<String, AnalysisParameters>, AnalysisData) - Static method in class peridot.Operations
 
start() - Method in class peridot.script.ScriptExec
 
start() - Method in class peridot.script.Task
 
started - Variable in class peridot.script.ScriptExec
 
startInstallations() - Method in class peridot.script.r.InstallationBatch
 
startsWithQuotes(String) - Static method in class peridot.Global
 
status - Variable in class peridot.script.r.InstallationBatch
 
Status() - Constructor for enum peridot.script.r.InstallationBatch.Status
 
status - Variable in class peridot.script.r.PackageInstaller
 
Status() - Constructor for enum peridot.script.r.PackageInstaller.Status
 
statusWatcher - Variable in class peridot.script.Task
 
stop() - Method in class peridot.script.r.InstallationBatch
 
stop() - Method in class peridot.script.r.PackageInstaller
 
stopFlag - Variable in class peridot.script.r.InstallationBatch
 
stopListeningFlag - Variable in class peridot.script.r.Script
 
storeTimeOfUpdate() - Method in class peridot.Output
 
stringIsLettersAndDigits(String) - Static method in class peridot.Global
 
stringToFile(String, String) - Static method in class peridot.Archiver.Manager
 
successFlag - Variable in class peridot.script.ScriptExec
 
successfulScripts - Variable in class peridot.script.Task
 
A B C D E F G H I J K L M N O P Q R S T U V W Z _ 
Skip navigation links