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A

abort() - Method in class peridot.script.ScriptExec
 
abortAll() - Method in class peridot.script.Task
 
abortAllFlag - Variable in class peridot.script.Task
 
addFinished(String, boolean) - Method in class peridot.script.Task
 
addInterpreter(String) - Static method in class peridot.CLI.PeridotCmd
 
addInterpreter(String) - Static method in class peridot.script.r.Interpreter
 
addToQueue(PackageInstaller) - Method in class peridot.script.r.InstallationBatch
 
afterEnd() - Method in class peridot.script.r.Script
 
afterStart(boolean) - Method in class peridot.script.r.Script
 
afterStart() - Method in class peridot.script.ScriptExec
 
allInfo - Variable in class peridot.CLI.AnalysisFile
 
allInfo - Variable in class peridot.CLI.AnalysisFileParser
 
allInfoSet() - Method in class peridot.Archiver.Spreadsheet.Info
 
analyseInterpreter() - Method in class peridot.script.r.Interpreter
 
AnalysisData - Class in peridot
Manages the count reads file and all the meta-information about it.
AnalysisData(File, File, Spreadsheet.Info, String, int) - Constructor for class peridot.AnalysisData
 
AnalysisData(File, SortedMap<IndexedString, String>, Spreadsheet.Info, String, int) - Constructor for class peridot.AnalysisData
 
AnalysisFile - Class in peridot.CLI
A file with all the definitions necessary to do an analysis.
AnalysisFile(File) - Constructor for class peridot.CLI.AnalysisFile
 
AnalysisFile() - Constructor for class peridot.CLI.AnalysisFile
 
analysisFile - Variable in class peridot.CLI.AnalysisFileParser
 
AnalysisFileParser - Class in peridot.CLI
Parses an AnalysisFile file to the AnalysisFile object.
AnalysisFileParser(File) - Constructor for class peridot.CLI.AnalysisFileParser
 
AnalysisFileParser.ParseException - Exception in peridot.CLI
 
AnalysisModule - Class in peridot.script
 
AnalysisModule(String, String, Map<String, Class>, Set<String>, Set<String>) - Constructor for class peridot.script.AnalysisModule
 
AnalysisModule(File) - Constructor for class peridot.script.AnalysisModule
 
AnalysisParameters - Class in peridot
The parameters necessary for an analysis.
AnalysisParameters() - Constructor for class peridot.AnalysisParameters
Creates an empty AnalysisParameters
AnalysisParameters(Map<String, Class>) - Constructor for class peridot.AnalysisParameters
Creates AnalysisParameters defining the required parameters.
AnalysisParameters(Map<String, Class>, Map<String, Object>) - Constructor for class peridot.AnalysisParameters
Creates a ready AnalysisParameters, with both definition of required parameters and parameters.
appendChar(char) - Method in class peridot.Output
 
appendLine(String) - Method in class peridot.Output
 
applyConditionsToExprFileSamples(File, Spreadsheet.Info, SortedMap<IndexedString, String>) - Static method in class peridot.AnalysisData
 
args - Variable in class peridot.CLI.Command
 
askToUpdateInterpreter(int) - Static method in class peridot.CLI.PeridotCmd
 
availableInterpreters - Variable in class peridot.Archiver.PeridotConfig
 
availableModules - Static variable in class peridot.script.RModule
 
availablePackages - Variable in class peridot.script.r.Interpreter
 
availableParamTypes - Static variable in class peridot.AnalysisParameters
 
availableParamTypes - Static variable in class peridot.script.RModule
 
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