- cancel() - Method in class peridot.script.ScriptExec
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- cancelInstallations() - Method in class peridot.script.r.InstallationBatch
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- changeLoadingState(String) - Static method in class peridot.Operations
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- checkForSuccess(String) - Method in class peridot.script.Task
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- clean() - Static method in class peridot.Operations
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- cleanLocalResults() - Method in class peridot.script.RModule
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- cleanTempFiles() - Method in class peridot.script.RModule
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- clearEnvironment() - Method in class peridot.script.RModule
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- clearParameters() - Method in class peridot.script.RModule
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- clearResults() - Method in class peridot.script.RModule
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- CmdParseException(String) - Constructor for exception peridot.CLI.Command.CmdParseException
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- Command - Class in peridot.CLI
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Parent class of all R-Peridot commands
- Command(String[]) - Constructor for class peridot.CLI.Command
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- Command.CmdParseException - Exception in peridot.CLI
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- commandArray - Variable in class peridot.script.r.Script
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- commandArray - Variable in class peridot.script.ScriptRunnable
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- commandArrayToCommandString(String[]) - Static method in class peridot.script.r.Script
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- commands - Variable in class peridot.script.r.RInfoParser
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- commandStr - Variable in class peridot.CLI.Command
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- commandString - Variable in class peridot.script.ScriptRunnable
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- compareTo(IndexedString) - Method in class peridot.IndexedString
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- compareTo(VersionNumber) - Method in class peridot.script.r.VersionNumber
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- concluded - Variable in class peridot.script.r.InstallationBatch
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- conditionInputFile - Static variable in class peridot.Archiver.Places
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The file that describes what is the condition of each sample.
- conditionInputFileName - Static variable in class peridot.Archiver.Places
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The name of the file that describes what is the condition of each sample.
- conditions - Variable in class peridot.AnalysisData
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- conditionsFile - Variable in class peridot.AnalysisData
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- conditionsFile - Variable in class peridot.CLI.AnalysisFileParser
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- conditionsStr - Static variable in class peridot.CLI.AnalysisFileParser
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- configFile - Variable in class peridot.script.RModule
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- copyExternalScriptToWorkingDir(String, String) - Method in class peridot.script.RModule
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- correctNoFirstCell(List<String[]>) - Static method in class peridot.Archiver.Spreadsheet
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Assuming that the table has no first cell (line 0, column 0), corrects the first line.
- countLines(String) - Static method in class peridot.Archiver.Manager
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Counts the number of lines in a text file
- countReadsFile - Variable in class peridot.CLI.AnalysisFileParser
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- countReadsInputFile - Static variable in class peridot.Archiver.Places
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The file that stores the count reads for the modules to use.
- countReadsInputFileName - Static variable in class peridot.Archiver.Places
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The name of the file that stores the count reads for the modules to use.
- countReadsThreshold - Variable in class peridot.AnalysisData
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- createClassDescription() - Method in class peridot.script.RModule
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- createConditionsFile(File, SortedMap<IndexedString, String>, boolean, boolean) - Static method in class peridot.AnalysisData
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- createConfig() - Method in class peridot.script.RModule
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- createConfigFile() - Method in class peridot.script.RModule
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- createEnvironment(String) - Method in class peridot.script.RModule
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Cria o diretorio temporario (workingdirectory) onde serĂ£o guardados o script, os resultados e etc.
- createExampleFileFor(File) - Static method in class peridot.CLI.AnalysisFile
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- createExampleOperation - Static variable in class peridot.CLI.Commands.RUN
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- createNecessaryDirs() - Static method in class peridot.Operations
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- createPeridotDir() - Static method in class peridot.Archiver.Places
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Creates peridotDir and finalResultsDir, if they do not yet.
- currentInstallation - Variable in class peridot.script.r.InstallationBatch
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