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 _ 

C

cancel() - Method in class peridot.script.ScriptExec
 
cancelInstallations() - Method in class peridot.script.r.InstallationBatch
 
changeLoadingState(String) - Static method in class peridot.Operations
 
checkForSuccess(String) - Method in class peridot.script.Task
 
clean() - Static method in class peridot.Operations
 
cleanLocalResults() - Method in class peridot.script.RModule
 
cleanTempFiles() - Method in class peridot.script.RModule
 
clearEnvironment() - Method in class peridot.script.RModule
 
clearParameters() - Method in class peridot.script.RModule
 
clearResults() - Method in class peridot.script.RModule
 
CmdParseException(String) - Constructor for exception peridot.CLI.Command.CmdParseException
 
Command - Class in peridot.CLI
Parent class of all R-Peridot commands
Command(String[]) - Constructor for class peridot.CLI.Command
 
Command.CmdParseException - Exception in peridot.CLI
 
commandArray - Variable in class peridot.script.r.Script
 
commandArray - Variable in class peridot.script.ScriptRunnable
 
commandArrayToCommandString(String[]) - Static method in class peridot.script.r.Script
 
commands - Variable in class peridot.script.r.RInfoParser
 
commandStr - Variable in class peridot.CLI.Command
 
commandString - Variable in class peridot.script.ScriptRunnable
 
compareTo(IndexedString) - Method in class peridot.IndexedString
 
compareTo(VersionNumber) - Method in class peridot.script.r.VersionNumber
 
concluded - Variable in class peridot.script.r.InstallationBatch
 
conditionInputFile - Static variable in class peridot.Archiver.Places
The file that describes what is the condition of each sample.
conditionInputFileName - Static variable in class peridot.Archiver.Places
The name of the file that describes what is the condition of each sample.
conditions - Variable in class peridot.AnalysisData
 
conditionsFile - Variable in class peridot.AnalysisData
 
conditionsFile - Variable in class peridot.CLI.AnalysisFileParser
 
conditionsStr - Static variable in class peridot.CLI.AnalysisFileParser
 
configFile - Variable in class peridot.script.RModule
 
copyExternalScriptToWorkingDir(String, String) - Method in class peridot.script.RModule
 
correctNoFirstCell(List<String[]>) - Static method in class peridot.Archiver.Spreadsheet
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
Counts the number of lines in a text file
countReadsFile - Variable in class peridot.CLI.AnalysisFileParser
 
countReadsInputFile - Static variable in class peridot.Archiver.Places
The file that stores the count reads for the modules to use.
countReadsInputFileName - Static variable in class peridot.Archiver.Places
The name of the file that stores the count reads for the modules to use.
countReadsThreshold - Variable in class peridot.AnalysisData
 
createClassDescription() - Method in class peridot.script.RModule
 
createConditionsFile(File, SortedMap<IndexedString, String>, boolean, boolean) - Static method in class peridot.AnalysisData
 
createConfig() - Method in class peridot.script.RModule
 
createConfigFile() - Method in class peridot.script.RModule
 
createEnvironment(String) - Method in class peridot.script.RModule
Cria o diretorio temporario (workingdirectory) onde serĂ£o guardados o script, os resultados e etc.
createExampleFileFor(File) - Static method in class peridot.CLI.AnalysisFile
 
createExampleOperation - Static variable in class peridot.CLI.Commands.RUN
 
createNecessaryDirs() - Static method in class peridot.Operations
 
createPeridotDir() - Static method in class peridot.Archiver.Places
Creates peridotDir and finalResultsDir, if they do not yet.
currentInstallation - Variable in class peridot.script.r.InstallationBatch
 
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