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G

GeneIdType - Class in peridot
Lists the types of IDs available to be used on GeneOntology
GeneIdType(String) - Constructor for class peridot.GeneIdType
 
get() - Static method in class peridot.Archiver.PeridotConfig
 
getAlreadyInstalled() - Method in class peridot.script.r.InstallationBatch
 
getAlternativeFileName(File) - Static method in class peridot.Archiver.Manager
 
getAnalysisParamsFromMap(Map<String, String>, Map<String, Class>) - Method in class peridot.CLI.AnalysisFileParser
 
getAvailableAnalysisModules() - Static method in class peridot.script.RModule
 
getAvailableInterpreters() - Static method in class peridot.script.r.Interpreter
 
getAvailableModules() - Static method in class peridot.script.RModule
 
getAvailableOrganisms() - Static method in class peridot.Organism
Defines the default list of IDs available
getAvailableParamTypes() - Static method in class peridot.AnalysisParameters
 
getAvailablePostAnalysisModules() - Static method in class peridot.script.RModule
 
getCommandArray(String) - Method in class peridot.script.r.Script
 
getCommands() - Method in class peridot.Output
 
getConditionOf(String) - Method in class peridot.AnalysisData
 
getConditionsFromExpressionFile(File, Spreadsheet.Info) - Static method in class peridot.AnalysisData
 
getConfigFile() - Method in class peridot.script.RModule
 
getConfigPath() - Method in class peridot.script.RModule
 
getConfigs() - Static method in class peridot.Archiver.PeridotConfig
 
getCurrentWorkingDir() - Static method in class peridot.Archiver.Manager
 
getDefaultColumnNames(int) - Static method in class peridot.Archiver.Spreadsheet
 
getDefaultHeader(int) - Static method in class peridot.Archiver.Spreadsheet
 
getDefaultIDTypes() - Static method in class peridot.GeneIdType
Defines the default list of IDs available
getDefaultModulesDir() - Static method in class peridot.Archiver.Places
 
getDefaultParameters() - Static method in class peridot.script.DiffExpressionModule
 
getDefaultParameters() - Static method in class peridot.script.PostAnalysisOntology
 
getDefaultRequiredFiles() - Static method in class peridot.script.DiffExpressionModule
 
getDefaultRequiredFiles() - Static method in class peridot.script.PostAnalysisOntology
 
getDefaultResults() - Static method in class peridot.script.DiffExpressionModule
 
getDefaultResults() - Static method in class peridot.script.PostAnalysisOntology
 
getDefaultRexecs() - Static method in class peridot.Archiver.Places
 
getDefaultValues() - Static method in class peridot.AnalysisParameters
 
getDescriptionFile() - Method in class peridot.script.RModule
 
getFailed() - Method in class peridot.script.r.InstallationBatch
 
getFirstCellPresent() - Method in class peridot.Archiver.Spreadsheet.Info
 
getFirstLinesFromFile(File, int) - Static method in class peridot.Global
 
getFirstRowFromFile(File, String) - Static method in class peridot.Archiver.Spreadsheet
 
getFromQueue() - Method in class peridot.Output
 
getHeaderOnFirstLine() - Method in class peridot.Archiver.Spreadsheet.Info
 
getInfo() - Method in class peridot.Archiver.Spreadsheet
 
getInputFiles() - Method in class peridot.script.RModule
 
getInterpreterNumber() - Static method in class peridot.CLI.PeridotCmd
 
getInterpretersStr() - Static method in class peridot.script.r.Interpreter
 
getJarFolder() - Static method in class peridot.Archiver.Places
 
getLabelsOnFirstCol() - Method in class peridot.Archiver.Spreadsheet.Info
 
getLinuxEnvVars() - Method in class peridot.script.r.Interpreter
 
getLogger() - Static method in class peridot.Log
 
getMandatoryResults() - Static method in class peridot.script.DiffExpressionModule
 
getName() - Method in class peridot.script.ScriptExec
 
getNamesAndConditions() - Method in class peridot.AnalysisData
 
getNaturallyWritenString(String) - Static method in class peridot.Global
Changes a String from programming notation to a more "natural" form.
getNoPermission() - Method in class peridot.script.r.InstallationBatch
 
getNotExistantResults() - Method in class peridot.script.RModule
 
getNumber() - Method in class peridot.IndexedString
 
getNumberOfConditions() - Method in class peridot.AnalysisData
 
getNumberOfGenes() - Method in class peridot.AnalysisData
 
getNumberOfSamples() - Method in class peridot.AnalysisData
 
getOutputStr() - Method in class peridot.script.r.PackageInstaller
 
getOutputStream() - Method in class peridot.script.r.Script
 
getOutputString() - Method in class peridot.script.r.Script
 
getPackage() - Method in class peridot.script.r.PackageInstaller
 
getPackageListStr(Collection<Package>) - Static method in class peridot.CLI.PeridotCmd
 
getPackageName() - Method in class peridot.script.r.PackageInstaller
 
getPackagesToInstall() - Method in class peridot.script.r.Interpreter
 
getParamsDescription() - Method in class peridot.script.RModule
 
getRequiredParametersFromModules() - Static method in class peridot.script.RModule
 
getRequiredParamsFromModules() - Method in class peridot.CLI.AnalysisFileParser
 
getRequiredScripts() - Static method in class peridot.script.PostAnalysisOntology
 
getRows() - Method in class peridot.Archiver.Spreadsheet
 
getRows(int) - Method in class peridot.Archiver.Spreadsheet
 
getRowsFromTable(File, int, String) - Static method in class peridot.Archiver.Spreadsheet
 
getRunningTask() - Static method in class peridot.script.Task
 
getRVersion() - Method in class peridot.script.r.Interpreter
 
getScriptFile() - Method in class peridot.script.RModule
 
getScriptPath() - Method in class peridot.script.RModule
 
getScriptType() - Method in class peridot.script.RModule
 
getSeparator() - Method in class peridot.Archiver.Spreadsheet
 
getSpecification() - Static method in class peridot.CLI.AnalysisFile
 
getSpecificParams() - Method in class peridot.CLI.AnalysisFileParser
 
getSubDirs(File) - Static method in class peridot.Archiver.Manager
Retrieves the subdirectories of a directory
getSuccessful() - Method in class peridot.script.r.InstallationBatch
 
getText() - Method in class peridot.IndexedString
 
getText() - Method in class peridot.Output
 
getUserHomePath() - Static method in class peridot.Archiver.Places
 
getWin64And32ExecsFrom(String) - Static method in class peridot.Archiver.Places
 
getWorkingDirectory() - Method in class peridot.script.RModule
 
getWorkingDirectoryPath() - Method in class peridot.script.RModule
 
Global - Class in peridot
Global general purpose functions.
Global() - Constructor for class peridot.Global
 
Global.RoundingMode - Enum in peridot
 
guessLineSeparator(File) - Static method in class peridot.Archiver.Spreadsheet.Info
 
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