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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
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