A C D E F G H I L M R S T U V

A

addFolderToPathForJavaSession(File) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem

Add a folder to the path variable for the session, in a few places.

addFolderToPathPermanent(File) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem

Add a folder to the permanent path variable.

C

callExe() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.CommandExecutor

Deprecated.

This method should not be used anymore, developers should instead provide an empty list to execute().

closeGraphicsDevice() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Closes the graphics device, whatever it was.

CommandExecutor - Class in uk.ac.liv.pgb.analytica.lib.wrappedr

Manages execution of an executable/command.

CommandExecutor(File) - Constructor for class uk.ac.liv.pgb.analytica.lib.wrappedr.CommandExecutor

Creates an instance of this class using the given executable/command.

compatibleWith(File) - Method in class uk.ac.liv.pgb.analytica.lib.RTaskWithManifest

Checks whether the given file is compatible with this task.

compatibleWith(File) - Method in class uk.ac.liv.pgb.analytica.lib.RTaskWithoutManifest

Checks whether the given file is compatible with this task.

compatibleWith(File) - Method in interface uk.ac.liv.pgb.analytica.lib.Task

Checks whether the given file is compatible with this task.

convert(File, File) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.converters.MzQuantMLToLFConverter

Conversion the given input file to the given output file.

convert(File, File) - Method in interface uk.ac.liv.pgb.analytica.lib.wrappedr.converters.RDataConverter

Converts an input file to an output file.

D

deleteRecursive(File) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem

Recursively deletes the path represented by the given file..

E

error(String, Exception) - Static method in class uk.ac.liv.pgb.analytica.lib.TaskExecutionResult

Creates an instance of this class denoting an unsuccessful task execution.

error(String, Exception) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.converters.RDataConversionResult

Creates an instance of this class denoting an unsuccessful conversion.

execute(File, GraphicsPolicy) - Method in class uk.ac.liv.pgb.analytica.lib.RTaskWithManifest

Executes this R task with the given file and graphics policy.

execute(File, GraphicsPolicy) - Method in class uk.ac.liv.pgb.analytica.lib.RTaskWithoutManifest

Executes this R task with the given file and graphics policy.

execute(File, GraphicsPolicy) - Method in interface uk.ac.liv.pgb.analytica.lib.Task

Executes this task with the given file and graphics policy.

execute(List<String>) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.CommandExecutor

Executes an executable/command given some arguments.

execute(String) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Execute naked R code.

executeFunction(String, String...) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Executes the given function by name, with the specified arguments.

executeTask(Task, File) - Method in class uk.ac.liv.pgb.analytica.lib.TaskManager

Executes the given task with the given file.

F

FileSystem - Class in uk.ac.liv.pgb.analytica.lib.wrappedr

Utility class to help to find files/executables and to manipulate environments.

FileSystem.SystemType - Enum in uk.ac.liv.pgb.analytica.lib.wrappedr

The system type.

fillFromFile(File) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RManifest

Reads data from an R manifest file into this instance.

findExecutionCommand(String) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem

Finds a executable/command from its name.

findExecutionCommand(String, Iterable<File>) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem

Finds a executable/command from its name, given some location hints.

findFile(String, File) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem

Finds a file from its name in the given directories..

findFile(String, File, boolean, boolean) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem

Finds a file from its name in the given directories..

findTask(String) - Method in class uk.ac.liv.pgb.analytica.lib.TaskManager

Finds a task given the name.

G

getConverters() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RDataTransformations

Gets the collection of available transformations/converters.

getError() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.CommandExecutor

Gets the standard error reported by the executable/command.

getErrorMessage() - Method in class uk.ac.liv.pgb.analytica.lib.TaskExecutionResult

Gets the error message, if any.

getErrorMessage() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.converters.RDataConversionResult

Gets the error message in this result, if any.

getException() - Method in class uk.ac.liv.pgb.analytica.lib.TaskExecutionResult

Gets the exception contained in this result, if any.

getException() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.converters.RDataConversionResult

Gets the exception in this result, if any.

getFunctionName() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RManifest

Gets the task's function name.

getInstance() - Static method in class uk.ac.liv.pgb.analytica.lib.TaskManager

Gets the singleton instance of this class.

getInstance() - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.converters.MzQuantMLToLFConverter

Get the singleton instance of this class.

getInstance() - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RDataTransformations

Gets the singleton instance of this class.

getInstance() - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Gets the singleton instance of this class.

getInstance() - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RSourceScanner

Gets the singleton instance of this class.

getManifest() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RSourceFile

Get the manifest file.

getName() - Method in class uk.ac.liv.pgb.analytica.lib.RTaskWithManifest

Gets the name of associated with this task.

getName() - Method in class uk.ac.liv.pgb.analytica.lib.RTaskWithoutManifest

Gets the name of associated with this task.

getName() - Method in interface uk.ac.liv.pgb.analytica.lib.Task

Get the name of the task.

getOutput() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.CommandExecutor

Gets the standard output reported by the command/executable.

getOutputFilePrefix() - Method in class uk.ac.liv.pgb.analytica.lib.GraphicsPolicy

Gets the output file prefix.

getScannedFiles() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RSourceScanner

Gets the R source files, with any manifests, that have been successfully scanned.

getSourceFile() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RSourceFile

Get the R source file.

getState() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Gets the current state of this runtime.

getSuccessMessage() - Method in class uk.ac.liv.pgb.analytica.lib.TaskExecutionResult

Gets the success message in this result, if any.

getSuccessMessage() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.converters.RDataConversionResult

Gets the success message in this result, if any.

getSupportedInputs() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.converters.MzQuantMLToLFConverter

Get the supported input formats for this converter.

getSupportedInputs() - Method in interface uk.ac.liv.pgb.analytica.lib.wrappedr.converters.RDataConverter

Gets the supported inputs.

getSupportedOutput() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.converters.MzQuantMLToLFConverter

Get the supported output format for this converter.

getSupportedOutput() - Method in interface uk.ac.liv.pgb.analytica.lib.wrappedr.converters.RDataConverter

Gets the supported output.

getSystemType() - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem

Gets the system type.

getTaskDependencies() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RManifest

Gets the task's package dependencies.

getTaskDescription() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RManifest

Gets the description of the task.

getTaskName() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RManifest

Gets the name of the task.

getTaskPrettyName() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RManifest

Gets the pretty name of the task.

getTaskSupportedFormats() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RManifest

Gets the task's supported input formats.

GraphicsPolicy - Class in uk.ac.liv.pgb.analytica.lib

Manages the manner in which graphics output is processed.

GraphicsPolicy() - Constructor for class uk.ac.liv.pgb.analytica.lib.GraphicsPolicy

H

hasManifest() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RSourceFile

Check whether this instance has a manifest file.

I

isAvailable() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Checks whether the R engine is available for use.

isToFileDevice() - Method in class uk.ac.liv.pgb.analytica.lib.GraphicsPolicy

Checks whether the graphics output goes to a file or not.

L

loadFileGraphicsDevice(File) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Loads the file graphics device, as a PNG in the specified file.

loadJavaGraphicsDevice() - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Loads the java graphics device.

loadPackageDependency(String) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Install and load a package.

M

MzQuantMLToLFConverter - Class in uk.ac.liv.pgb.analytica.lib.wrappedr.converters

Converts from mzQuantML to LF (label free) format.

R

rBusy(Rengine, int) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Indicate that the engine has changed its busy state.

rChooseFile(Rengine, int) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Choose file for use in console.

RDataConversionResult - Class in uk.ac.liv.pgb.analytica.lib.wrappedr.converters

RDataConverter - Interface in uk.ac.liv.pgb.analytica.lib.wrappedr.converters

Represents actions that an R data converter must support.

RDataTransformations - Class in uk.ac.liv.pgb.analytica.lib.wrappedr

Describes the supported R data transformations/converters.

registerGraphicsPolicy(GraphicsPolicy) - Method in class uk.ac.liv.pgb.analytica.lib.TaskManager

Registers the given graphics policy with this class.

rFlushConsole(Rengine) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Flush any buffered output.

rLoadHistory(Rengine, String) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Load the history from file.

RManifest - Class in uk.ac.liv.pgb.analytica.lib.wrappedr

Describes the information contained in an R manifest file.

RManifest() - Constructor for class uk.ac.liv.pgb.analytica.lib.wrappedr.RManifest

rReadConsole(Rengine, String, int) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Read text into the console.

RRuntime - Class in uk.ac.liv.pgb.analytica.lib.wrappedr

Manages the interaction with the R runtime itself.

RRuntime.RRuntimeState - Enum in uk.ac.liv.pgb.analytica.lib.wrappedr

The possible states of the runtime.

rSaveHistory(Rengine, String) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Save the history to file.

rShowMessage(Rengine, String) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Show warning/error text.

RSourceFile - Class in uk.ac.liv.pgb.analytica.lib.wrappedr

Describes an R source file, and manifest file if available.

RSourceFile() - Constructor for class uk.ac.liv.pgb.analytica.lib.wrappedr.RSourceFile

RSourceScanner - Class in uk.ac.liv.pgb.analytica.lib.wrappedr

Manages the R source file and manifest files, both bundled and user provided.

RTaskWithManifest - Class in uk.ac.liv.pgb.analytica.lib

Wraps a piece of R code that has a manifest describing what to do with it.

RTaskWithManifest(RSourceFile) - Constructor for class uk.ac.liv.pgb.analytica.lib.RTaskWithManifest

Creates an instance of the class with the given R source object.

RTaskWithoutManifest - Class in uk.ac.liv.pgb.analytica.lib

Wraps a piece of R code that does not have a manifest describing what to do with it.

RTaskWithoutManifest() - Constructor for class uk.ac.liv.pgb.analytica.lib.RTaskWithoutManifest

rWriteConsole(Rengine, String, int) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Write text to the console.

S

setEnvironmentVariableForJavaSession(String, String) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem

Set an environment variable for the session.

setEnvironmentVariablePermanent(String, String) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem

Set an environment variable permanently.

setManifest(RManifest) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RSourceFile

Set the manifest file.

setOutputFilePrefix(String) - Method in class uk.ac.liv.pgb.analytica.lib.GraphicsPolicy

Sets the output file prefix.

setSourceFile(File) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RSourceFile

Set the R source file.

setToFileDevice(boolean) - Method in class uk.ac.liv.pgb.analytica.lib.GraphicsPolicy

Sets whether the graphics output goes to a file or not.

source(File) - Method in class uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime

Reads and evaluates an R source file.

success(String) - Static method in class uk.ac.liv.pgb.analytica.lib.TaskExecutionResult

Creates an instance of this class denoting a successful task execution.

success(String) - Static method in class uk.ac.liv.pgb.analytica.lib.wrappedr.converters.RDataConversionResult

Creates an instance of this class denoting a successful conversion.

T

Task - Interface in uk.ac.liv.pgb.analytica.lib

Represents actions that a task, of any type, must support.

TaskExecutionResult - Class in uk.ac.liv.pgb.analytica.lib

Describes the result of a task.

TaskManager - Class in uk.ac.liv.pgb.analytica.lib

Manages all available tasks.

U

uk.ac.liv.pgb.analytica.lib - package uk.ac.liv.pgb.analytica.lib

uk.ac.liv.pgb.analytica.lib.wrappedr - package uk.ac.liv.pgb.analytica.lib.wrappedr

uk.ac.liv.pgb.analytica.lib.wrappedr.converters - package uk.ac.liv.pgb.analytica.lib.wrappedr.converters

V

valueOf(String) - Static method in enum uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem.SystemType

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime.RRuntimeState

Returns the enum constant of this type with the specified name.

values() - Static method in enum uk.ac.liv.pgb.analytica.lib.wrappedr.FileSystem.SystemType

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum uk.ac.liv.pgb.analytica.lib.wrappedr.RRuntime.RRuntimeState

Returns an array containing the constants of this enum type, in the order they are declared.

A C D E F G H I L M R S T U V