Index (anchor-launcher 1.1.1 API)

A C D E G H I L M N O P R S T U V
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

addAdditionalOptions(Options) - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Adds additional options to the command-line parser.
addAdditionalOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions: Adds additional options to the Options object.
addBasicOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions: Adds basic options to the Options object.
addFrom(CommandLineExtracter, InputArguments) - Static method in class org.anchoranalysis.launcher.options.process.AddInputOptions: Adds options to change the inputs from the command-line.
addFrom(CommandLineExtracter, OutputArguments) - Static method in class org.anchoranalysis.launcher.options.process.AddOutputOptions: Adds options to add/remove change the outputs the inputs from the command-line.
addInputOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions: Adds input-related options to the Options object.
AddInputOptions - Class in org.anchoranalysis.launcher.options.process: Adds options relating to inputting from the command-line.
addOptionsFromCommandLine() - Method in class org.anchoranalysis.launcher.options.process.AddInputOptions
addOptionsFromCommandLine() - Method in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Maybe add options to the arguments from the command-line.
addOptionsFromCommandLine() - Method in class org.anchoranalysis.launcher.options.process.AddOutputOptions
AddOptionsFromCommandLine<T> - Class in org.anchoranalysis.launcher.options.process: Base class for adding options from command-line arguments.
AddOptionsFromCommandLine(CommandLineExtracter, T) - Constructor for class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Creates a new AddOptionsFromCommandLine instance.
AddOutputOptions - Class in org.anchoranalysis.launcher.options.process: Adds options relating to outputting from the command-line.
AnchorWebsiteLinks - Class in org.anchoranalysis.launcher: A centralized location for hyperlinks to the Anchor website.
ArgumentConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path.convert: Converts string passed as arguments.
associated - Variable in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: An associated entity which consumers accept.

C

classInCurrentJar() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Provides a class which is used to determine the base location for LauncherConfig.pathRelativeProperties().
CommandLineException - Exception Class in org.anchoranalysis.launcher: An exception thrown at run-time while processing command-line arguments.
CommandLineException(String) - Constructor for exception class org.anchoranalysis.launcher.CommandLineException: Constructs a new CommandLineException with the specified detail message.
CommandLineExtracter - Class in org.anchoranalysis.launcher.options: Adds methods to CommandLine for querying and extracting options, with and without arguments.
CommandLineExtracter(CommandLine) - Constructor for class org.anchoranalysis.launcher.options.CommandLineExtracter: Creates a new CommandLineExtracter instance.
CommandLineOptions - Class in org.anchoranalysis.launcher.options: All command-line options used by the launcher.
create(CommandLine, Path, Path) - Static method in class org.anchoranalysis.launcher.executor.ExperimentExecutorFactory: Creates an experiment-executor from a command line that EITHER: uses a default-experiment OR accepts a path passed as the first command-line argument.
createArguments(CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Creates execution arguments from the command line.
createExperimentExecutor(CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Creates an experiment executor from the command line.
customizeExperimentExecutor(ExperimentExecutor, CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Customizes the experiment executor with additional configuration.

D

defaultExperimentOrCustom(CommandLine, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.experiment.ExperimentFactory: Chooses either a path to the default-experiment or a path to a custom experiment.
describe() - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam: Provides a string that can be displayed to the user to describe this particular SelectParam.
describe() - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
doJobOnInput(InputBound<S, NoSharedState>) - Method in class org.anchoranalysis.launcher.run.tasks.HelloWorld

E

equals(Object) - Method in class org.anchoranalysis.launcher.config.HelpConfig
executeExperiment(ExecutionArguments, boolean, Logger) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: Executes an experiment after finding a single experiment XML file, and reading the experiment from this file.
ExperimentExecutor - Class in org.anchoranalysis.launcher.executor: Runs a particular experiment after identifying necessary paths and input files.
ExperimentExecutorFactory - Class in org.anchoranalysis.launcher.executor: Creates an ExperimentExecutor.
ExperimentFactory - Class in org.anchoranalysis.launcher.executor.selectparam.experiment: SelectParam<Path> factory for experiments.
experimentSelectParam(CommandLine, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Creates a SelectParam for experiment selection.

G

getCommandName() - Method in class org.anchoranalysis.launcher.config.HelpConfig: The application command as described in the help message.
getFirstArgument() - Method in class org.anchoranalysis.launcher.config.HelpConfig: The application's first argument as described in the help message.
getInput() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The input selection parameter.
getOutput() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The output selection parameter.
getTask() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The task selection parameter.

H

hashCode() - Method in class org.anchoranalysis.launcher.config.HelpConfig
hasOption(String) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter: Identical to CommandLine.hasOption(java.lang.String).
hasOptionWithoutArgument(String) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter: Checks if an option exists, but without any argument(s) specified.
hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.launcher.run.tasks.HelloWorld
HelloWorld<S> - Class in org.anchoranalysis.launcher.run.tasks: A dummy task that simply writes a message to all log files, specifically: 1.
HelloWorld() - Constructor for class org.anchoranalysis.launcher.run.tasks.HelloWorld
help() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
HelpConfig - Class in org.anchoranalysis.launcher.config: Configuration for help messages in the launcher.
HelpConfig(String, String) - Constructor for class org.anchoranalysis.launcher.config.HelpConfig: Creates a new HelpConfig instance.

I

ifOptionWithoutArgument(String, Consumer<T>) - Method in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Executes consumer if an option exists without any argument.
ifPresentMultiple(String, CheckedConsumer<String[], ExperimentExecutionException>) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter: Executes a Consumer if an option is present - allowing that option to occur multiple times.
ifPresentMultiple(String, CheckedConsumer<String[], ExperimentExecutionException>) - Method in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Executes consumer if one or more options exists with a single argument.
ifPresentSingle(String, CheckedConsumer<String, ExperimentExecutionException>) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter: Executes a Consumer if an option is present - allowing that option to occur only once.
ifPresentSingle(String, CheckedConsumer<String, ExperimentExecutionException>) - Method in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Executes consumer if maximally one option exists with a single argument - without passing associated.
ifPresentSingleAssociated(String, CheckedBiConsumer<T, String, ExperimentExecutionException>) - Method in class org.anchoranalysis.launcher.options.process.AddOptionsFromCommandLine: Executes consumer if maximally one option exists with a single argument - passing associated.
InputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path: SelectParam<Path> factory for inputs.
inputSelectParam(CommandLine) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Creates a SelectParam for input selection.
inputTypesExpected() - Method in class org.anchoranalysis.launcher.run.tasks.HelloWorld
InvalidPathArgumentException - Exception Class in org.anchoranalysis.launcher.executor.selectparam.path.convert: An exception thrown if an invalid path is inputted as an argument.
InvalidPathArgumentException(String) - Constructor for exception class org.anchoranalysis.launcher.executor.selectparam.path.convert.InvalidPathArgumentException: Creates an exception with a custom message.
InvalidPathArgumentException(String, InvalidPathException) - Constructor for exception class org.anchoranalysis.launcher.executor.selectparam.path.convert.InvalidPathArgumentException: Creates an exception for an invalid path argument.
isDefault() - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam: Checks if this is the default option that occurs without any additional user effort.
isDefault() - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
isOpenInDesktop() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: Whether to open the output directory in the desktop GUI after execution (if supported on the O/S).

L

Launch - Class in org.anchoranalysis.launcher: A command-line interface used for launching experiments.
LauncherConfig - Class in org.anchoranalysis.launcher.config: Specifies a configuration of the launcher for a particular application.
LauncherConfig() - Constructor for class org.anchoranalysis.launcher.config.LauncherConfig
LONG_OPTION_GROUP - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Activates grouping from a subset of the identifier's elements.
LONG_OPTION_INPUT_RANDOM_SAMPLE - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Randomly samples a number of inputs.
LONG_OPTION_OUTPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Changes output manager.
LONG_OPTION_OUTPUT_CONSOLE_ONLY - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Output console only.

M

main(String[]) - Static method in class org.anchoranalysis.launcher.Launch: Entry point for command-line application.

N

newlinesBeforeError() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Determines if extra newlines should be inserted before error messages.

O

org.anchoranalysis.launcher - package org.anchoranalysis.launcher: Parent package and entry-point classes for the Anchor command-line launcher application.
org.anchoranalysis.launcher.config - package org.anchoranalysis.launcher.config: Specifies a configuration of the launcher for a particular application.
org.anchoranalysis.launcher.executor - package org.anchoranalysis.launcher.executor: Runs a particular experiment after identifying necessary paths and input files.
org.anchoranalysis.launcher.executor.selectparam - package org.anchoranalysis.launcher.executor.selectparam: Different methods of selecting a object T that is used as a parameter for an experiment.
org.anchoranalysis.launcher.executor.selectparam.experiment - package org.anchoranalysis.launcher.executor.selectparam.experiment: SelectParams for loading a Experiment.
org.anchoranalysis.launcher.executor.selectparam.path - package org.anchoranalysis.launcher.executor.selectparam.path: SelectParams for loading a Optional<Path> for inputs, outputs or tasks.
org.anchoranalysis.launcher.executor.selectparam.path.convert - package org.anchoranalysis.launcher.executor.selectparam.path.convert: Converting paths to/from different formats as needed by org.anchoranalysis.launcher.executor.selectparam.path.
org.anchoranalysis.launcher.options - package org.anchoranalysis.launcher.options: A centralized location for all command-line options used by the launcher.
org.anchoranalysis.launcher.options.process - package org.anchoranalysis.launcher.options.process: Adding/removing/changing the arguments (input and output) from the experiment via command-line-options.
org.anchoranalysis.launcher.resources - package org.anchoranalysis.launcher.resources: Reading and integrating resources for the launcher.
org.anchoranalysis.launcher.run - package org.anchoranalysis.launcher.run: Parses command-line arguments and runs an experiment.
org.anchoranalysis.launcher.run.tasks - package org.anchoranalysis.launcher.run.tasks: Loading and displaying pre-defined tasks.
OutputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path: SelectParam<Path> factory for outputs.
outputSelectParam(CommandLine) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Creates a SelectParam for output selection.

P

parseAndRun(String[], LauncherConfig) - Method in class org.anchoranalysis.launcher.run.ParseArgumentsAndRunExperiment: Parses the arguments to a command-line experiment and runs an experiment.
ParseArgumentsAndRunExperiment - Class in org.anchoranalysis.launcher.run: Parses command-line arguments and runs an experiment.
ParseArgumentsAndRunExperiment(Logger) - Constructor for class org.anchoranalysis.launcher.run.ParseArgumentsAndRunExperiment: Creates a new ParseArgumentsAndRunExperiment instance.
pathFromArgument(String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.convert.ArgumentConverter: Converts the string passed as a command-line argument to a path.
pathOrDirectory(String[], boolean) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.OutputFactory: Creates a SelectParam for output paths or directories.
pathOrDirectoryOrGlobOrExtension(String[]) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.InputFactory: Creates a SelectParam for path, directory, glob, or file extension inputs.
pathOrTaskName(String[], Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.TaskFactory: Creates a SelectParam for a path or task name.
pathOrTaskNameOrDefault(CommandLine, String, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Creates a SelectParam for a path, task name, or default.
pathRelativeProperties() - Method in class org.anchoranalysis.launcher.config.LauncherConfig: Provides the path to a property file that defines a relative-path to the default experiment in bean XML.
PredefinedTasks - Class in org.anchoranalysis.launcher.run.tasks: Loading and printing predefined-tasks.
prettyPath(String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.convert.PrettyPathConverter: Converts a string path to either a normalized absolute-path or relative-path depending on which is prettier to the user.
prettyPath(Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.convert.PrettyPathConverter: Converts a Path to either a normalized absolute-path or relative-path depending on which is prettier to the user.
PrettyPathConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path.convert: Utility class for converting paths to a more user-friendly representation.
printTasksToConsole(Path, Resources, PrintStream) - Static method in class org.anchoranalysis.launcher.run.tasks.PredefinedTasks: Prints names of the predefined tasks that are available to the application.

R

resources() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
Resources - Class in org.anchoranalysis.launcher.resources: Accesses resource-files associated with this application.
Resources(ClassLoader, String, String, String, String, Optional<String>) - Constructor for class org.anchoranalysis.launcher.resources.Resources: Creates a new Resources instance.
runCommandLineApplication(String[], LauncherConfig, Logger) - Static method in class org.anchoranalysis.launcher.Launch: Runs a command-line application, by parsing arguments, and then executing an experiment.

S

select(ExecutionArguments) - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam: Retrieves the parameter.
select(ExecutionArguments) - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
SelectParam<T> - Interface in org.anchoranalysis.launcher.executor.selectparam: Different methods of selecting an object T that is used as a parameter for an experiment.
SelectParamFactory - Class in org.anchoranalysis.launcher.executor.selectparam: Creates an appropriate SelectParam based upon the options passed to the command-line.
setDefaultBehaviourString(Optional<String>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: If present, a string is printed in the description if the default-experiment is used, otherwise ignored.
setInput(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The input selection parameter.
setOpenInDesktop(boolean) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: Whether to open the output directory in the desktop GUI after execution (if supported on the O/S).
setOutput(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The output selection parameter.
setTask(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: The task selection parameter.
SHORT_OPTION_DEBUG - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Enables debug-mode: runs only the first available input [whose name contains string].
SHORT_OPTION_GROUP - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Activates grouping from a subset of the identifier's elements.
SHORT_OPTION_HELP - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Displays help message with all command-line options.
SHORT_OPTION_INPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Changes inputs.
SHORT_OPTION_INPUT_COPY_NON_INPUTS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Additionally copies any files in the input directory, unused as inputs.
SHORT_OPTION_INPUT_LIMIT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Imposes an upper limit on the number of inputs.
SHORT_OPTION_INPUT_RANDOM_SAMPLE - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Randomly samples a number of inputs.
SHORT_OPTION_INPUT_RELATIVE_PATH - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Derives the unique identifier from the **entire relative filename or path** (excluding file extension).
SHORT_OPTION_INPUT_SHUFFLE - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Shuffles the order of the inputs.
SHORT_OPTION_INPUT_SUBSET_IDENTIFIER - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Subsets the identifier.
SHORT_OPTION_LOG_ERROR - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Logs initial BeanXML errors in greater detail to a file-path.
SHORT_OPTION_OUTPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Changes output manager.
SHORT_OPTION_OUTPUT_CONSOLE_ONLY - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Output console only.
SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Disables specific output(s).
SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Enables specific output(s).
SHORT_OPTION_OUTPUT_ENABLE_ALL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Enables all outputs.
SHORT_OPTION_OUTPUT_IMAGE_FILE_FORMAT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Suggests an output image file format: e.g -of jpg or -of ome.xml.
SHORT_OPTION_OUTPUT_INCREMENTING_NUMBER - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Outputs with an incrementing number instead of the input identifier.
SHORT_OPTION_OUTPUT_OMIT_EXPERIMENT_IDENTIFIER - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Ignores the experiment identifier, when forming an output-path.
SHORT_OPTION_OUTPUT_SUPPRESS_DIRECTORIES - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Suppressed the subdirectory structure when outputting file identifiers.
SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Shows additional argument information, otherwise executes as normal.
SHORT_OPTION_SHOW_TASKS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Prints the names of predefined tasks that can be easily used with -t.
SHORT_OPTION_TASK - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Changes task.
SHORT_OPTION_TASK_NUMBER_PROCESSORS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Suggests a maximum number of processors to use for the task.
SHORT_OPTION_TASK_SIZE - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Suggests dimensions or a scaling factor for certain tasks.
SHORT_OPTION_VERSION - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions: Displays version and authorship information.

T

taskDirectory() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor: Gets the path to the task directory.
TaskFactory - Class in org.anchoranalysis.launcher.executor.selectparam.path: Determines Paths related to tasks.
tasksFooter() - Method in class org.anchoranalysis.launcher.resources.Resources: Footer-message used after "show tasks".
toCommandLineException() - Method in exception class org.anchoranalysis.launcher.executor.selectparam.path.convert.InvalidPathArgumentException: Converts this exception to a CommandLineException.
toString() - Method in class org.anchoranalysis.launcher.config.HelpConfig

U

URL_OUTPUT_OPTIONS - Static variable in class org.anchoranalysis.launcher.AnchorWebsiteLinks: A URL for showing command-line options relating to outputting.
URL_PREDEFIEND_TASKS - Static variable in class org.anchoranalysis.launcher.AnchorWebsiteLinks: A URL for showing predefined tasks that can be used.
usageFooter() - Method in class org.anchoranalysis.launcher.resources.Resources: Footer-message that describes usage.
usageHeader() - Method in class org.anchoranalysis.launcher.resources.Resources: Header-message that describes usage.
useDefault() - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory: Creates a SelectParam that uses the default manager.
UseDefaultManager - Class in org.anchoranalysis.launcher.executor.selectparam: Uses whatever default-manager exists
UseDefaultManager() - Constructor for class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager

V

versionFooter() - Method in class org.anchoranalysis.launcher.resources.Resources: Footer-message that accompanies a version message, if it exists.
versionFromMavenProperties() - Method in class org.anchoranalysis.launcher.resources.Resources: Gets the current version of the software by reading a properties-file provided by the Maven build

A C D E G H I L M N O P R S T U V
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form