de.jstacs.tools

Interface JstacsTool

public interface JstacsTool

Interface for a generic Jstacs tool. Implementations of this interface may be used in the CLI, Galaxy, and JavaFX-based GUI classes for creating generic interfaces to tools created using Jstacs

Author:

Jan Grau

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	JstacsTool.ResultEntry Representation of default results.

Method Summary

Methods

Modifier and Type	Method and Description
JstacsTool.ResultEntry[]	getDefaultResultInfos() Returns JstacsTool.ResultEntrys for the default results of this JstacsTool.
String	getDescription() Returns a short description (half a sentence) on what this tool does.
String	getHelpText() Returns a detailed help text for this tool, describing the purpose of the tool, all parameters and results.
String	getShortName() Returns a name (preferably short and without spaces) for referring to this tool on the command line.
String	getToolName() Returns a descriptive, human readable name for this tool.
ParameterSet	getToolParameters() Returns the input parameters of this tool.
String	getToolVersion() Returns a descriptive, human readable version for this tool.
ToolResult	run(ParameterSet parameters, Protocol protocol, ProgressUpdater progress, int threads) Runs the tool using the provided (now filled) parameters, which are in structure identical to those returned by getToolParameters().

Method Detail

getToolParameters

ParameterSet getToolParameters()

Returns the input parameters of this tool. The parameters should be empty but may have default values, which are used in all interface variants (command line, Galaxy, JavaFX GUI).

Returns:

the input parameters

run

ToolResult run(ParameterSet parameters,
             Protocol protocol,
             ProgressUpdater progress,
             int threads)
               throws Exception

Runs the tool using the provided (now filled) parameters, which are in structure identical to those returned by getToolParameters(). These parameters should only be used for this run and should not affect subsequent runs of the same tool. Protocol and ProgressUpdater may be used for indicating the tool's progress. Depending on the implementation and interface variant, these may be rendered differently (or not at all). This method returns all results of this tool encapsulated in a ToolResult.

Parameters:

parameters - the input parameters

protocol - the protocol

progress - the progress updater

threads - the maximum number of threads that may be used for this run of the tool

Returns:

the results of this tool

Throws:

Exception - if the tool can not be run properly

getToolName

String getToolName()

Returns a descriptive, human readable name for this tool.

Returns:

the name

getToolVersion

String getToolVersion()

Returns a descriptive, human readable version for this tool.

Returns:

the version

getShortName

String getShortName()

Returns a name (preferably short and without spaces) for referring to this tool on the command line.

Returns:

the short name

getDescription

String getDescription()

Returns a short description (half a sentence) on what this tool does.

Returns:

the description

getHelpText

String getHelpText()

Returns a detailed help text for this tool, describing the purpose of the tool, all parameters and results. May use reStructureText markup.

Returns:

the help text

getDefaultResultInfos

JstacsTool.ResultEntry[] getDefaultResultInfos()

Returns JstacsTool.ResultEntrys for the default results of this JstacsTool. These results must be a subset of all results that are returned by successful runs of this tool regardless of the input parameters. If no results should be defined as defaults, this method may return null. Currently, this information is only used in the Galaxy environment, but may be used in the JavaFX GUI in the future for building workflows as well. For each entry either the format or the result class should be supplied. If a format is specified this overrides the default formats for this Result type. Default formats for a given Result class may be obtained from GalaxyAdaptor.getDefaultExtension(Class). If this method returns null, the output format may be guessed by the environment (e.g., Galaxy). Results are matched to default results by their name (AnnotatedEntity.getName()) and result class, so the name supplied to JstacsTool.ResultEntry.JstacsTool.ResultEntry(Class, String, String) must be identical to that of the final Result and should be unique (otherwise only one appearance of this name will be considered a default result) within a result class. The set of default results must always be returned in the same order.

Returns:

the default results (or null for no default results).