Plugin (SeqWare 1.1.2 API)

java.lang.Object
- net.sourceforge.seqware.pipeline.plugin.Plugin

All Implemented Interfaces:

PluginInterface

Direct Known Subclasses:

AttributeAnnotator, BasicDecider, BundleManager, CheckDB, CycleChecker, DeletionDB, FileLinker, FileProvenanceQueryTool, FileProvenanceReporter, HelloWorld, MarkdownPlugin, Metadata, ModuleRunner, OozieXML2Dot, ProcessingDataStructure2Dot, SanityCheck, UserSettingsPlugin, WorkflowLauncher, WorkflowLifecycle, WorkflowRelauncher, WorkflowRescheduler, WorkflowRunFilesInitialPopulationPlugin, WorkflowRunReporter, WorkflowScheduler, WorkflowStatusChecker, WorkflowWatcher
```
public abstract class Plugin
extends Object
implements PluginInterface
```
Abstract Plugin class.

Version:

$Id: $Id

Author:

boconnor

Field Summary

Fields
Modifier and Type	Field and Description
`protected Map<String,String>`	`config`
`protected Metadata`	`metadata`
`protected joptsimple.OptionSet`	`options`
`protected String[]`	`params`
`protected joptsimple.OptionParser`	`parser`

Constructor Summary

Constructors
Constructor and Description

Plugin()
Constructor for Plugin.

Constructors
Constructor and Description
`Plugin()` Constructor for Plugin.

Method Summary

Methods
Modifier and Type	Method and Description
`String`	`get_description()` Generates a short description of the plugin, preferably one line.
`String`	`get_syntax()` Generates a "help" message for the user of the plugin.
`ReturnValue`	`parse_parameters()` Parameter validation code goes here.
`void`	`print(String output)` print.
`void`	`println(String output)` println.
`void`	`setConfig(Map<String,String> config)` Let's you set the config this object should use.
`void`	`setMetadata(Metadata metadata)` Lets you set the metadata object
`void`	`setParams(List<String> params)` Lets you set a List of params so the plugin can deal with parameters

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.sourceforge.seqware.pipeline.plugin.PluginInterface
clean_up, do_run, do_test, init

- Field Detail
  - parser
```
protected joptsimple.OptionParser parser
```
  - options
```
protected joptsimple.OptionSet options
```
  - params
```
protected String[] params
```
  - metadata
```
protected Metadata metadata
```
  - config
```
protected Map<String,String> config
```
- Constructor Detail
  - Plugin
```
public Plugin()
```
    Constructor for Plugin.
- Method Detail
  - setConfig
```
public void setConfig(Map<String,String> config)
```
    Let's you set the config this object should use.
    
    Specified by:
    
    setConfig in interface PluginInterface
    
    Parameters:
    config - A map that includes the key/values from the SeqWare settings file.
  - setParams
```
public void setParams(List<String> params)
```
    Lets you set a List of params so the plugin can deal with parameters
    
    Specified by:
    
    setParams in interface PluginInterface
    
    Parameters:
    params - The parameters specifically passed in to the plugin.
  - setMetadata
```
public void setMetadata(Metadata metadata)
```
    Lets you set the metadata object
    
    Specified by:
    
    setMetadata in interface PluginInterface
    
    Parameters:
    metadata - a Metadata object.
  - get_syntax
```
public String get_syntax()
```
    Generates a "help" message for the user of the plugin. This will be called by the PluginRunner to provide information about using the plugin. It is up to the implementation to defined the format for the returned message. This is triggered if no options are provided to the PluginRunner.
    
    Specified by:
    
    get_syntax in interface PluginInterface
    
    Returns:
    Description of the command line parameters for this plugin.
  - get_description
```
public String get_description()
```
    Generates a short description of the plugin, preferably one line.
    
    Specified by:
    
    get_description in interface PluginInterface
    
    Returns:
    Description of the plugin.
  - parse_parameters
```
public ReturnValue parse_parameters()
```
    Parameter validation code goes here. Use to make sure all required parameters are available, that parameters are known, that they have reasonable values, etc. Validation involving multiple options happens here where the existence and content of input data files will be checked.
    
    Specified by:
    
    parse_parameters in interface PluginInterface
    
    Returns:
    Success or failure info from this phase, along with any console output.
  - print
```
public void print(String output)
```
    print.
    
    Parameters:
    output - a String object.
  - println
```
public void println(String output)
```
    println.
    
    Parameters:
    output - a String object.

Class Plugin

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface net.sourceforge.seqware.pipeline.plugin.PluginInterface

Field Detail

parser

options

params

metadata

config

Constructor Detail

Plugin

Method Detail

setConfig

setParams

setMetadata

get_syntax

get_description

parse_parameters

print

println