org.ginsim

Class ScriptLauncher

java.lang.Object

org.ginsim.ScriptLauncher

public class ScriptLauncher
extends Object

A helper when running GINsim in script mode. It provides a proxy to common actions:

• open and save graphs
• run services
• create reports

Author:

Aurelien Naldi

Field Summary

Fields

Modifier and Type	Field and Description
String[]	args Arguments passed to the script

Constructor Summary

Constructors

Constructor and Description
ScriptLauncher()

Method Summary

Modifier and Type	Method and Description
Object	associated(Graph<?,?> g, String key, boolean create) Get or create associated data.
Object	associated(Graph g, String key) Get (existing) associated data
DocumentWriter	createReport(String path, Map<String,String> properties) Create a report file, this creates the file and DocumentWriter, don't forget to close it.
void	help() Show some help about services and data available for scripts
RegulatoryGraph	load(org.colomoto.biolqm.LogicalModel model)
Graph<?,?>	load(String filename) Open a graph from a file.
org.colomoto.biolqm.service.LQMServiceManager	LQM() Grab a proxy to the bioLQM API
String	nameState(byte[] state, RegulatoryGraph graph) Deprecated.
Graph<?,?>	open(String filename) Deprecated. see load(String)
BasicProgressListener	progressListener()
void	run(String filename, String[] args) Run a script: the method is called by the main launcher to launch a GINsim script
Service	service(Class<Service> cl) Get a service instance
Service	service(String name) Get a service instance by name

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

args

public String[] args

Arguments passed to the script

Constructor Detail

ScriptLauncher

public ScriptLauncher()

Method Detail

run

public void run(String filename,
                String[] args)

Run a script: the method is called by the main launcher to launch a GINsim script

Parameters:

filename - script filename

args - additional arguments passed on the command line

LQM

public org.colomoto.biolqm.service.LQMServiceManager LQM()

Grab a proxy to the bioLQM API

Returns:

a LQM script launcher

load

public Graph<?,?> load(String filename)
                throws GsException

Open a graph from a file.

Parameters:

filename -

Returns:

the parsed graph

Throws:

GsException

load

public RegulatoryGraph load(org.colomoto.biolqm.LogicalModel model)
                     throws GsException

Throws:

GsException

open

@Deprecated
public Graph<?,?> open(String filename)
                            throws GsException

Deprecated. see load(String)

Throws:

GsException

nameState

@Deprecated
public String nameState(byte[] state,
                                    RegulatoryGraph graph)

Deprecated.

Lookup a named state matching the given state. Marked as deprecated as it should be part of the initial state service.

Parameters:

state -

graph -

Returns:

the name or null

service

public Service service(Class<Service> cl)

Get a service instance

Parameters:

cl - the service class

Returns:

the service or null if not found

service

public Service service(String name)

Get a service instance by name

Parameters:

name - the service name (class name or alias)

Returns:

the service or null if not found

associated

public Object associated(Graph g,
                         String key)

Get (existing) associated data

Parameters:

g -

key -

Returns:

the associated object or null if it was not created.

associated

public Object associated(Graph<?,?> g,
                         String key,
                         boolean create)

Get or create associated data.

Parameters:

g -

key -

create -

Returns:

the associated object, created if needed or null if the key is invalid

createReport

public DocumentWriter createReport(String path,
                                   Map<String,String> properties)

Create a report file, this creates the file and DocumentWriter, don't forget to close it.

Parameters:

path -

properties -

Returns:

a new DocumentWriter

help

public void help()

Show some help about services and data available for scripts

progressListener

public BasicProgressListener progressListener()