compbio.ws.client
Class Jws2Client

java.lang.Object
  compbio.ws.client.Jws2Client

public class Jws2Client
extends Object

A command line client for JAva Bioinformatics Analysis Web Services

Version:

1.0

Author:

pvtroshin

Method Summary

static JABAService	connect(String host, Services service) Connects to a web service by the host and the service name web service type
static RegistryWS	connectToRegistry(String host) Get a connection of JABAWS registry
static Set<Services>	getServices(String hostname)
static void	main(String[] args) Starts command line client, if no parameter are supported print help.
static void	testService(String hostname, Services service, PrintWriter writer) Asks registry to test the service on the host hostname
static boolean	validURL(String urlstr) Attempt to construct the URL object from the string

Methods inherited from class java.lang.Object

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

Method Detail

validURL

public static boolean validURL(String urlstr)

Attempt to construct the URL object from the string

Parameters:

urlstr -

Returns:

true if it succeed false otherwise

testService

public static void testService(String hostname,
                               Services service,
                               PrintWriter writer)
                        throws ConnectException,
                               WebServiceException

Asks registry to test the service on the host hostname

Parameters:

hostname -

service -

writer -

Throws:

ConnectException

WebServiceException

getServices

public static Set<Services> getServices(String hostname)
                                 throws WebServiceException,
                                        ConnectException

Throws:

WebServiceException

ConnectException

connect

public static JABAService connect(String host,
                                  Services service)
                           throws WebServiceException,
                                  ConnectException

Connects to a web service by the host and the service name web service type

Parameters:

host - the fully qualified name of JABAWS server including JABAWS context name e.g http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba

service - the name of the JABAWS service to connect to

Returns:

JABAService

Throws:

WebServiceException

ConnectException - if fails to connect to the service on the host

connectToRegistry

public static RegistryWS connectToRegistry(String host)
                                    throws WebServiceException,
                                           ConnectException

Get a connection of JABAWS registry

Parameters:

host - the fully qualified name of JABAWS server including JABAWS context name e.g http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba

Returns:

compbio.data.msa.RegistryWS - instance of a RegistryWS web service

Throws:

WebServiceException

ConnectException

main

public static void main(String[] args)

Starts command line client, if no parameter are supported print help. Two parameters are required for successful call the JWS2 host name and a service name.

Parameters:

args - Usage: -h=host_and_context -s=serviceName ACTION [OPTIONS] -h= - a full URL to the JWS2 web server including context path e.g. http://10.31.1.159:8080/ws -s= - one of [MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS] ACTIONS: -i= - full path to fasta formatted sequence file, from which to align sequences -parameters - lists parameters supported by web service -presets - lists presets supported by web service -limits - lists web services limits Please note that if input file is specified other actions are ignored OPTIONS: (only for use with -i action): -r= - name of the preset to use -o= - full path to the file where to write an alignment -f= - the name of the file with the list of parameters to use. Please note that -r and -f options cannot be used together. Alignment is done with either preset or a parameters from the file, but not both!