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 <T> MsaWS<T>	connect(String host, Services service) Connects to a web service by the host and the service name
static String	getHost(String[] cmd) Extracts host name from the command line
static String	getServiceName(String[] cmd) Extracts service name from the command line
static void	main(String[] args) Starts command line client, if no parameter are supported print help.
static boolean	validURL(String urlstr) Attempt to construct the URL object from the string

Methods inherited from class java.lang.Object

clone, equals, finalize, 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

getServiceName

public static String getServiceName(String[] cmd)

Extracts service name from the command line

Parameters:

cmd - command line options

Returns:

service name or null if it is not defined

getHost

public static String getHost(String[] cmd)

Extracts host name from the command line

Parameters:

cmd - command line options

Returns:

host name or null if it is not defined

connect

public static <T> MsaWS<T> connect(String host,
                                   Services service)
                        throws WebServiceException

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

Type Parameters:

T - web service type

Parameters:

host -

service -

Returns:

MsaWS

Throws:

WebServiceException

main

public static void main(String[] args)

Starts command line client, if no parameter are supported print help. Two parameters are required for successfull 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!