-Jws2Client -

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- -compbio.ws.client -
-Class Jws2Client

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

public class Jws2Client
extends Object
extends Object

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-A command line client for JAva Bioinformatics Analysis Web Services -

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Version:: 1.0
Author:: pvtroshin

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-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) - -
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-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
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Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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-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`

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-Method Detail
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-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

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-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

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-getServices

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

Throws: -: WebServiceException -; ConnectException

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-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

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-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

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-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!

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