+Jws2Client +

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fcompbio%2Fws%2Fclient%2FJws2Client.html;fp=website%2Fdm_javadoc%2Fcompbio%2Fws%2Fclient%2FJws2Client.html;h=c94a02b5b4a1567ee38d0bb7b82afb2f3b37f1cf;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/dm_javadoc/compbio/ws/client/Jws2Client.html b/website/dm_javadoc/compbio/ws/client/Jws2Client.html new file mode 100644 index 0000000..c94a02b --- /dev/null +++ b/website/dm_javadoc/compbio/ws/client/Jws2Client.html @@ -0,0 +1,399 @@ + + + + + + +Jws2Client + + + + + + + + + + + + +

+ + + + + + + + + + + + + + + + + + + +

+ + + + + + + + + + + + +

Overview

Package

Class

Use

Tree

Deprecated

Index

Help

+ +

+ PREV CLASS + NEXT CLASS

+ FRAMES + NO FRAMES + + + + +

+ SUMMARY: NESTED | FIELD | CONSTR | METHOD

+DETAIL: FIELD | CONSTR | METHOD

+ + + +

+ +

+ +compbio.ws.client +
+Class Jws2Client

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

public class Jws2Client
extends java.lang.Object
extends java.lang.Object

+ + +

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

+ +

Version:: 1.0
Author:: pvtroshin

+ +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static JABAService connect(java.lang.String host, + Services service) + +
+          Connects to a web service by the host and the service name web service + type
+static RegistryWS connectToRegistry(java.lang.String host) + +
+          Get a connection of JABAWS registry
+static java.util.Set<Services> getServices(java.lang.String hostname) + +
+
+static void main(java.lang.String[] args) + +
+          Starts command line client, if no parameter are supported print help.
+static void testService(java.lang.String hostname, + Services service, + java.io.PrintWriter writer) + +
+          Asks registry to test the service on the host hostname
+static boolean validURL(java.lang.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 Summary
+`static JABAService`	`connect(java.lang.String host, + Services service)` + + + Connects to a web service by the host and the service name web service + type
+`static RegistryWS`	`connectToRegistry(java.lang.String host)` + + + Get a connection of JABAWS registry
+`static java.util.Set<Services>`	`getServices(java.lang.String hostname)` + + +
+`static void`	`main(java.lang.String[] args)` + + + Starts command line client, if no parameter are supported print help.
+`static void`	`testService(java.lang.String hostname, + Services service, + java.io.PrintWriter writer)` + + + Asks registry to test the service on the host hostname
+`static boolean`	`validURL(java.lang.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(java.lang.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(java.lang.String hostname,
+                               Services service,
+                               java.io.PrintWriter writer)
+                        throws java.net.ConnectException,
+                               javax.xml.ws.WebServiceException

Asks registry to test the service on the host hostname +

Parameters:: hostname -; service -; writer - +
Throws: +: java.net.ConnectException +; javax.xml.ws.WebServiceException

+ +

+getServices

+public static java.util.Set<Services> getServices(java.lang.String hostname)
+                                           throws javax.xml.ws.WebServiceException,
+                                                  java.net.ConnectException

Throws: +: javax.xml.ws.WebServiceException +; java.net.ConnectException

+ +

+connect

+public static JABAService connect(java.lang.String host,
+                                  Services service)
+                           throws javax.xml.ws.WebServiceException,
+                                  java.net.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: +: javax.xml.ws.WebServiceException +; java.net.ConnectException - if fails to connect to the service on the host

+ +

+connectToRegistry

+public static RegistryWS connectToRegistry(java.lang.String host)
+                                    throws javax.xml.ws.WebServiceException,
+                                           java.net.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: +: javax.xml.ws.WebServiceException +; java.net.ConnectException

+ +

+main

+public static void main(java.lang.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!

+ +