compbio.ws.client

Class Jws2Client

java.lang.Object

compbio.ws.client.Jws2Client

public class Jws2Client
extends java.lang.Object

A command line client for JAva Bioinformatics Analysis Web Services

Version:

1.0

Author:

pvtroshin

Field Summary

Fields

Modifier and Type	Field and Description
private static java.util.logging.Logger	log Use java.util.Logger instead of log4j logger to reduce the size of the client package

Constructor Summary

Constructors

Constructor and Description
Jws2Client(java.lang.String[] cmd) Connects to the service and do the job as requested, if something goes wrong reports or/and prints usage help.

Method Summary

Modifier and Type	Method and Description
(package private) static <T> Alignment	align(java.io.File file, MsaWS<T> msaws, Preset<T> preset, java.util.List<Option<T>> customOptions) Align sequences from the file using MsaWS
(package private) static <T> ScoreManager	analize(java.io.File file, SequenceAnnotation<T> wsproxy, Preset<T> preset, java.util.List<Option<T>> customOptions) Calculate conservation for sequences loaded from the file
(package private) static <T> ScoreManager	analize(java.util.List<FastaSequence> fastalist, SequenceAnnotation<T> wsproxy, Preset<T> preset, java.util.List<Option<T>> customOptions) Calculate conservation for sequences loaded from a FASTA record list structure
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
private static void	listAllServices(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

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

Field Detail

log

private static final java.util.logging.Logger log

Use java.util.Logger instead of log4j logger to reduce the size of the client package

Constructor Detail

Jws2Client

Jws2Client(java.lang.String[] cmd)
    throws java.io.IOException

Connects to the service and do the job as requested, if something goes wrong reports or/and prints usage help.

Type Parameters:

T - web service type

Parameters:

cmd - command line options

Throws:

java.io.IOException

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

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

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

listAllServices

private static void listAllServices(java.lang.String hostname)
                             throws javax.xml.ws.WebServiceException,
                                    java.io.IOException

Throws:

javax.xml.ws.WebServiceException

java.io.IOException

analize

static <T> ScoreManager analize(java.util.List<FastaSequence> fastalist,
                                SequenceAnnotation<T> wsproxy,
                                Preset<T> preset,
                                java.util.List<Option<T>> customOptions)

Calculate conservation for sequences loaded from a FASTA record list structure

Parameters:

fastalist - the list of FASTA records

wsproxy - a web service proxy

preset - Preset to use optional

customOptions - the list of options

Returns:

Set the conservation scores

Throws:

UnknownFileFormatException

analize

static <T> ScoreManager analize(java.io.File file,
                                SequenceAnnotation<T> wsproxy,
                                Preset<T> preset,
                                java.util.List<Option<T>> customOptions)

Calculate conservation for sequences loaded from the file

Parameters:

wsproxy - a web service proxy

file - the file to read the results from

preset - Preset to use optional

customOptions - the list of options

Returns:

Set the conservation scores

Throws:

java.io.IOException

UnknownFileFormatException

align

static <T> Alignment align(java.io.File file,
                           MsaWS<T> msaws,
                           Preset<T> preset,
                           java.util.List<Option<T>> customOptions)

Align sequences from the file using MsaWS

Type Parameters:

T - web service type e.g. Clustal

Parameters:

file - to write the resulting alignment to

msaws - MsaWS required

preset - Preset to use optional

customOptions - file which contains new line separated list of options

Returns:

Alignment

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!