compbio.ws.client

Class AAConClient

java.lang.Object

compbio.ws.client.AAConClient

public class AAConClient
extends java.lang.Object

A command line client for AACon web service

Version:

1.0

Author:

pvtroshin

Field Summary

Fields

Modifier and Type	Field and Description
(package private) static java.lang.String	hostname Web service host
private static java.util.logging.Logger	log Use java.util.Logger instead of log4j logger to reduce the size of the client package
(package private) static java.lang.String	QUALIFIED_SERVICE_NAME The fully qualified web service namespace
(package private) static java.lang.String	serviceName Web service name

Constructor Summary

Constructors

Constructor and Description
AAConClient(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 ScoreManager	analize(java.io.File file, SequenceAnnotation<AAConWS> wsproxy, Preset<AAConWS> preset, java.util.List<Option<AAConWS>> customOptions) Calculate conservation for sequences loaded from the file
static SequenceAnnotation<AAConWS>	connect() Connects to a AACon web service by the host and the service name
static void	main(java.lang.String[] args) Starts command line client, if no parameters are supplied prints help.
(package private) static void	printUsage(int exitStatus) Prints AAConClient usage information to standard out
(package private) static void	writeOut(java.io.Writer writer, ScoreManager result) Outputs AAcon results into the file represented by the outStream

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

QUALIFIED_SERVICE_NAME

static final java.lang.String QUALIFIED_SERVICE_NAME

The fully qualified web service namespace

See Also:

Constant Field Values

hostname

static final java.lang.String hostname

Web service host

See Also:

Constant Field Values

serviceName

static final java.lang.String serviceName

Web service name

See Also:

Constant Field Values

Constructor Detail

AAConClient

AAConClient(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.

Parameters:

cmd - command line options

Throws:

java.io.IOException - if the system cannot read/write from/into the file system

Method Detail

writeOut

static void writeOut(java.io.Writer writer,
                     ScoreManager result)

Outputs AAcon results into the file represented by the outStream

Parameters:

outStream -

result - the AACon scores to output

connect

public static SequenceAnnotation<AAConWS> connect()
                                           throws javax.xml.ws.WebServiceException

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

Returns:

AlignmentAnnotation

Throws:

javax.xml.ws.WebServiceException - if cannot connect to a web service

analize

static ScoreManager analize(java.io.File file,
                            SequenceAnnotation<AAConWS> wsproxy,
                            Preset<AAConWS> preset,
                            java.util.List<Option<AAConWS>> 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:

UnknownFileFormatException

printUsage

static void printUsage(int exitStatus)

Prints AAConClient usage information to standard out

Parameters:

exitStatus -

main

public static void main(java.lang.String[] args)

Starts command line client, if no parameters are supplied prints help.

Parameters:

args - Usage: ACTION [OPTIONS] -i= - full path to fasta or Clustal formatted alignment file -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 results -f= - the name of the file with the list of parameters to use. Please note that -r and -f options cannot be used together. Conservation is calculated with either a preset or parameters from the file, but not both!