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/* Copyright (c) 2011 Peter Troshin
*
* JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
*
* This library is free software; you can redistribute it and/or modify it under the terms of the
* Apache License version 2 as published by the Apache Software Foundation
*
* This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
* even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
* License for more details.
*
* A copy of the license is in apache_license.txt. It is also available here:
* @see: http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Any republication or derived work distributed in source code form
* must include this copyright and license notice.
*/
package compbio.ws.client;
class Constraints {
final static String pseparator = "=";
// Parameters for required command line options
final static String hostkey = "-h";
final static String servicekey = "-s";
final static String listServices = "-list";
final static String listServicesOld = "-list_services";
final static String testKey = "-test";
// Actions
final static String inputkey = "-i";
final static String paramList = "-parameters";
final static String presetList = "-presets";
final static String limitList = "-limits";
// Options
final static String paramFile = "-f";
final static String outputkey = "-o";
final static String parameterkey = "-p";
final static String presetkey = "-r";
final static String help_text = "\r\n" +
"Usage: java -jar <JAR file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n" +
"\r\n" +
" -h=<host_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws\r\n" +
" -s=<ServiceName> - a name of servise (the full list can be obtain with the option -list)\r\n" +
" <serviceName> is required for all ACTIONS except -list\r\n\r\n" +
"ACTIONS: \r\n" +
" -i=<inputFile> - defines an input file. For most services this is a FASTA file with initial sequences\r\n" +
" -list - lists all available web services\r\n" +
" -test - tests functioning of <ServiceName> \r\n" +
" -parameters - lists parameters supported by <ServiceName>\r\n" +
" -presets - lists presets supported by <ServiceName>\r\n" +
" -limits - lists limits of <ServiceName>\r\n" +
"\r\n" +
"N.B. If an input file is specified with -i other actions are ignored!\r\n\r\n" +
"OPTIONS (used with the -i action only):\r\n" +
" -r=<presetName> - name of the preset to use\r\n" +
" -o=<outputFile> - file with output results\r\n" +
" -f=<paramFile> - file with the list of parameters to use.\r\n\r\n" +
"Please note that -r and -f options cannot be used together. \r\n" +
"Alignment/Prediction is done with either preset or a parameters from the file, but not both!\r\n\r\n" +
"EXAMPLES: \r\n" +
"<THECLIENT> is java -jar <JAR file name>\r\n\r\n" +
"1) List all available services on the host:\r\n" +
" <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -list\r\n" +
"\r\n" +
"2) Test Clustal web service:\r\n" +
" <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n" +
"\r\n" +
"3) Align sequence from file input.txt with Probcons. Record resulting alignment \r\n" +
" into the output.txt:\r\n" +
" <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r\n" +
"\r\n" +
"4) Calculate disorder with Disembl take input from input.txt with output results\r\n " +
" to be printed out to the standard output:\r\n" +
" <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r\n" +
"\r\n" +
"5) List all parameters available for AAconWS service:\r\n" +
" <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r\n" +
"\r\n" +
"6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment \r\n" +
" from input.txt and report the scores to the standard output:\r\n" +
" <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r\n" +
"\r\n" +
" Where the content of prm.txt file is -m=LANDGRAF\r\n" +
"N.B. The list of the supported parameters can be obtained as shown in the example 5.\r\n" +
"";
}
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