1 /* Copyright (c) 2011 Peter Troshin
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3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0
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5 * This library is free software; you can redistribute it and/or modify it under the terms of the
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6 * Apache License version 2 as published by the Apache Software Foundation
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8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
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9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
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10 * License for more details.
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12 * A copy of the license is in apache_license.txt. It is also available here:
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13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
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15 * Any republication or derived work distributed in source code form
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16 * must include this copyright and license notice.
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18 package compbio.ws.client;
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22 final static String pseparator = "=";
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24 // Parameters for required command line options
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25 final static String hostkey = "-h";
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26 final static String servicekey = "-s";
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28 final static String listServices = "-list";
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29 final static String testKey = "-test";
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32 final static String inputkey = "-i";
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34 final static String paramList = "-parameters";
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35 final static String presetList = "-presets";
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36 final static String limitList = "-limits";
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39 final static String paramFile = "-f";
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40 final static String outputkey = "-o";
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41 final static String parameterkey = "-p";
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42 final static String presetkey = "-r";
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44 final static String help_text = "\r\n" +
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45 "Usage: java -jar <JAR file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n" +
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47 " -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" +
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48 " -s=<ServiceName> - a name of servise (the full list can be obtain with the option -list)\r\n" +
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49 " <serviceName> is required for all ACTIONS except -list\r\n\r\n" +
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51 " -i=<inputFile> - defines an input file. For most services this is a FASTA file with initial sequences\r\n" +
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52 " -list - lists all available web services\r\n" +
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53 " -test - tests functioning of <ServiceName> \r\n" +
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54 " -parameters - lists parameters supported by <ServiceName>\r\n" +
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55 " -presets - lists presets supported by <ServiceName>\r\n" +
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56 " -limits - lists limits of <ServiceName>\r\n" +
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58 "N.B. If an input file is specified with -i other actions are ignored!\r\n\r\n" +
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59 "OPTIONS (used with the -i action only):\r\n" +
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60 " -r=<presetName> - name of the preset to use\r\n" +
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61 " -o=<outputFile> - file with output results\r\n" +
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62 " -f=<paramFile> - file with the list of parameters to use.\r\n\r\n" +
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63 "Please note that -r and -f options cannot be used together. \r\n" +
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64 "Alignment/Prediction is done with either preset or a parameters from the file, but not both!\r\n\r\n" +
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66 "<THECLIENT> is java -jar <JAR file name>\r\n\r\n" +
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67 "1) List all available services on the host:\r\n" +
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68 " <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -list\r\n" +
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70 "2) Test Clustal web service:\r\n" +
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71 " <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n" +
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73 "3) Align sequence from file input.txt with Probcons. Record resulting alignment \r\n" +
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74 " into the output.txt:\r\n" +
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75 " <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r\n" +
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77 "4) Calculate disorder with Disembl take input from input.txt with output results\r\n " +
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78 " to be printed out to the standard output:\r\n" +
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79 " <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r\n" +
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81 "5) List all parameters available for AAconWS service:\r\n" +
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82 " <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r\n" +
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84 "6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment \r\n" +
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85 " from input.txt and report the scores to the standard output:\r\n" +
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86 " <THECLIENT> -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r\n" +
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88 " Where the content of prm.txt file is -m=LANDGRAF\r\n" +
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89 "N.B. The list of the supported parameters can be obtained as shown in the example 5.\r\n" +
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