X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FConstraints.java;h=2454424704d0b955a4f90464bd8a51303a0f8c9e;hb=4c022b67a736b6f79dbe212d73016607cf298422;hp=e76ee6a84006352165562fdbcc3731ca488affa1;hpb=603a6be6b9459625f535bf42c6d8ec5462e218e2;p=jabaws.git diff --git a/webservices/compbio/ws/client/Constraints.java b/webservices/compbio/ws/client/Constraints.java index e76ee6a..2454424 100644 --- a/webservices/compbio/ws/client/Constraints.java +++ b/webservices/compbio/ws/client/Constraints.java @@ -1,3 +1,20 @@ +/* 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 { @@ -8,7 +25,8 @@ class Constraints { final static String hostkey = "-h"; final static String servicekey = "-s"; - final static String listServices = "-list_services"; + final static String listServices = "-list"; + final static String listServicesOld = "-list_services"; final static String testKey = "-test"; // Actions @@ -24,71 +42,52 @@ class Constraints { final static String parameterkey = "-p"; final static String presetkey = "-r"; - final static String help_text = "\r\n" - + "JABAWS client v2.0 June 2011 http://www.compbio.dundee.ac.uk/jabaws \r\n" - + " \r\n" - + "Usage: -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n" - + "\r\n" - + "-h= - a full URL to the JABAWS web server including context \r\n" - + " path e.g. http://10.31.1.159:8080/ws\r\n" - + "-s= - one of [MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS, \r\n" - + " AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]\r\n" - + " is required for all ACTIONS but -list_services\r\n" - + "\r\n" - + "ACTIONS: \r\n" - + "-list_services - list available services\r\n" - + "-test - test service \r\n" - + "-i= - full path to fasta formatted sequence file, from which to align \r\n" - + " sequences\r\n" - + "-parameters - lists parameters supported by web service\r\n" - + "-presets - lists presets supported by web service\r\n" - + "-limits - lists web services limits\r\n" - + "\r\n" - + "Please note that if input file is specified other actions are ignored\r\n" - + "\r\n" - + "OPTIONS (only for use with -i action):\r\n" - + "-r= - name of the preset to use\r\n" - + "-o= - full path to the file where to write an alignment\r\n" - + "-f= - the name of the file with the list of parameters to use.\r\n" - + "\r\n" - + "Please note that -r and -f options cannot be used together. Alignment is done with \r\n" - + "either preset or a parameters from the file, but not both!\r\n" - + "\r\n" - + "EXAMPLES: \r\n" - + "\r\n" - + "1) List all available services on the host \r\n" - + "\r\n" - + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -list_services\r\n" - + "\r\n" - + "2) Test Clustal web service \r\n" - + "\r\n" - + "Jws2Client -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" - + "\r\n" - + "Jws2Client -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, output results to \r\n" - + "the console \r\n" - + "\r\n" - + "Jws2Client -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" - + "\r\n" - + "Jws2Client -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 console \r\n" - + "\r\n" - + "Jws2Client -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" - + "The list of the supported parameters can be obtained as shown in the example 5. \r\n" - + "\r\n" - + "Citation: Peter V. Troshin, James B. Procter and Geoffrey J. Barton - \"Java \r\n" - + "Bioinformatics Analysis Web Services for Multiple Sequence Alignment - \r\n" - + "JABAWS:MSA\" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.\r\n" - + ""; + final static String help_text = "\r\n" + + "Usage: java -jar -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n" + + "\r\n" + + " -h= - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws\r\n" + + " -s= - a name of servise (the full list can be obtain with the option -list)\r\n" + + " is required for all ACTIONS except -list\r\n\r\n" + + "ACTIONS: \r\n" + + " -i= - 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 \r\n" + + " -parameters - lists parameters supported by \r\n" + + " -presets - lists presets supported by \r\n" + + " -limits - lists limits of \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= - name of the preset to use\r\n" + + " -o= - file with output results\r\n" + + " -f= - 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" + + " is java -jar \r\n\r\n" + + "1) List all available services on the host:\r\n" + + " -h=http://www.compbio.dundee.ac.uk/jabaws -list\r\n" + + "\r\n" + + "2) Test Clustal web service:\r\n" + + " -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" + + " -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" + + " -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" + + " -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" + + " -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" + + ""; }