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Clustal Omega web service wrapper and tester
[jabaws.git] / webservices / compbio / ws / client / Constraints.java
diff --git a/webservices/compbio/ws/client/Constraints.java b/webservices/compbio/ws/client/Constraints.java
index e76ee6a..412d9f2 100644 (file)
--- a/webservices/compbio/ws/client/Constraints.java
+++ b/webservices/compbio/ws/client/Constraints.java
@@ -24,71 +24,71 @@ class Constraints {
        final static String parameterkey = "-p";\r
        final static String presetkey = "-r";\r
 \r
-       final static String help_text = "\r\n"\r
-                       + "JABAWS client v2.0 June 2011 http://www.compbio.dundee.ac.uk/jabaws \r\n"\r
-                       + " \r\n"\r
-                       + "Usage: <Class or Jar file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n"\r
-                       + "\r\n"\r
-                       + "-h=<host_context>  - a full URL to the JABAWS web server including context \r\n"\r
-                       + "                     path e.g. http://10.31.1.159:8080/ws\r\n"\r
-                       + "-s=<ServiceName>   - one of [MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS, \r\n"\r
-                       + "                     AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]\r\n"\r
-                       + "                     <serviceName> is required for all ACTIONS but -list_services\r\n"\r
-                       + "\r\n"\r
-                       + "ACTIONS: \r\n"\r
-                       + "-list_services    - list available services\r\n"\r
-                       + "-test             - test service \r\n"\r
-                       + "-i=<inputFile>    - full path to fasta formatted sequence file, from which to align \r\n"\r
-                       + "                    sequences\r\n"\r
-                       + "-parameters       - lists parameters supported by web service\r\n"\r
-                       + "-presets          - lists presets supported by web service\r\n"\r
-                       + "-limits           - lists web services limits\r\n"\r
-                       + "\r\n"\r
-                       + "Please note that if input file is specified other actions are ignored\r\n"\r
-                       + "\r\n"\r
-                       + "OPTIONS (only for use with -i action):\r\n"\r
-                       + "-r=<presetName>   - name of the preset to use\r\n"\r
-                       + "-o=<outputFile>   - full path to the file where to write an alignment\r\n"\r
-                       + "-f=<PrmInputFile> - the name of the file with the list of parameters to use.\r\n"\r
-                       + "\r\n"\r
-                       + "Please note that -r and -f options cannot be used together. Alignment is done with \r\n"\r
-                       + "either preset or a parameters from the file, but not both!\r\n"\r
-                       + "\r\n"\r
-                       + "EXAMPLES: \r\n"\r
-                       + "\r\n"\r
-                       + "1) List all available services on the host \r\n"\r
-                       + "\r\n"\r
-                       + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -list_services\r\n"\r
-                       + "\r\n"\r
-                       + "2) Test Clustal web service \r\n"\r
-                       + "\r\n"\r
-                       + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n"\r
-                       + "\r\n"\r
-                       + "3) Align sequence from file input.txt with Probcons. Record resulting alignment \r\n"\r
-                       + "into the output.txt \r\n"\r
-                       + "\r\n"\r
-                       + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r\n"\r
-                       + "\r\n"\r
-                       + "4) Calculate disorder with Disembl take input from input.txt, output results to \r\n"\r
-                       + "the console \r\n"\r
-                       + "\r\n"\r
-                       + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r\n"\r
-                       + "\r\n"\r
-                       + "5) List all parameters available for AAconWS service \r\n"\r
-                       + "\r\n"\r
-                       + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r\n"\r
-                       + "\r\n"\r
-                       + "6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment \r\n"\r
-                       + "from input.txt and report  the scores to the console \r\n"\r
-                       + "\r\n"\r
-                       + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r\n"\r
-                       + "\r\n"\r
-                       + "Where the content of prm.txt file is -m=LANDGRAF\r\n"\r
-                       + "The list of the supported parameters can be obtained as shown in the example 5. \r\n"\r
-                       + "\r\n"\r
-                       + "Citation: Peter V. Troshin, James B. Procter and Geoffrey J. Barton - \"Java \r\n"\r
-                       + "Bioinformatics Analysis Web Services for Multiple Sequence Alignment - \r\n"\r
-                       + "JABAWS:MSA\" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.\r\n"\r
-                       + "";\r
+       final static String help_text = "\r\n" + \r
+                       "JABAWS2 client August 2011 http://www.compbio.dundee.ac.uk/jabaws \r\n" + \r
+                       " \r\n" + \r
+                       "Usage: <Class or Jar file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n" + \r
+                       "\r\n" + \r
+                       "-h=<host_context>  - a full URL to the JABAWS web server including context \r\n" + \r
+                       "                     path e.g. http://10.31.1.159:8080/ws\r\n" + \r
+                       "-s=<ServiceName>   - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, \r\n" + \r
+                       "                                        ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]\r\n" + \r
+                       "                     <serviceName> is required for all ACTIONS but -list_services\r\n" + \r
+                       "\r\n" + \r
+                       "ACTIONS: \r\n" + \r
+                       "-list_services    - list available services\r\n" + \r
+                       "-test             - test service \r\n" + \r
+                       "-i=<inputFile>    - full path to fasta formatted sequence file, from which to align \r\n" + \r
+                       "                    sequences\r\n" + \r
+                       "-parameters       - lists parameters supported by web service\r\n" + \r
+                       "-presets          - lists presets supported by web service\r\n" + \r
+                       "-limits           - lists web services limits\r\n" + \r
+                       "\r\n" + \r
+                       "Please note that if input file is specified other actions are ignored\r\n" + \r
+                       "\r\n" + \r
+                       "OPTIONS (only for use with -i action):\r\n" + \r
+                       "-r=<presetName>   - name of the preset to use\r\n" + \r
+                       "-o=<outputFile>   - full path to the file where to write an alignment\r\n" + \r
+                       "-f=<PrmInputFile> - the name of the file with the list of parameters to use.\r\n" + \r
+                       "\r\n" + \r
+                       "Please note that -r and -f options cannot be used together. Alignment is done with \r\n" + \r
+                       "either preset or a parameters from the file, but not both!\r\n" + \r
+                       "\r\n" + \r
+                       "EXAMPLES: \r\n" + \r
+                       "\r\n" + \r
+                       "1) List all available services on the host \r\n" + \r
+                       "\r\n" + \r
+                       "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -list_services\r\n" + \r
+                       "\r\n" + \r
+                       "2) Test Clustal web service \r\n" + \r
+                       "\r\n" + \r
+                       "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n" + \r
+                       "\r\n" + \r
+                       "3) Align sequence from file input.txt with Probcons. Record resulting alignment \r\n" + \r
+                       "into the output.txt \r\n" + \r
+                       "\r\n" + \r
+                       "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r\n" + \r
+                       "\r\n" + \r
+                       "4) Calculate disorder with Disembl take input from input.txt, output results to \r\n" + \r
+                       "the console \r\n" + \r
+                       "\r\n" + \r
+                       "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r\n" + \r
+                       "\r\n" + \r
+                       "5) List all parameters available for AAconWS service \r\n" + \r
+                       "\r\n" + \r
+                       "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r\n" + \r
+                       "\r\n" + \r
+                       "6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment \r\n" + \r
+                       "from input.txt and report  the scores to the console \r\n" + \r
+                       "\r\n" + \r
+                       "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r\n" + \r
+                       "\r\n" + \r
+                       "Where the content of prm.txt file is -m=LANDGRAF\r\n" + \r
+                       "The list of the supported parameters can be obtained as shown in the example 5. \r\n" + \r
+                       "\r\n" + \r
+                       "Citation: Peter V. Troshin, James B. Procter and Geoffrey J. Barton - \"Java \r\n" + \r
+                       "Bioinformatics Analysis Web Services for Multiple Sequence Alignment - \r\n" + \r
+                       "JABAWS:MSA\" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.\r\n" + \r
+                       "";\r
 \r
 }\r