X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=webservices%2Fcompbio%2Fws%2Fclient%2FConstraints.java;h=412d9f2a93cb9d86180ea2a1ac38b698515465bf;hb=88d252a4d6e1b4bdfc03f617c5a97d2d7bb9d050;hp=e76ee6a84006352165562fdbcc3731ca488affa1;hpb=40f197693d886791ac801db40f28f4e0f0fb805c;p=jabaws.git

diff --git a/webservices/compbio/ws/client/Constraints.java b/webservices/compbio/ws/client/Constraints.java
index e76ee6a..412d9f2 100644
--- 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";
 	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: <Class or 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 \r\n"
-			+ "                     path e.g. http://10.31.1.159:8080/ws\r\n"
-			+ "-s=<ServiceName>   - one of [MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS, \r\n"
-			+ "                     AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]\r\n"
-			+ "                     <serviceName> 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=<inputFile>    - 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=<presetName>   - name of the preset to use\r\n"
-			+ "-o=<outputFile>   - full path to the file where to write an alignment\r\n"
-			+ "-f=<PrmInputFile> - 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" + 
+			"JABAWS2 client August 2011 http://www.compbio.dundee.ac.uk/jabaws \r\n" + 
+			" \r\n" + 
+			"Usage: <Class or 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 \r\n" + 
+			"                     path e.g. http://10.31.1.159:8080/ws\r\n" + 
+			"-s=<ServiceName>   - one of [MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, \r\n" + 
+			"					 ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]\r\n" + 
+			"                     <serviceName> 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=<inputFile>    - 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=<presetName>   - name of the preset to use\r\n" + 
+			"-o=<outputFile>   - full path to the file where to write an alignment\r\n" + 
+			"-f=<PrmInputFile> - 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" + 
+			"";
 
 }