- 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