webservices/compbio/ws/client/Constraints.java

   1 package compbio.ws.client;\r
   2 \r
   3 class Constraints {\r
   4 \r
   5         final static String pseparator = "=";\r
   6 \r
   7         // Parameters for required command line options\r
   8         final static String hostkey = "-h";\r
   9         final static String servicekey = "-s";\r
  10 \r
  11         final static String listServices = "-list_services";\r
  12         final static String testKey = "-test";\r
  13 \r
  14         // Actions\r
  15         final static String inputkey = "-i";\r
  16 \r
  17         final static String paramList = "-parameters";\r
  18         final static String presetList = "-presets";\r
  19         final static String limitList = "-limits";\r
  20 \r
  21         // Options\r
  22         final static String paramFile = "-f";\r
  23         final static String outputkey = "-o";\r
  24         final static String parameterkey = "-p";\r
  25         final static String presetkey = "-r";\r
  26 \r
  27         final static String help_text = "\r\n"\r
  28                         + "JABAWS client v2.0 June 2011 http://www.compbio.dundee.ac.uk/jabaws \r\n"\r
  29                         + " \r\n"\r
  30                         + "Usage: <Class or Jar file name> -h=host_and_context <-s=serviceName> ACTION [OPTIONS] \r\n"\r
  31                         + "\r\n"\r
  32                         + "-h=<host_context>  - a full URL to the JABAWS web server including context \r\n"\r
  33                         + "                     path e.g. http://10.31.1.159:8080/ws\r\n"\r
  34                         + "-s=<ServiceName>   - one of [MafftWS, MuscleWS, ClustalWS, TcoffeeWS, ProbconsWS, \r\n"\r
  35                         + "                     AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS]\r\n"\r
  36                         + "                     <serviceName> is required for all ACTIONS but -list_services\r\n"\r
  37                         + "\r\n"\r
  38                         + "ACTIONS: \r\n"\r
  39                         + "-list_services    - list available services\r\n"\r
  40                         + "-test             - test service \r\n"\r
  41                         + "-i=<inputFile>    - full path to fasta formatted sequence file, from which to align \r\n"\r
  42                         + "                    sequences\r\n"\r
  43                         + "-parameters       - lists parameters supported by web service\r\n"\r
  44                         + "-presets          - lists presets supported by web service\r\n"\r
  45                         + "-limits           - lists web services limits\r\n"\r
  46                         + "\r\n"\r
  47                         + "Please note that if input file is specified other actions are ignored\r\n"\r
  48                         + "\r\n"\r
  49                         + "OPTIONS (only for use with -i action):\r\n"\r
  50                         + "-r=<presetName>   - name of the preset to use\r\n"\r
  51                         + "-o=<outputFile>   - full path to the file where to write an alignment\r\n"\r
  52                         + "-f=<PrmInputFile> - the name of the file with the list of parameters to use.\r\n"\r
  53                         + "\r\n"\r
  54                         + "Please note that -r and -f options cannot be used together. Alignment is done with \r\n"\r
  55                         + "either preset or a parameters from the file, but not both!\r\n"\r
  56                         + "\r\n"\r
  57                         + "EXAMPLES: \r\n"\r
  58                         + "\r\n"\r
  59                         + "1) List all available services on the host \r\n"\r
  60                         + "\r\n"\r
  61                         + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -list_services\r\n"\r
  62                         + "\r\n"\r
  63                         + "2) Test Clustal web service \r\n"\r
  64                         + "\r\n"\r
  65                         + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n"\r
  66                         + "\r\n"\r
  67                         + "3) Align sequence from file input.txt with Probcons. Record resulting alignment \r\n"\r
  68                         + "into the output.txt \r\n"\r
  69                         + "\r\n"\r
  70                         + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r\n"\r
  71                         + "\r\n"\r
  72                         + "4) Calculate disorder with Disembl take input from input.txt, output results to \r\n"\r
  73                         + "the console \r\n"\r
  74                         + "\r\n"\r
  75                         + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r\n"\r
  76                         + "\r\n"\r
  77                         + "5) List all parameters available for AAconWS service \r\n"\r
  78                         + "\r\n"\r
  79                         + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r\n"\r
  80                         + "\r\n"\r
  81                         + "6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment \r\n"\r
  82                         + "from input.txt and report  the scores to the console \r\n"\r
  83                         + "\r\n"\r
  84                         + "Jws2Client -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r\n"\r
  85                         + "\r\n"\r
  86                         + "Where the content of prm.txt file is -m=LANDGRAF\r\n"\r
  87                         + "The list of the supported parameters can be obtained as shown in the example 5. \r\n"\r
  88                         + "\r\n"\r
  89                         + "Citation: Peter V. Troshin, James B. Procter and Geoffrey J. Barton - \"Java \r\n"\r
  90                         + "Bioinformatics Analysis Web Services for Multiple Sequence Alignment - \r\n"\r
  91                         + "JABAWS:MSA\" Bioinformatics 2011; doi: 10.1093/bioinformatics/btr304.\r\n"\r
  92                         + "";\r
  93 \r
  94 }\r