src/jalview/ws/rest/clientdefs/ShmrRestClient.java

   1 package jalview.ws.rest.clientdefs;
   2
   3 import jalview.io.packed.DataProvider.JvDataType;
   4 import jalview.util.MessageManager;
   5 import jalview.ws.rest.InputType;
   6 import jalview.ws.rest.RestClient;
   7 import jalview.ws.rest.RestServiceDescription;
   8 import java.util.Hashtable;
   9
  10 public class ShmrRestClient
  11 {
  12
  13   public static RestClient makeShmmrRestClient()
  14   {
  15     String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
  16             .getString("label.multiharmony");
  17     Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
  18     jalview.ws.rest.params.JobConstant toolp;
  19     // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
  20     // iparams.put(toolp.token, toolp);
  21     // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
  22     // iparams.put(toolp.token, toolp);
  23     // toolp = new
  24     // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
  25     // iparams.put(toolp.token, toolp);
  26     // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
  27     // iparams.put(toolp.token, toolp);
  28     // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
  29     // iparams.put(toolp.token, toolp);
  30
  31     jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
  32     // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
  33     // so we always upload our files.
  34     aliinput.token = "ali_file";
  35     aliinput.writeAsFile = true;
  36     iparams.put(aliinput.token, aliinput);
  37     jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
  38     sgroups.setMinsize(2);
  39     sgroups.min = 2;// need at least two group defined to make a partition
  40     iparams.put("groups", sgroups);
  41     sgroups.token = "groups";
  42     sgroups.sep = " ";
  43     RestServiceDescription shmrService = new RestServiceDescription(
  44             action,
  45             description,
  46             name,
  47             "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
  48             "?tool=jalview", iparams, true, false, '-');
  49     // a priori knowledge of the data returned from the service
  50     shmrService.addResultDatatype(JvDataType.ANNOTATION);
  51     return new RestClient(shmrService);
  52   }
  53
  54 }