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 jalview.ws.rest.params.Alignment;
   9 import jalview.ws.rest.params.JobConstant;
  10 import jalview.ws.rest.params.SeqGroupIndexVector;
  11
  12 import java.util.Hashtable;
  13
  14 public class ShmrRestClient
  15 {
  16
  17   public static RestClient makeShmmrRestClient()
  18   {
  19     String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
  20             .getString("label.multiharmony");
  21     Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
  22     jalview.ws.rest.params.JobConstant toolp;
  23     // toolp = new jalview.ws.rest.JobConstant("tool","jalview");
  24     // iparams.put(toolp.token, toolp);
  25     // toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
  26     // iparams.put(toolp.token, toolp);
  27     // toolp = new
  28     // jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
  29     // iparams.put(toolp.token, toolp);
  30     // toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
  31     // iparams.put(toolp.token, toolp);
  32     // toolp = new jalview.ws.rest.params.JobConstant("blast","0");
  33     // iparams.put(toolp.token, toolp);
  34
  35     jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
  36     // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
  37     // so we always upload our files.
  38     aliinput.token = "ali_file";
  39     aliinput.writeAsFile = true;
  40     iparams.put(aliinput.token, aliinput);
  41     jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
  42     sgroups.setMinsize(2);
  43     sgroups.min = 2;// need at least two group defined to make a partition
  44     iparams.put("groups", sgroups);
  45     sgroups.token = "groups";
  46     sgroups.sep = " ";
  47     RestServiceDescription shmrService = new RestServiceDescription(
  48             action,
  49             description,
  50             name,
  51             "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
  52             "?tool=jalview", iparams, true, false, '-');
  53     // a priori knowledge of the data returned from the service
  54     shmrService.addResultDatatype(JvDataType.ANNOTATION);
  55     return new RestClient(shmrService);
  56   }
  57
  58 }