- public static RestClient makeShmmrRestClient()
- {
- String action = "Analysis", description = "Sequence Harmony and Multi-Relief (UNSTABLE!)", name = "Sequence Harmony";
- Hashtable<String, InputType> iparams = new Hashtable<String, InputType>();
- jalview.ws.rest.params.JobConstant toolp;
- //toolp = new jalview.ws.rest.JobConstant("tool","jalview");
- //iparams.put(toolp.token, toolp);
- toolp = new jalview.ws.rest.params.JobConstant("mbjob[method]","shmr");
- iparams.put(toolp.token, toolp);
- toolp = new jalview.ws.rest.params.JobConstant("mbjob[description]","step 1");
- iparams.put(toolp.token, toolp);
- toolp = new jalview.ws.rest.params.JobConstant("start_search","1");
- iparams.put(toolp.token, toolp);
- toolp = new jalview.ws.rest.params.JobConstant("blast","0");
- iparams.put(toolp.token, toolp);
-
- jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
- aliinput.token = "ali";//_file";
- aliinput.writeAsFile=false;//true;
- //aliinput.token = "ali_file";
- //aliinput.writeAsFile=true;
- iparams.put(aliinput.token, aliinput);
- jalview.ws.rest.params.SeqGroupIndexVector sgroups = new jalview.ws.rest.params.SeqGroupIndexVector();
- sgroups.setMinsize(2);
- sgroups.min=2;// need at least two group defined to make a partition
- iparams.put("groups", sgroups);
- sgroups.token = "groups";
- sgroups.sep = " ";
- RestServiceDescription shmrService = new RestServiceDescription(
- action,
- description,
- name,
- "http://www.ibi.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
- "?tool=jalview", iparams, true, false, '-');
- // a priori knowledge of the data returned from the service
- shmrService.addResultDatatype(JvDataType.ANNOTATION);
- return new RestClient(shmrService);
- }
-