Merge branch 'develop' into spike/JAL-1950_hmmer3client

[jalview.git] / src / jalview / ws / rest / RestClient.java

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index 7fbae89..54e0e04 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -28,15 +28,14 @@ import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.gui.WebserviceInfo;
-import jalview.io.packed.DataProvider.JvDataType;
 import jalview.util.MessageManager;
 import jalview.ws.WSClient;
 import jalview.ws.WSClientI;
 import jalview.ws.WSMenuEntryProviderI;
+import jalview.ws.rest.clientdefs.ShmrRestClient;
 
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
-import java.util.Hashtable;
 import java.util.Vector;
 
 import javax.swing.JMenu;
@@ -336,47 +335,6 @@ public class RestClient extends WSClient implements WSClientI,
     }
   }
 
-  public static RestClient makeShmmrRestClient()
-  {
-    String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager
-            .getString("label.multiharmony");
-    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();
-    // SHMR server has a 65K limit for content pasted into the 'ali' parameter,
-    // so we always upload our files.
-    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://zeus.few.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);
-  }
-
   public AlignmentPanel recoverAlignPanelForView()
   {
     AlignmentPanel[] aps = Desktop
@@ -411,7 +369,7 @@ public class RestClient extends WSClient implements WSClientI,
         for (RestServiceDescription descr : RestServiceDescription
                 .parseDescriptions(jalview.bin.Cache.getDefault(
                         RSBS_SERVICES,
-                        makeShmmrRestClient().service.toString())))
+                        ShmrRestClient.makeShmmrRestClient().service.toString())))
         {
           services.add(descr.toString());
         }