X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2Frest%2FRestClient.java;h=b04030d466e3b607fbe66ffa97b2a759deb22e55;hb=f3133c4f086cbdf59a7ce7fe465d2a5fa4a0fd60;hp=a71b70d62a72db33a6bdcc4d4be6aed3f24d47a4;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index a71b70d..b04030d 100644
--- 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;
@@ -339,46 +338,6 @@ public class RestClient extends WSClient
     }
   }
 
-  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
@@ -411,9 +370,9 @@ public class RestClient extends WSClient
       try
       {
         for (RestServiceDescription descr : RestServiceDescription
-                .parseDescriptions(
-                        jalview.bin.Cache.getDefault(RSBS_SERVICES,
-                                makeShmmrRestClient().service.toString())))
+                .parseDescriptions(jalview.bin.Cache.getDefault(
+                        RSBS_SERVICES,
+                        ShmrRestClient.makeShmmrRestClient().service.toString())))
         {
           services.add(descr.toString());
         }