JAL-715 JAL-724 refactored multi harmony definition out of core class

diff --git a/src/jalview/gui/RestServiceEditorPane.java b/src/jalview/gui/RestServiceEditorPane.java
index ec8e7f1..961ec4c 100644 (file)
--- a/src/jalview/gui/RestServiceEditorPane.java
+++ b/src/jalview/gui/RestServiceEditorPane.java
@@ -472,7 +472,7 @@ public class RestServiceEditorPane extends GRestServiceEditorPane
             df.getContentPane().setLayout(new BorderLayout());
             df.getContentPane().add(
                     (nulserv = !nulserv) ? new RestServiceEditorPane(
-                            jalview.ws.rest.RestClient
+                            jalview.ws.rest.clientdefs.ShmrRestClient
                                     .makeShmmrRestClient()
                                     .getRestDescription())
                             : new RestServiceEditorPane(),

diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java
index 1fb9259..1abe36e 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -27,15 +27,14 @@ import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 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());
         }

diff --git a/src/jalview/ws/rest/clientdefs/ShmrRestClient.java b/src/jalview/ws/rest/clientdefs/ShmrRestClient.java
new file mode 100644 (file)
index 0000000..a10931b
--- /dev/null
+++ b/src/jalview/ws/rest/clientdefs/ShmrRestClient.java
@@ -0,0 +1,58 @@
+package jalview.ws.rest.clientdefs;
+
+import jalview.io.packed.DataProvider.JvDataType;
+import jalview.util.MessageManager;
+import jalview.ws.rest.InputType;
+import jalview.ws.rest.RestClient;
+import jalview.ws.rest.RestServiceDescription;
+import jalview.ws.rest.params.Alignment;
+import jalview.ws.rest.params.JobConstant;
+import jalview.ws.rest.params.SeqGroupIndexVector;
+
+import java.util.Hashtable;
+
+public class ShmrRestClient
+{
+
+  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);
+  }
+
+}

diff --git a/test/jalview/ws/rest/ShmmrRSBSService.java b/test/jalview/ws/rest/ShmmrRSBSService.java
index 30383f7..a9989fd 100644 (file)
--- a/test/jalview/ws/rest/ShmmrRSBSService.java
+++ b/test/jalview/ws/rest/ShmmrRSBSService.java
@@ -24,6 +24,7 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.gui.AlignFrame;
+import jalview.ws.rest.clientdefs.ShmrRestClient;
 
 import java.util.Map;
 
@@ -43,13 +44,13 @@ public class ShmmrRSBSService
     assertTrue(
             "Test Rsd Exchange using using default Shmmr service failed.",
             testRsdExchange("Test using default Shmmr service",
-                    RestClient.makeShmmrRestClient().service));
+                    ShmrRestClient.makeShmmrRestClient().service));
   }
 
   @Test(groups = { "Functional" })
   public void testShmmrServiceDataprep() throws Exception
   {
-    RestClient _rc = RestClient.makeShmmrRestClient();
+    RestClient _rc = ShmrRestClient.makeShmmrRestClient();
     assertNotNull(_rc);
     AlignFrame alf = new jalview.io.FileLoader(false)
             .LoadFileWaitTillLoaded("examples/testdata/smad.fa",