Merge branch 'Jalview-JS/develop' into merge_js_develop

[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 5d1a288..2d39db5 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -30,15 +30,14 @@ 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;
@@ -120,12 +119,12 @@ public static final String RSBS_SERVICES = "RSBS_SERVICES";
   {
     WebServiceJobTitle = MessageManager
             .formatMessage("label.webservice_job_title", new String[]
-            { service.details.Action, service.details.Name });
-    WebServiceName = service.details.Name;
+            { service.details.getAction(), service.details.getName() });
+    WebServiceName = service.details.getName();
     WebServiceReference = "No reference - go to url for more info";
-    if (service.details.description != null)
+    if (service.details.getDescription() != null)
     {
-      WebServiceReference = service.details.description;
+      WebServiceReference = service.details.getDescription();
     }
     if (!headless)
     {
@@ -162,10 +161,10 @@ public static final String RSBS_SERVICES = "RSBS_SERVICES";
   public void attachWSMenuEntry(final JMenu wsmenu,
           final AlignFrame alignFrame)
   {
-    JMenuItem submit = new JMenuItem(service.details.Name);
+    JMenuItem submit = new JMenuItem(service.details.getName());
     submit.setToolTipText(MessageManager
             .formatMessage("label.rest_client_submit", new String[]
-            { service.details.Action, service.details.Name }));
+            { service.details.getAction(), service.details.getName() }));
     submit.addActionListener(new ActionListener()
     {
 
@@ -360,46 +359,6 @@ public static final String RSBS_SERVICES = "RSBS_SERVICES";
     }
   }
 
-  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
@@ -429,13 +388,13 @@ public static final String RSBS_SERVICES = "RSBS_SERVICES";
   {
     if (services == null)
     {
-      services = new Vector<String>();
+      services = new Vector<>();
       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());
         }
@@ -458,7 +417,7 @@ public static final String RSBS_SERVICES = "RSBS_SERVICES";
 
   public String getAction()
   {
-    return service.details.Action;
+    return service.details.getAction();
   }
 
   public RestServiceDescription getRestDescription()
@@ -468,7 +427,7 @@ public static final String RSBS_SERVICES = "RSBS_SERVICES";
 
   public static Vector<String> getRsbsDescriptions()
   {
-    Vector<String> rsbsDescrs = new Vector<String>();
+    Vector<String> rsbsDescrs = new Vector<>();
     for (RestClient rsbs : getRestClients())
     {
       rsbsDescrs.add(rsbs.getRestDescription().toString());