revised shmr service

[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 5a4cf61..df9050b 100644 (file)
--- a/src/jalview/ws/rest/RestClient.java
+++ b/src/jalview/ws/rest/RestClient.java
@@ -20,8 +20,10 @@ import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceGroup;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.WebserviceInfo;
+import jalview.io.packed.DataProvider.JvDataType;
 import jalview.ws.WSClient;
 import jalview.ws.WSClientI;
 import jalview.ws.WSMenuEntryProviderI;
@@ -82,6 +84,7 @@ public class RestClient extends WSClient implements WSClientI,
     {
       wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n"
               + WebServiceReference);
+      wsInfo.setRenderAsHtml(true);
     }
 
   }
@@ -172,14 +175,17 @@ public class RestClient extends WSClient implements WSClientI,
    */
   protected boolean isAlignmentModified()
   {
-    if (undoredo == null)
+    if (undoredo == null || av==null || av.getAlignment()==null)
     {
+      // always return modified if we don't have access to live GUI elements anymore.
       return true;
     }
     if (av.isUndoRedoHashModified(undoredo))
     {
-
+      // alignment has been modified in some way. 
+      return true;
     }
+    // TODO: look deeper into modification of selection state, etc that may affect RestJobThread.realiseResults(boolean merge); 
     return false;
 
   }
@@ -266,6 +272,7 @@ public class RestClient extends WSClient implements WSClientI,
     }
     else
     {
+      // TODO: try to tell the user why the job couldn't be started.
       JOptionPane.showMessageDialog(Desktop.desktop,
               "Unable to start web service analysis",
               "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
@@ -274,7 +281,7 @@ public class RestClient extends WSClient implements WSClientI,
 
   public static RestClient makeShmmrRestClient()
   {
-    String action = "Analyse", description = "Sequence Harmony and Multi-Relief", name = "SHMR";
+    String action = "Analyse", 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");
@@ -289,10 +296,13 @@ public class RestClient extends WSClient implements WSClientI,
     iparams.put(toolp.token, toolp);
     
     jalview.ws.rest.params.Alignment aliinput = new jalview.ws.rest.params.Alignment();
-    aliinput.token = "ali_file";
-    aliinput.writeAsFile=true;
-    iparams.put("ali_file", aliinput);
+    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.minsize=2;
     iparams.put("groups", sgroups);
     sgroups.token = "groups";
     sgroups.sep = " ";
@@ -302,7 +312,28 @@ public class RestClient extends WSClient implements WSClientI,
             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);
   }
 
+  public AlignmentPanel recoverAlignPanelForView()
+  {
+    AlignmentPanel[] aps = Desktop.getAlignmentPanels(av.getSequenceSetId());
+    for (AlignmentPanel alp:aps)
+    {
+      if (alp.av == av)
+      {
+        return alp;
+      }
+    }
+    return null;
+  }
+
+  public boolean isShowResultsInNewView()
+  {
+    // TODO make this a property of the service
+    return true;
+  }
+
 }