X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FSequenceAnnotationWSClient.java;h=e3f3674928cc5568af8842cddfcfc93c6ec79afe;hb=7526a82c54f0ef8434f826a1f2323ca5ec1eb3b1;hp=3e4cbe15eb86c37200b076d26c6be289c9c415c6;hpb=6709b4d7eaeb41020a0e8101730400507c8005a7;p=jalview.git

diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
index 3e4cbe1..e3f3674 100644
--- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
+++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java
@@ -9,12 +9,15 @@ import java.util.List;
 
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
 
 import compbio.metadata.Argument;
 
 import jalview.api.AlignCalcWorkerI;
 import jalview.datamodel.AlignmentView;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.JalviewDialog;
 import jalview.gui.JvSwingUtils;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.params.WsParamSetI;
@@ -38,37 +41,69 @@ public class SequenceAnnotationWSClient extends Jws2Client
           AlignFrame alignFrame, WsParamSetI preset, boolean editParams)
   {
     super(alignFrame, preset, null);
-    List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
-            .getCalcManager()
-            .getRegisteredWorkersOfClass(AAConsClient.class);
-    if (clnts == null || clnts.size() == 0)
+    if (alignFrame.getViewport().getAlignment().isNucleotide())
     {
+      JOptionPane
+              .showMessageDialog(
+                      Desktop.desktop,
+                      sh.serviceType+" can only be used\nfor amino acid alignments.",
+                      "Wrong type of sequences!",
+                      JOptionPane.WARNING_MESSAGE);
+      return;
+
+    }
+    if (sh.action.toLowerCase().contains("conservation"))
+    {
+      // Build an AACons style client - take alignment, return annotation for columns
+
+      List<AlignCalcWorkerI> clnts = alignFrame.getViewport()
+              .getCalcManager()
+              .getRegisteredWorkersOfClass(AAConsClient.class);
+      if (clnts == null || clnts.size() == 0)
+      {
+        if (!processParams(sh, editParams))
+        {
+          return;
+        }
+        alignFrame
+                .getViewport()
+                .getCalcManager()
+                .registerWorker(
+                        new AAConsClient(sh, alignFrame, preset, paramset));
+      }
+      else
+      {
+        AAConsClient worker = (AAConsClient) clnts.get(0);
+        if (editParams)
+        {
+          paramset = worker.getArguments();
+          preset = worker.getPreset();
+        }
+
+        if (!processParams(sh, editParams, true))
+          return;
+        // reinstate worker if it was blacklisted (might have happened due to
+        // invalid parameters)
+        alignFrame.getViewport().getCalcManager().workerMayRun(worker);
+        worker.updateParameters(preset, paramset);
+
+      }
+    }
+    if (sh.action.toLowerCase().contains("disorder"))
+    {
+      // build IUPred style client. take sequences, returns annotation per sequence.
       if (!processParams(sh, editParams))
       {
         return;
       }
+
       alignFrame
               .getViewport()
               .getCalcManager()
-              .registerWorker(
-                      new AAConsClient(sh, alignFrame, preset, paramset));
+              .startWorker(
+                      new AADisorderClient(sh, alignFrame, preset, paramset));
     }
-    else
-    {
-      AAConsClient worker = (AAConsClient) clnts.get(0);
-      if (editParams)
-      {
-        paramset = worker.getArguments();
-        preset = worker.getPreset();
-      }
-
-      if (!processParams(sh, editParams, true))
-        return;
-      // reinstate worker if it was blacklisted (might have happened due to invalid parameters)
-      alignFrame.getViewport().getCalcManager().workerMayRun(worker);
-      worker.updateParameters(preset, paramset);
 
-    }
   }
 
   /*
@@ -80,63 +115,61 @@ public class SequenceAnnotationWSClient extends Jws2Client
   public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service,
           final AlignFrame alignFrame)
   {
-    if (service.serviceType.toLowerCase().contains("aaconws"))
+    boolean hasparams = service.hasParameters();
+    // Assume name ends in WS
+    String calcName = service.serviceType.substring(0,service.serviceType.length()-2);
+
+    JMenuItem aacons = new JMenuItem(calcName + " Defaults");
+    aacons.addActionListener(new ActionListener()
     {
-      boolean hasparams = service.hasParameters();
-      String calcName = "AACons";
-      System.out.println("Making an aacons client!");
-      JMenuItem aacons = new JMenuItem("AACons Defaults");
-      aacons.addActionListener(new ActionListener()
+
+      @Override
+      public void actionPerformed(ActionEvent e)
       {
+        new SequenceAnnotationWSClient(service, alignFrame, null, false);
+      }
+    });
+    wsmenu.add(aacons);
+    if (hasparams)
+    {
+      // only add these menu options if the service has user-modifiable
+      // arguments
+      aacons = new JMenuItem("Edit settings and run ...");
+      aacons.setToolTipText("View and change parameters before running calculation");
 
-        @Override
+      aacons.addActionListener(new ActionListener()
+      {
         public void actionPerformed(ActionEvent e)
         {
-          new SequenceAnnotationWSClient(service, alignFrame, null, false);
+          new SequenceAnnotationWSClient(service, alignFrame, null, true);
         }
       });
       wsmenu.add(aacons);
-      if (hasparams)
+      List<WsParamSetI> presets = service.getParamStore().getPresets();
+      if (presets != null && presets.size() > 0)
       {
-        // only add these menu options if the service has user-modifiable
-        // arguments
-        aacons = new JMenuItem("Edit settings and run ...");
-        aacons.setToolTipText("View and change the parameters before alignment.");
+        JMenu presetlist = new JMenu("Run " + calcName + "with preset");
 
-        aacons.addActionListener(new ActionListener()
+        for (final WsParamSetI preset : presets)
         {
-          public void actionPerformed(ActionEvent e)
+          final JMenuItem methodR = new JMenuItem(preset.getName());
+          methodR.setToolTipText("<html><p>"
+                  + JvSwingUtils.wrapTooltip("<strong>"
+                          + (preset.isModifiable() ? "User Preset"
+                                  : "Service Preset") + "</strong><br/>"
+                          + preset.getDescription() + "</p>") + "</html>");
+          methodR.addActionListener(new ActionListener()
           {
-            new SequenceAnnotationWSClient(service, alignFrame, null, true);
-          }
-        });
-        wsmenu.add(aacons);
-        List<WsParamSetI> presets = service.getParamStore().getPresets();
-        if (presets != null && presets.size() > 0)
-        {
-          JMenu presetlist = new JMenu("Run " + calcName + "with preset");
-
-          for (final WsParamSetI preset : presets)
-          {
-            final JMenuItem methodR = new JMenuItem(preset.getName());
-            methodR.setToolTipText("<html><p>"
-                    + JvSwingUtils.wrapTooltip("<strong>"
-                            + (preset.isModifiable() ? "User Preset"
-                                    : "Service Preset") + "</strong><br/>"
-                            + preset.getDescription() + "</p>") + "</html>");
-            methodR.addActionListener(new ActionListener()
+            public void actionPerformed(ActionEvent e)
             {
-              public void actionPerformed(ActionEvent e)
-              {
-                new SequenceAnnotationWSClient(service, alignFrame, preset,
-                        false);
-              }
-
-            });
-            presetlist.add(methodR);
-          }
-          wsmenu.add(presetlist);
+              new SequenceAnnotationWSClient(service, alignFrame, preset,
+                      false);
+            }
+
+          });
+          presetlist.add(methodR);
         }
+        wsmenu.add(presetlist);
       }
 
     }