JAL-3066 Implement clustaloWS using slivka system.

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 18000bd..5a5df3b 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -33,6 +33,7 @@ import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureSettingsControllerI;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.SimilarityParamsI;
@@ -108,6 +109,7 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.WsParamSetI;
 import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.ws.slivkaws.SlivkaWSDiscoverer;
 
 import java.awt.BorderLayout;
 import java.awt.Component;
@@ -1198,13 +1200,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public boolean alignmentIsSufficient(int required)
   {
-    if (getViewport().getAlignment().getSequences().size() < required)
-    {
-      JOptionPane.showMessageDialog(this,
-              MessageManager.getString("label.not_enough_sequences"));
-      return false;
-    }
-    return true;
+      if (getViewport().getSequenceSelection().length < required)
+      {
+        JOptionPane.showMessageDialog(this,
+                MessageManager.getString("label.not_enough_sequences"));
+        return false;
+      }
+      return true;
   }
 
   /**
@@ -3786,6 +3788,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     alignPanel.paintAlignment(true, false);
   }
 
+  @Override
+  public void sortEValueMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByEValue(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+
+  @Override
+  public void sortBitScoreMenuItem_actionPerformed(ActionEvent e)
+  {
+    SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+    AlignmentSorter.sortByBitScore(viewport.getAlignment());
+    addHistoryItem(new OrderCommand("Group Sort", oldOrder,
+            viewport.getAlignment()));
+    alignPanel.paintAlignment(true, false);
+
+  }
+  
   /**
    * DOCUMENT ME!
    * 
@@ -4400,7 +4424,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       jws2servs.attachWSMenuEntry(webService, me);
                       for (Jws2Instance sv : jws2servs.getServices())
                       {
-                        if (sv.description.toLowerCase().contains("jpred"))
+                        if (sv.getName().toLowerCase().contains("jpred"))
                         {
                           for (JMenuItem jmi : legacyItems)
                           {
@@ -4420,6 +4444,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   }
                 }
                 build_urlServiceMenu(me.webService);
+
+
+                // TODO Mateusz - follow pattern for adding web service
+                // JMenuItems for slivka-based services
+
+                SlivkaWSDiscoverer slivkaDiscoverer = SlivkaWSDiscoverer.getInstance();
+                slivkaDiscoverer.attachWSMenuEntry(webService, me);
+
+
                 build_fetchdbmenu(webService);
                 for (JMenu item : wsmenu)
                 {
@@ -5211,6 +5244,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               @Override
               public void finished()
               {
+
+                for (FeatureSettingsModelI srcSettings : dbRefFetcher
+                        .getFeatureSettingsModels())
+                {
+
+                  alignPanel.av.mergeFeaturesStyle(srcSettings);
+                }
                 AlignFrame.this.setMenusForViewport();
               }
             });
@@ -5296,6 +5336,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                                   @Override
                                   public void finished()
                                   {
+                                    FeatureSettingsModelI srcSettings = dassource[0]
+                                            .getFeatureColourScheme();
+                                    alignPanel.av.mergeFeaturesStyle(
+                                            srcSettings);
                                     AlignFrame.this.setMenusForViewport();
                                   }
                                 });