Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppre...

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 07baa2e..6f57d83 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,8 +20,6 @@
  */
 package jalview.gui;
 
-import java.util.Locale;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -59,6 +57,7 @@ import java.util.Deque;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
+import java.util.Locale;
 import java.util.Vector;
 
 import javax.swing.ButtonGroup;
@@ -369,8 +368,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       // modifyPID.setEnabled(false);
     }
 
-    String sortby = Cache.getDefault("SORT_ALIGNMENT",
-            "No sort");
+    String sortby = Cache.getDefault("SORT_ALIGNMENT", "No sort");
 
     if (sortby.equals("Id"))
     {
@@ -489,8 +487,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             });
     if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
             .indexOf("devel") > -1
-            || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
-                    .indexOf("test") > -1)
+            || Cache.getDefault("VERSION", "DEVELOPMENT")
+                    .toLowerCase(Locale.ROOT).indexOf("test") > -1)
     {
       formatMenu.add(vsel);
     }
@@ -579,7 +577,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           if (viewport.cursorMode)
           {
-            alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown());
+            alignPanel.getSeqPanel().moveCursor(0, -1, evt.isShiftDown());
           }
 
           break;
@@ -3359,6 +3357,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
+   * Set or clear 'Show Sequence Feature Counts'
+   * 
+   * @param evt
+   *          DOCUMENT ME!
+   */
+  @Override
+  protected void showSeqFeatureCounts_actionPerformed(
+          ActionEvent actionEvent)
+  {
+    viewport.setShowSequenceFeatureCounts(
+            showSeqFeatureCounts.isSelected());
+    alignPanel.paintAlignment(true, true);
+  }
+
+  /**
    * Action on toggle of the 'Show annotations' menu item. This shows or hides
    * the annotations panel as a whole.
    * 
@@ -4289,9 +4302,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                   webService.add(me.webServiceNoServices);
                 }
                 // TODO: move into separate menu builder class.
-                boolean new_sspred = false;
-                if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
                 {
+                  // logic for 2.11.1.4 is
+                  // always look to see if there is a discover. if there isn't
+                  // we can't show any Jws2 services
+                  // if there are services available, show them - regardless of
+                  // the 'show JWS2 preference'
+                  // if the discoverer is running then say so
+                  // otherwise offer to trigger discovery if 'show JWS2' is not
+                  // enabled
                   Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
                   if (jws2servs != null)
                   {
@@ -4300,7 +4319,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       jws2servs.attachWSMenuEntry(webService, me);
                       for (Jws2Instance sv : jws2servs.getServices())
                       {
-                        if (sv.description.toLowerCase(Locale.ROOT).contains("jpred"))
+                        if (sv.description.toLowerCase(Locale.ROOT)
+                                .contains("jpred"))
                         {
                           for (JMenuItem jmi : legacyItems)
                           {
@@ -4308,8 +4328,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                           }
                         }
                       }
-
                     }
+
                     if (jws2servs.isRunning())
                     {
                       JMenuItem tm = new JMenuItem(
@@ -4317,6 +4337,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       tm.setEnabled(false);
                       webService.add(tm);
                     }
+                    else if (!Cache.getDefault("SHOW_JWS2_SERVICES", true))
+                    {
+                      JMenuItem enableJws2 = new JMenuItem(
+                              "Discover Web Services");
+                      enableJws2.setToolTipText(
+                              "Select to start JABA Web Service discovery (or enable option in Web Service preferences)");
+                      enableJws2.setEnabled(true);
+                      enableJws2.addActionListener(new ActionListener()
+                      {
+
+                        @Override
+                        public void actionPerformed(ActionEvent e)
+                        {
+                          // start service discoverer, but ignore preference
+                          Desktop.instance.startServiceDiscovery(false,
+                                  true);
+                        }
+                      });
+                      webService.add(enableJws2);
+                    }
                   }
                 }
                 build_urlServiceMenu(me.webService);
@@ -4472,8 +4512,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       al = dna.translateCdna(codeTable);
     } catch (Exception ex)
     {
-      Console.error(
-              "Exception during translation. Please report this !", ex);
+      Console.error("Exception during translation. Please report this !",
+              ex);
       final String msg = MessageManager.getString(
               "label.error_when_translating_sequences_submit_bug_report");
       final String errorTitle = MessageManager