From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 1 Apr 2015 13:57:24 +0000 (+0100)
Subject: JAL-1264 reinstate Show annotations menu item
X-Git-Tag: Jalview_2_9~69^2~17
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c640b1c17cbfbc41723b0441f049cd416267dcc3;p=jalview.git

JAL-1264 reinstate Show annotations menu item
---

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 3e919f6..93bd155 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -113,9 +113,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   public AlignViewport viewport;
 
-  int DEFAULT_WIDTH = 700;
+  // width and height may be overridden by applet parameters
+  int frameWidth = 700;
 
-  int DEFAULT_HEIGHT = 500;
+  int frameHeight = 500;
 
   String jalviewServletURL;
 
@@ -176,13 +177,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         if (param != null)
         {
           int width = Integer.parseInt(param);
-          DEFAULT_WIDTH = width;
+          frameWidth = width;
         }
         param = applet.getParameter("windowHeight");
         if (param != null)
         {
           int height = Integer.parseInt(param);
-          DEFAULT_HEIGHT = height;
+          frameHeight = height;
         }
       } catch (Exception ex)
       {
@@ -203,6 +204,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     showSequenceLogo.setState(viewport.isShowSequenceLogo());
     normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
     applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
+    annotationPanelMenuItem.setState(viewport.isShowAnnotation());
     showAlignmentAnnotations.setState(viewport.isShowAnnotation());
     showSequenceAnnotations.setState(viewport.isShowAnnotation());
 
@@ -1964,8 +1966,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
           }
         }
 
-        jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
-                DEFAULT_HEIGHT);
+        jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
+                frameHeight);
       }
       else
       {
@@ -3596,8 +3598,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     /*
      * Annotations menu
      */
-    // annotationsMenu.add(annotationPanelMenuItem);
-    // annotationsMenu.addSeparator();
+    annotationsMenu.add(annotationPanelMenuItem);
+    annotationsMenu.addSeparator();
     annotationsMenu.add(showAlignmentAnnotations);
     annotationsMenu.add(showSequenceAnnotations);
     annotationsMenu.add(sortAnnBySequence);
@@ -3771,8 +3773,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       add(alignPanel, BorderLayout.CENTER);
       // and register with the applet so it can pass external API calls to us
       jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
-              DEFAULT_WIDTH,
-              DEFAULT_HEIGHT);
+              frameWidth,
+              frameHeight);
     }
   }
 
diff --git a/src/jalview/appletgui/SplitFrame.java b/src/jalview/appletgui/SplitFrame.java
index cdd1605..59b66c6 100644
--- a/src/jalview/appletgui/SplitFrame.java
+++ b/src/jalview/appletgui/SplitFrame.java
@@ -1,16 +1,17 @@
 package jalview.appletgui;
 
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+import java.awt.GridLayout;
+import java.awt.Panel;
+
 import jalview.analysis.AlignmentUtils;
+import jalview.api.AlignmentViewPanel;
 import jalview.api.ViewStyleI;
 import jalview.bin.JalviewLite;
 import jalview.datamodel.AlignmentI;
 import jalview.structure.StructureSelectionManager;
 
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.GridLayout;
-import java.awt.Panel;
-
 public class SplitFrame extends EmbmenuFrame
 {
   private static final long serialVersionUID = 1L;
@@ -65,6 +66,14 @@ public class SplitFrame extends EmbmenuFrame
       ssm.addCommandListener(protein);
     }
 
+    /*
+     * Now mappings exist, can compute cDNA consensus on protein alignment
+     */
+    protein.initComplementConsensus();
+    AlignmentViewPanel ap = topAlignment.isNucleotide() ? bottomFrame.alignPanel
+            : topFrame.alignPanel;
+    protein.updateConsensus(ap);
+
     adjustLayout();
   }
 
@@ -178,9 +187,9 @@ public class SplitFrame extends EmbmenuFrame
     else
     {
       this.add(outermost);
-      int width = Math.max(topFrame.DEFAULT_WIDTH,
-              bottomFrame.DEFAULT_WIDTH);
-      int height = topFrame.DEFAULT_HEIGHT + bottomFrame.DEFAULT_HEIGHT;
+      int width = Math.max(topFrame.frameWidth,
+              bottomFrame.frameWidth);
+      int height = topFrame.frameHeight + bottomFrame.frameHeight;
       jalview.bin.JalviewLite
               .addFrame(this, this.getTitle(), width, height);
     }
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 5317d4c..2528841 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2263,6 +2263,13 @@ public class Jalview2XML
     int height = (int) (dnaFrame.getBounds().getHeight()
             + proteinFrame.getBounds().getHeight() + 50);
     Desktop.addInternalFrame(splitFrame, title, width, height);
+
+    /*
+     * And compute cDNA consensus (couldn't do earlier with consensus as
+     * mappings were not yet present)
+     */
+    proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
+
     return splitFrame;
   }
 
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 7054ed3..1270c15 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -1731,7 +1731,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
    * If this is a protein alignment and there are mappings to cDNA, add the cDNA
    * consensus annotation.
    */
-  protected void initComplementConsensus()
+  public void initComplementConsensus()
   {
     if (!alignment.isNucleotide())
     {