selected states set in updateMenusFromViewport

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2b4b7e0..7ef0e25 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -59,8 +59,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
 
   /** DOCUMENT ME!! */
   public String currentFileFormat = null;
-  Stack historyList = new Stack();
-  Stack redoList = new Stack();
+
   private int treeCount = 0;
 
   /**
@@ -136,13 +135,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
      setGUINucleotide(viewport.alignment.isNucleotide());
    }
 
-   if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))
+   setMenusFromViewport(viewport);
+
+   if (viewport.wrapAlignment)
    {
-     wrapMenuItem.setSelected(true);
      wrapMenuItem_actionPerformed(null);
    }
 
    addKeyListener();
+
+
   }
 
   void addKeyListener()
@@ -177,6 +179,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
                 if(viewport.viewName==null)
                   viewport.viewName="View 1";
 
+                newview.historyList = viewport.historyList;
+                newview.redoList = viewport.redoList;
+
                 newview.sequenceSetID = viewport.getSequenceSetId();
                 newview.viewName = "View " +
                     (Desktop.getViewCount(viewport.getSequenceSetId())+1);
@@ -464,10 +469,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   public void setGUINucleotide(boolean nucleotide)
   {
     showTranslation.setVisible( nucleotide );
-    //sequenceFeatures.setVisible(!nucleotide );
-    //featureSettings.setVisible( !nucleotide );
-    conservationMenuItem.setVisible( !nucleotide );
-    modifyConservation.setVisible(   !nucleotide );
+    conservationMenuItem.setEnabled( !nucleotide );
+    modifyConservation.setEnabled(   !nucleotide );
 
     //Remember AlignFrame always starts as protein
     if(!nucleotide)
@@ -476,6 +479,34 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
     }
   }
 
+  /**
+   * Need to call this method when tabs are selected for multiple views,
+   * or when loading from Jalview2XML.java
+   * @param av AlignViewport
+   */
+  void setMenusFromViewport(AlignViewport av)
+  {
+    colourTextMenuItem.setSelected(av.showColourText);
+    abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
+    conservationMenuItem.setSelected(av.getConservationSelected());
+    seqLimits.setSelected(av.getShowJVSuffix());
+    renderGapsMenuItem.setSelected(av.renderGaps);
+    wrapMenuItem.setSelected(av.wrapAlignment);
+    annotationPanelMenuItem.setState(av.showAnnotation);
+    viewBoxesMenuItem.setSelected(av.showBoxes);
+    viewTextMenuItem.setSelected(av.showText);
+
+    setColourSelected(ColourSchemeProperty.
+                      getColourName(av.getGlobalColourScheme()));
+
+    showSeqFeatures.setSelected(av.showSequenceFeatures);
+    hiddenMarkers.setState(av.showHiddenMarkers);
+    applyToAllGroups.setState(av.colourAppliesToAllGroups);
+    smoothFont.setState(av.antiAlias);
+
+    updateEditMenuBar();
+  }
+
 
   Hashtable progressBars;
   public void setProgressBar(String message, long id)
@@ -823,10 +854,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   void updateEditMenuBar()
   {
 
-    if (historyList.size() > 0)
+    if (viewport.historyList.size() > 0)
     {
       undoMenuItem.setEnabled(true);
-      CommandI command = (CommandI) historyList.peek();
+      CommandI command = (CommandI) viewport.historyList.peek();
       undoMenuItem.setText("Undo " + command.getDescription());
     }
     else
@@ -835,11 +866,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
       undoMenuItem.setText("Undo");
     }
 
-    if (redoList.size() > 0)
+    if (viewport.redoList.size() > 0)
     {
       redoMenuItem.setEnabled(true);
 
-      CommandI command = (CommandI) redoList.peek();
+      CommandI command = (CommandI) viewport.redoList.peek();
       redoMenuItem.setText("Redo " + command.getDescription());
     }
     else
@@ -854,8 +885,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
   {
     if(command.getSize()>0)
     {
-      historyList.push(command);
-      redoList.clear();
+      viewport.historyList.push(command);
+      viewport.redoList.clear();
       updateEditMenuBar();
       viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
     }
@@ -870,8 +901,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void undoMenuItem_actionPerformed(ActionEvent e)
   {
-    CommandI command = (CommandI)historyList.pop();
-    redoList.push(command);
+    CommandI command = (CommandI)viewport.historyList.pop();
+    viewport.redoList.push(command);
     command.undoCommand();
 
     viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;
@@ -887,8 +918,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
    */
   protected void redoMenuItem_actionPerformed(ActionEvent e)
   {
-    CommandI command = (CommandI) redoList.pop();
-    historyList.push(command);
+    CommandI command = (CommandI) viewport.redoList.pop();
+    viewport.historyList.push(command);
     command.doCommand();
     viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null;
 
@@ -1489,7 +1520,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener
         }
       }
 
-      viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+      viewport.firePropertyChange("alignment", null,
+                                  viewport.getAlignment().getSequences());
     }
   }
 
@@ -3100,6 +3132,7 @@ public void drop(DropTargetDropEvent evt)
     {
       alignPanel = (AlignmentPanel) alignPanels.elementAt(index);
       viewport = alignPanel.av;
+      setMenusFromViewport(viewport);
     }
   }
 

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 4287e70..cbe888a 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -827,7 +827,6 @@ public class GAlignFrame
       }\r
     });\r
     applyToAllGroups.setText("Apply Colour To All Groups");\r
-    applyToAllGroups.setState(true);\r
     applyToAllGroups.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -958,14 +957,7 @@ public class GAlignFrame
       }\r
     });\r
 \r
-   /* tabbedPane.addChangeListener(new ChangeListener()\r
-        {\r
-          public void stateChanged(ChangeEvent ece)\r
-          {\r
 \r
-            tabSelected();\r
-          }\r
-        });*/\r
     featureSettings.setText("Feature Settings...");\r
     featureSettings.addActionListener(new ActionListener()\r
     {\r
@@ -990,7 +982,7 @@ public class GAlignFrame
         smoothFont_actionPerformed(e);\r
       }\r
     });\r
-    smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
+\r
     annotationColour.setText("By Annotation...");\r
     annotationColour.addActionListener(new ActionListener()\r
     {\r
@@ -1093,7 +1085,6 @@ public class GAlignFrame
       }\r
     });\r
     hiddenMarkers.setText("Hidden Markers");\r
-    hiddenMarkers.setState(true);\r
     hiddenMarkers.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r