From e0c4027fce496e56101696f10559eb3ea94c7e7e Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 13 Apr 2015 15:59:59 +0100
Subject: [PATCH] JAL-1690 show 'scale protein' in protein _and_ dna menus;
 default true

---
 src/jalview/appletgui/FontChooser.java      |   15 +++++++++++---
 src/jalview/gui/FontChooser.java            |   28 +++++++++++++++++++--------
 src/jalview/viewmodel/styles/ViewStyle.java |    2 +-
 3 files changed, 33 insertions(+), 12 deletions(-)

diff --git a/src/jalview/appletgui/FontChooser.java b/src/jalview/appletgui/FontChooser.java
index ae59470..6456878 100644
--- a/src/jalview/appletgui/FontChooser.java
+++ b/src/jalview/appletgui/FontChooser.java
@@ -204,6 +204,13 @@ public class FontChooser extends Panel implements ItemListener
   {
     if (ap != null)
     {
+      ap.av.setScaleProteinAsCdna(oldScaleProtein);
+      if (ap.av.getCodingComplement() != null)
+      {
+        ap.av.getCodingComplement().setScaleProteinAsCdna(oldScaleProtein);
+        ap.alignFrame.getSplitFrame().repaint();
+      }
+
       ap.av.setFont(oldFont);
       ViewStyleI style = ap.av.getViewStyle();
       if (style.getCharWidth() != oldCharWidth)
@@ -390,11 +397,10 @@ public class FontChooser extends Panel implements ItemListener
     optionsPanel.add(stylePanel, null);
 
     /*
-     * Only show 'scale protein as cDNA' in protein half of a SplitFrame
+     * Only show 'scale protein as cDNA' in a SplitFrame
      */
     this.add(optionsPanel, BorderLayout.NORTH);
-    if (ap.alignFrame.getSplitFrame() != null
-            && !ap.av.getAlignment().isNucleotide())
+    if (ap.alignFrame.getSplitFrame() != null)
     {
       this.add(scalePanel, BorderLayout.CENTER);
     }
@@ -408,8 +414,11 @@ public class FontChooser extends Panel implements ItemListener
   protected void scaleAsCdna_actionPerformed()
   {
     ap.av.setScaleProteinAsCdna(scaleAsCdna.getState());
+    ap.av.getCodingComplement().setScaleProteinAsCdna(
+            scaleAsCdna.getState());
     ap.alignFrame.getSplitFrame().adjustLayout();
     ap.paintAlignment(true);
+    ap.alignFrame.getSplitFrame().repaint();
   }
 
 }
diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index 72b7bd6..5e13781 100755
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -91,11 +91,10 @@ public class FontChooser extends GFontChooser
     smoothFont.setSelected(ap.av.antiAlias);
 
     /*
-     * Enable 'scale protein as cDNA' in protein half of a SplitFrame view. The
-     * selection is stored in the ViewStyle of the Viewport
+     * Enable 'scale protein as cDNA' in a SplitFrame view. The selection is
+     * stored in the ViewStyle of both dna and protein Viewport
      */
-    if (ap.av.getCodingComplement() != null
-            && !ap.av.getAlignment().isNucleotide())
+    if (ap.av.getCodingComplement() != null)
     {
       scaleAsCdna.setVisible(true);
       scaleAsCdna.setSelected(ap.av.isScaleProteinAsCdna());
@@ -189,6 +188,11 @@ public class FontChooser extends GFontChooser
       ap.av.setFont(oldFont, true);
       ap.av.setScaleProteinAsCdna(oldProteinScale);
       ap.paintAlignment(true);
+      if (scaleAsCdna.isEnabled())
+      {
+        ap.av.setScaleProteinAsCdna(oldProteinScale);
+        ap.av.getCodingComplement().setScaleProteinAsCdna(oldProteinScale);
+      }
     }
     else if (tp != null)
     {
@@ -314,10 +318,10 @@ public class FontChooser extends GFontChooser
   }
 
   /**
-   * DOCUMENT ME!
+   * Make selected settings the defaults by storing them (via Cache class) in
+   * the .jalview_properties file (the file is only written when Jalview exits)
    * 
    * @param e
-   *          DOCUMENT ME!
    */
   public void defaultButton_actionPerformed(ActionEvent e)
   {
@@ -326,6 +330,8 @@ public class FontChooser extends GFontChooser
     Cache.setProperty("FONT_SIZE", fontSize.getSelectedItem().toString());
     Cache.setProperty("ANTI_ALIAS",
             Boolean.toString(smoothFont.isSelected()));
+    Cache.setProperty(Preferences.SCALE_PROTEIN_TO_CDNA,
+            Boolean.toString(scaleAsCdna.isSelected()));
   }
 
   /**
@@ -336,7 +342,13 @@ public class FontChooser extends GFontChooser
   protected void scaleAsCdna_actionPerformed(ActionEvent e)
   {
     ap.av.setScaleProteinAsCdna(scaleAsCdna.isSelected());
-    ((SplitFrame) ap.alignFrame.getSplitViewContainer()).adjustLayout();
-    ap.paintAlignment(true);
+    ap.av.getCodingComplement().setScaleProteinAsCdna(
+            scaleAsCdna.isSelected());
+    final SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+            .getSplitViewContainer();
+    splitFrame.adjustLayout();
+    splitFrame.repaint();
+    // ap.paintAlignment(true);
+    // TODO would like to repaint
   }
 }
diff --git a/src/jalview/viewmodel/styles/ViewStyle.java b/src/jalview/viewmodel/styles/ViewStyle.java
index fc34be8..adc2baf 100644
--- a/src/jalview/viewmodel/styles/ViewStyle.java
+++ b/src/jalview/viewmodel/styles/ViewStyle.java
@@ -149,7 +149,7 @@ public class ViewStyle implements ViewStyleI
    * If true, scale protein residues to 3 times width of cDNA bases (in
    * SplitFrame views only)
    */
-  private boolean scaleProteinAsCdna = false;
+  private boolean scaleProteinAsCdna = true;
 
   public ViewStyle(ViewStyleI viewStyle)
   {
-- 
1.7.10.2