From 92f2bdf5a7a89ceefe2bff76ca75414cf0fb633c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 7 Apr 2006 11:27:55 +0000
Subject: [PATCH] Autocalculate consensus set in preferences

---
 src/jalview/gui/AlignViewport.java  |    2 ++
 src/jalview/gui/Preferences.java    |    4 ++++
 src/jalview/jbgui/GAlignFrame.java  |    2 +-
 src/jalview/jbgui/GPreferences.java |    7 +++++++
 4 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 2c8172b..15c10e7 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -136,6 +136,8 @@ public class AlignViewport
       showQuality = Cache.getDefault("SHOW_QUALITY", true);
       showIdentity = Cache.getDefault("SHOW_IDENTITY", true);
 
+      autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
        String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
        String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;
        String fontSize = Cache.getDefault("FONT_SIZE", "10");
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index f322daa..8cbe03f 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -150,6 +150,8 @@ public class Preferences extends GPreferences
         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
 
+        autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+
   /****************************************************
    * Set up Connections
    */
@@ -277,6 +279,8 @@ public class Preferences extends GPreferences
         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
 
+        Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+                                                Boolean.toString(autoCalculateConsCheck.isSelected()));
 
         Cache.saveProperties();
         try
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 1cbe15c..422f9a7 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -979,7 +979,7 @@ public class GAlignFrame
       }
     });
     autoCalculate.setText("Autocalculate Consensus");
-    autoCalculate.setState(true);
+    autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
     autoCalculate.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 8b10c5f..58c7743 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -104,6 +104,8 @@ public class GPreferences extends JPanel
   protected JCheckBox seqLimit = new JCheckBox();
   GridLayout gridLayout3 = new GridLayout();
   protected JCheckBox smoothFont = new JCheckBox();
+  JPanel calcTab = new JPanel();
+  protected JCheckBox autoCalculateConsCheck = new JCheckBox();
   /**
      * Creates a new GPreferences object.
      */
@@ -357,6 +359,9 @@ public class GPreferences extends JPanel
     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
     smoothFont.setText("Smooth Font");
+    calcTab.setLayout(null);
+    autoCalculateConsCheck.setText("AutoCalculate Consensus");
+    autoCalculateConsCheck.setBounds(new Rectangle(16, 29, 209, 23));
     jPanel2.add(fullScreen);
 
     jPanel2.add(annotations);
@@ -439,6 +444,8 @@ public class GPreferences extends JPanel
     jPanel11.add(pfamjv);
     jPanel11.add(pileupjv);
     jPanel11.add(pirjv);
+    tabbedPane.add(calcTab, "Calculations");
+    calcTab.add(autoCalculateConsCheck);
 
     exportTab.add(epsLabel);
     exportTab.add(epsRendering);
-- 
1.7.10.2