showunconserved preference

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index bae40ca..60fae37 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -106,6 +106,7 @@ import org.biojava.dasobert.dasregistry.Das1Source;
  * (false) </li>
  * <li>SHOW_NPFEATS_TOOLTIP (true) show non-positional features in the Sequence ID tooltip</li>
  * <li>SHOW_DBREFS_TOOLTIP (true) show Database Cross References in the Sequence ID tooltip</li>
+ * <li>SHOW_UNCONSERVED (false) only render unconserved residues - conserved displayed as '.'</li>
  * <li> </li>
  * 
  * </ul>

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index e28581f..22a4737 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -20,6 +20,7 @@ package jalview.jbgui;
 
 import java.awt.*;
 import java.awt.event.*;
+
 import javax.swing.*;
 import javax.swing.border.*;
 import javax.swing.event.*;
@@ -187,6 +188,8 @@ public class GPreferences extends JPanel
 
   protected JCheckBox rightAlign = new JCheckBox();
 
+  protected JCheckBox showUnconserved = new JCheckBox();
+
   protected JCheckBox idItalics = new JCheckBox();
 
   protected JCheckBox openoverv = new JCheckBox();
@@ -266,6 +269,20 @@ public class GPreferences extends JPanel
         annotations_actionPerformed(e);
       }
     });
+    showUnconserved.setFont(verdana11);
+    showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
+    showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
+    //showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
+    showUnconserved.setSelected(true);
+    showUnconserved.setText("Show Unconserved");
+    showUnconserved.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        showunconserved_actionPerformed(e);
+      }
+    });
+    
     gapLabel.setFont(verdana11);
     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     gapLabel.setText("Gap Symbol ");
@@ -278,11 +295,11 @@ public class GPreferences extends JPanel
     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     fontLabel.setText("Font ");
     fontSizeCB.setFont(verdana11);
-    fontSizeCB.setBounds(new Rectangle(319, 111, 49, 21));
+    fontSizeCB.setBounds(new Rectangle(319, 101, 49, 21));
     fontStyleCB.setFont(verdana11);
-    fontStyleCB.setBounds(new Rectangle(367, 111, 70, 21));
+    fontStyleCB.setBounds(new Rectangle(367, 101, 70, 21));
     fontNameCB.setFont(verdana11);
-    fontNameCB.setBounds(new Rectangle(172, 111, 147, 21));
+    fontNameCB.setBounds(new Rectangle(172, 101, 147, 21));
     gapSymbolCB.setFont(verdana11);
     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 21));
     startupCheckbox.setText("Open file");
@@ -401,7 +418,7 @@ public class GPreferences extends JPanel
     sortLabel.setText("Sort by ");
     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
     jPanel2.setLayout(gridLayout2);
-    gridLayout2.setRows(12);
+    gridLayout2.setRows(13);
     jPanel3.setBounds(new Rectangle(173, 35, 274, 26));
     exportTab.setLayout(null);
     epsLabel.setFont(verdana11);
@@ -484,6 +501,7 @@ public class GPreferences extends JPanel
     jPanel2.add(seqLimit);
     jPanel2.add(rightAlign);
     jPanel2.add(fontLabel);
+    jPanel2.add(showUnconserved);
     jPanel2.add(idItalics);
     jPanel2.add(smoothFont);
     jPanel2.add(wrap);
@@ -504,6 +522,7 @@ public class GPreferences extends JPanel
     jPanel3.add(identity);
     jPanel3.add(quality);
     visualTab.add(jPanel2);
+
     linkPanel.add(editLinkButtons, BorderLayout.EAST);
     editLinkButtons.add(newLink, null);
     editLinkButtons.add(editLink, null);
@@ -571,6 +590,12 @@ public class GPreferences extends JPanel
     exportTab.add(jPanel11);
   }
 
+  protected void showunconserved_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
   /**
    * DOCUMENT ME!
    *