Merge branch 'develop' into menard

[jalview.git] / src / jalview / jbgui / GPreferences.java

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 1a1f9d3..64bcf5c 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -1,6 +1,6 @@
 /*
 /*

- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle

  * 
  * This file is part of Jalview.
  * 
  * 
  * This file is part of Jalview.
  * 

@@ -160,6 +160,11 @@ public class GPreferences extends JPanel
   JLabel epsLabel = new JLabel();
 
   protected JComboBox epsRendering = new JComboBox();
   JLabel epsLabel = new JLabel();
 
   protected JComboBox epsRendering = new JComboBox();

+  
+  protected JLabel userIdWidthlabel = new JLabel();
+  protected JCheckBox autoIdWidth = new JCheckBox();
+  protected JTextField userIdWidth = new JTextField();
+

 
   JLabel jLabel1 = new JLabel();
 
 
   JLabel jLabel1 = new JLabel();
 

@@ -181,7 +186,7 @@ public class GPreferences extends JPanel
 
   JPanel jPanel11 = new JPanel();
 
 
   JPanel jPanel11 = new JPanel();
 

-  Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
+  Font verdana11 = JvSwingUtils.getLabelFont();

 
   protected JCheckBox seqLimit = new JCheckBox();
 
 
   protected JCheckBox seqLimit = new JCheckBox();
 

@@ -241,6 +246,8 @@ public class GPreferences extends JPanel
 
   protected JCheckBox followHighlight = new JCheckBox();
 
 
   protected JCheckBox followHighlight = new JCheckBox();
 

+  protected JCheckBox sortByTree= new JCheckBox();
+

   /**
    * Creates a new GPreferences object.
    */
   /**
    * Creates a new GPreferences object.
    */

@@ -436,7 +443,7 @@ public class GPreferences extends JPanel
     });
     maxcolourLabel.setFont(verdana11);
     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     });
     maxcolourLabel.setFont(verdana11);
     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);

-    maxcolourLabel.setText("Maximumum Colour ");
+    maxcolourLabel.setText("Maximum Colour ");

     maxColour.setFont(verdana11);
     maxColour.setBorder(BorderFactory.createEtchedBorder());
     maxColour.setPreferredSize(new Dimension(40, 20));
     maxColour.setFont(verdana11);
     maxColour.setBorder(BorderFactory.createEtchedBorder());
     maxColour.setPreferredSize(new Dimension(40, 20));

@@ -447,6 +454,7 @@ public class GPreferences extends JPanel
           maxColour_actionPerformed();
       }
     });
           maxColour_actionPerformed();
       }
     });

+    

     startupCheckbox.setText("Open file");
     startupCheckbox.setFont(verdana11);
     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
     startupCheckbox.setText("Open file");
     startupCheckbox.setFont(verdana11);
     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);

@@ -622,32 +630,71 @@ public class GPreferences extends JPanel
     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
     smoothFont.setText("Smooth Font");
     calcTab.setLayout(null);
     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
     smoothFont.setText("Smooth Font");
     calcTab.setLayout(null);

-    autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN,
-            11));
+    autoCalculateConsCheck.setFont(JvSwingUtils.getLabelFont());

     autoCalculateConsCheck.setText("AutoCalculate Consensus");
     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
     autoCalculateConsCheck.setText("AutoCalculate Consensus");
     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));

-    padGaps.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    padGaps.setText("Pad gaps when editing");
+    padGaps.setFont(JvSwingUtils.getLabelFont());
+    padGaps.setText("Pad Gaps When Editing");

     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
     padGaps.setBounds(new Rectangle(22, 94, 168, 23));

-    modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    sortByTree.setFont(JvSwingUtils.getLabelFont());
+    sortByTree.setText("Sort With New Tree");
+    sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
+    sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
+    
+    autoIdWidth.setFont(JvSwingUtils.getLabelFont());
+    autoIdWidth.setText("Automatically set ID width");
+    autoIdWidth.setToolTipText("<html>"+JvSwingUtils.wrapTooltip("Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed")+"</html>");
+    autoIdWidth.setBounds(new Rectangle(228, 96,188,23));
+    autoIdWidth.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        autoIdWidth_actionPerformed();
+      }
+    });
+    userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
+    userIdWidthlabel.setText("Figure ID column width");
+    userIdWidth
+            .setToolTipText("<html>"+JvSwingUtils
+                    .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")+"</html>");
+    userIdWidthlabel
+            .setToolTipText("<html>"+JvSwingUtils
+                    .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")+"</html>");
+    userIdWidthlabel.setBounds(new Rectangle(236, 120,168,23));
+    userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
+    userIdWidth.setText("");
+    userIdWidth.setBounds(new Rectangle(232,144,84,23));
+    userIdWidth.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        userIdWidth_actionPerformed();
+      }
+    });
+    modellerOutput.setFont(JvSwingUtils.getLabelFont());

     modellerOutput.setText("Use Modeller Output");
     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
     modellerOutput.setText("Use Modeller Output");
     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));

+

     dasPanel.setLayout(borderLayout4);
     wsPanel.setLayout(borderLayout5);
     dasPanel.setLayout(borderLayout4);
     wsPanel.setLayout(borderLayout5);

-    wrap.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    wrap.setFont(JvSwingUtils.getLabelFont());

     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
     wrap.setText("Wrap Alignment");
     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
     wrap.setText("Wrap Alignment");

-    rightAlign.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    rightAlign.setFont(JvSwingUtils.getLabelFont());

     rightAlign.setForeground(Color.black);
     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
     rightAlign.setText("Right Align Ids");
     rightAlign.setForeground(Color.black);
     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
     rightAlign.setText("Right Align Ids");

-    idItalics.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    idItalics.setFont(JvSwingUtils.getLabelFont());

     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
     idItalics.setText("Sequence Name Italics");
     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
     idItalics.setText("Sequence Name Italics");

-    openoverv.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    openoverv.setFont(JvSwingUtils.getLabelFont());

     openoverv.setActionCommand("Open Overview");
     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
     openoverv.setActionCommand("Open Overview");
     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);

@@ -787,10 +834,15 @@ public class GPreferences extends JPanel
     jPanel11.add(pfamjv);
     jPanel11.add(pileupjv);
     jPanel11.add(pirjv);
     jPanel11.add(pfamjv);
     jPanel11.add(pileupjv);
     jPanel11.add(pirjv);

+    exportTab.add(autoIdWidth);
+    exportTab.add(userIdWidth);
+    exportTab.add(userIdWidthlabel);

     exportTab.add(modellerOutput);
     tabbedPane.add(calcTab, "Editing");
     calcTab.add(autoCalculateConsCheck);
     calcTab.add(padGaps);
     exportTab.add(modellerOutput);
     tabbedPane.add(calcTab, "Editing");
     calcTab.add(autoCalculateConsCheck);
     calcTab.add(padGaps);

+    calcTab.add(sortByTree);
+    

     tabbedPane.add(dasPanel, "DAS Settings");
     tabbedPane.add(wsPanel, "Web Services");
 
     tabbedPane.add(dasPanel, "DAS Settings");
     tabbedPane.add(wsPanel, "Web Services");
 

@@ -799,6 +851,18 @@ public class GPreferences extends JPanel
     exportTab.add(jPanel11);
   }
 
     exportTab.add(jPanel11);
   }
 

+  protected void autoIdWidth_actionPerformed()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void userIdWidth_actionPerformed()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+

   protected void maxColour_actionPerformed()
   {
     // TODO Auto-generated method stub
   protected void maxColour_actionPerformed()
   {
     // TODO Auto-generated method stub