update author list in license for (JAL-826)

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

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 42ffa5d..c37d230 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.
  * 
@@ -17,6 +17,8 @@
  */
 package jalview.jbgui;
 
+import jalview.gui.JvSwingUtils;
+
 import java.awt.*;
 import java.awt.event.*;
 
@@ -179,7 +181,7 @@ public class GPreferences extends JPanel
 
   JPanel jPanel11 = new JPanel();
 
-  Font verdana11 = new java.awt.Font("Verdana", Font.PLAIN, 11);
+  Font verdana11 = JvSwingUtils.getLabelFont();
 
   protected JCheckBox seqLimit = new JCheckBox();
 
@@ -239,22 +241,8 @@ public class GPreferences extends JPanel
 
   protected JCheckBox followHighlight = new JCheckBox();
 
-  public void addtoLayout(JPanel panel, String tooltip, JComponent label, JComponent valBox)
-  {
-    JPanel laypanel = new JPanel(),labPanel=new JPanel(), valPanel=new JPanel();
-    laypanel.setSize(panel.getWidth(),33);
-    labPanel.setBounds(new Rectangle(7, 7, 158, 23));
-    valPanel.setBounds(new Rectangle(172, 7, 270,23));
-    labPanel.setLayout(new GridLayout());
-    valPanel.setLayout(new GridLayout());
-    labPanel.add(label);
-    valPanel.add(valBox);
-    laypanel.add(labPanel);
-    laypanel.add(valPanel);
-    panel.add(laypanel);
-    valPanel.setToolTipText(tooltip);
-    labPanel.setToolTipText(tooltip);
-  }
+  protected JCheckBox sortByTree= new JCheckBox();
+
   /**
    * Creates a new GPreferences object.
    */
@@ -450,7 +438,7 @@ public class GPreferences extends JPanel
     });
     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));
@@ -461,6 +449,7 @@ public class GPreferences extends JPanel
           maxColour_actionPerformed();
       }
     });
+    
     startupCheckbox.setText("Open file");
     startupCheckbox.setFont(verdana11);
     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -636,32 +625,35 @@ public class GPreferences extends JPanel
     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));
-    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));
-    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));
+    modellerOutput.setFont(JvSwingUtils.getLabelFont());
     modellerOutput.setText("Use Modeller Output");
     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
     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");
-    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");
-    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");
-    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);
@@ -723,9 +715,13 @@ public class GPreferences extends JPanel
     tooltipSettings.add(showNpTooltip);
     visualTab.add(tooltipSettings);
     visualTab.add(jPanel2);
-    addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
-    addtoLayout(visual2Tab, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
-    addtoLayout(visual2Tab,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
+    JvSwingUtils.addtoLayout(visual2Tab, "Default Colourscheme for alignment", colourLabel, colour);
+    JPanel annotationShding=new JPanel();
+    annotationShding.setBorder(new TitledBorder("Annotation Shading Default"));
+    annotationShding.setLayout(new GridLayout(1,2));
+    JvSwingUtils.addtoLayout(annotationShding, "Default Minimum Colour for annotation shading", mincolourLabel,minColour);
+    JvSwingUtils.addtoLayout(annotationShding,"Default Maximum Colour for annotation shading", maxcolourLabel, maxColour);
+    visual2Tab.add(annotationShding); // , FlowLayout.LEFT);
 
 //    visual2panel.add(minColour);
 //    visual2panel.add(maxColour);
@@ -801,6 +797,8 @@ public class GPreferences extends JPanel
     tabbedPane.add(calcTab, "Editing");
     calcTab.add(autoCalculateConsCheck);
     calcTab.add(padGaps);
+    calcTab.add(sortByTree);
+    
     tabbedPane.add(dasPanel, "DAS Settings");
     tabbedPane.add(wsPanel, "Web Services");