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 aaa73a1..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.*;
 
@@ -46,6 +48,7 @@ public class GPreferences extends JPanel
   protected JCheckBox quality = new JCheckBox();
 
   JPanel visualTab = new JPanel();
+  JPanel visual2Tab = new JPanel();
 
   protected JCheckBox fullScreen = new JCheckBox();
 
@@ -55,6 +58,12 @@ public class GPreferences extends JPanel
 
   protected JCheckBox annotations = new JCheckBox();
 
+  protected JPanel minColour = new JPanel();
+  JLabel mincolourLabel = new JLabel();
+
+  protected JPanel maxColour = new JPanel();
+  JLabel maxcolourLabel = new JLabel();
+
   JLabel gapLabel = new JLabel();
 
   protected JComboBox colour = new JComboBox();
@@ -132,9 +141,12 @@ public class GPreferences extends JPanel
   JLabel sortLabel = new JLabel();
 
   JPanel jPanel2 = new JPanel();
+  JPanel visual2panel = new JPanel();
 
   GridLayout gridLayout2 = new GridLayout();
 
+  GridLayout gridLayout4 = new GridLayout();
+
   JPanel annsettingsPanel = new JPanel();
 
   JPanel autoAnnotSettings1 = new JPanel();
@@ -169,7 +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();
 
@@ -229,6 +241,8 @@ public class GPreferences extends JPanel
 
   protected JCheckBox followHighlight = new JCheckBox();
 
+  protected JCheckBox sortByTree= new JCheckBox();
+
   /**
    * Creates a new GPreferences object.
    */
@@ -276,6 +290,8 @@ public class GPreferences extends JPanel
     quality.setText("Quality");
     visualTab.setBorder(new TitledBorder("Open new alignment"));
     visualTab.setLayout(null);
+    visual2Tab.setBorder(new TitledBorder("Open new alignment"));
+    visual2Tab.setLayout(new FlowLayout());
     fullScreen.setFont(verdana11);
     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
@@ -395,7 +411,7 @@ public class GPreferences extends JPanel
     colour.setBounds(new Rectangle(172, 225, 155, 21));
     colourLabel.setFont(verdana11);
     colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    colourLabel.setText("Colour ");
+    colourLabel.setText("Alignment Colour ");
     fontLabel.setFont(verdana11);
     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     fontLabel.setText("Font ");
@@ -407,6 +423,33 @@ public class GPreferences extends JPanel
     fontNameCB.setBounds(new Rectangle(172, 104, 147, 23));
     gapSymbolCB.setFont(verdana11);
     gapSymbolCB.setBounds(new Rectangle(172, 204, 69, 23));
+    mincolourLabel.setFont(verdana11);
+    mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    mincolourLabel.setText("Minimum Colour");
+    minColour.setFont(verdana11);
+    minColour.setBorder(BorderFactory.createEtchedBorder());
+    minColour.setPreferredSize(new Dimension(40, 20));
+    minColour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+          minColour_actionPerformed();
+      }
+    });
+    maxcolourLabel.setFont(verdana11);
+    maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    maxcolourLabel.setText("Maximum Colour ");
+    maxColour.setFont(verdana11);
+    maxColour.setBorder(BorderFactory.createEtchedBorder());
+    maxColour.setPreferredSize(new Dimension(40, 20));
+    maxColour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+          maxColour_actionPerformed();
+      }
+    });
+    
     startupCheckbox.setText("Open file");
     startupCheckbox.setFont(verdana11);
     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -535,7 +578,7 @@ public class GPreferences extends JPanel
     sortLabel.setText("Sort by ");
     jPanel2.setBounds(new Rectangle(7, 17, 158, 278));
     jPanel2.setLayout(gridLayout2);
-    gridLayout2.setRows(13);
+    gridLayout2.setRows(12);
     exportTab.setLayout(null);
     epsLabel.setFont(verdana11);
     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
@@ -582,32 +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);
@@ -620,15 +666,13 @@ public class GPreferences extends JPanel
     jPanel2.add(showUnconserved);
     jPanel2.add(idItalics);
     jPanel2.add(smoothFont);
-    jPanel2.add(wrap);
     jPanel2.add(gapLabel);
-    jPanel2.add(colourLabel);
+    jPanel2.add(wrap);
     jPanel2.add(sortLabel);
     jPanel2.add(startupCheckbox);
     visualTab.add(annotations);
     visualTab.add(startupFileTextfield);
     visualTab.add(sortby);
-    visualTab.add(colour);
     visualTab.add(gapSymbolCB);
     visualTab.add(fontNameCB);
     visualTab.add(fontSizeCB);
@@ -671,6 +715,17 @@ public class GPreferences extends JPanel
     tooltipSettings.add(showNpTooltip);
     visualTab.add(tooltipSettings);
     visualTab.add(jPanel2);
+    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);
+//    visual2Tab.add(visual2panel);
 
     linkPanel.add(editLinkButtons, BorderLayout.EAST);
     editLinkButtons.add(newLink, null);
@@ -727,6 +782,7 @@ public class GPreferences extends JPanel
     gapSymbolCB.setRenderer(dlcr);
 
     tabbedPane.add(visualTab, "Visual");
+    tabbedPane.add(visual2Tab,"Colours");
     tabbedPane.add(connectTab, "Connections");
     tabbedPane.add(exportTab, "Output");
     jPanel11.add(jLabel1);
@@ -741,6 +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");
 
@@ -749,6 +807,18 @@ public class GPreferences extends JPanel
     exportTab.add(jPanel11);
   }
 
+  protected void maxColour_actionPerformed()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  protected void minColour_actionPerformed()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
   protected void showunconserved_actionPerformed(ActionEvent e)
   {
     // TODO Auto-generated method stub