default parameter for colours in annotation shading (JAL-234), ensure

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

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index aaa73a1..42ffa5d 100755 (executable)
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -46,6 +46,7 @@ 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 +56,12 @@ 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 +139,12 @@ 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();
@@ -229,6 +239,22 @@ 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);
+  }
   /**
    * Creates a new GPreferences object.
    */
@@ -276,6 +302,8 @@ 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 +423,7 @@ 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 +435,32 @@ 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("Maximumum 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 +589,7 @@ 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);
@@ -620,15 +674,13 @@ 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 +723,13 @@ 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);
+
+//    visual2panel.add(minColour);
+//    visual2panel.add(maxColour);
+//    visual2Tab.add(visual2panel);
 
     linkPanel.add(editLinkButtons, BorderLayout.EAST);
     editLinkButtons.add(newLink, null);
@@ -727,6 +786,7 @@ 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);
@@ -749,6 +809,18 @@ 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