X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=a1ec0a9669f46599e0a60c1a7b147ff828bdce56;hb=60ba5da3aa84fe3a8e82dc0b4d9c847594eedc31;hp=02756f1552c0556af8795213f42845e207c80883;hpb=7651849dd842b8663742e55f621ffb1c8e631466;p=jalview.git

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 02756f1..a1ec0a9 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -104,6 +104,10 @@ public class GPreferences extends JPanel
   protected JCheckBox seqLimit = new JCheckBox();
   GridLayout gridLayout3 = new GridLayout();
   protected JCheckBox smoothFont = new JCheckBox();
+  JPanel calcTab = new JPanel();
+  protected JCheckBox autoCalculateConsCheck = new JCheckBox();
+  protected JCheckBox padGaps = new JCheckBox();
+  protected JCheckBox modellerOutput = new JCheckBox();
   /**
      * Creates a new GPreferences object.
      */
@@ -185,7 +189,7 @@ public class GPreferences extends JPanel
         gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
         gapLabel.setText("Gap Symbol ");
     colour.setFont(verdana11);
-        colour.setBounds(new Rectangle(172, 180, 155, 21));
+        colour.setBounds(new Rectangle(171, 180, 155, 21));
         colourLabel.setFont(verdana11);
         colourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
         colourLabel.setText("Colour ");
@@ -199,14 +203,14 @@ public class GPreferences extends JPanel
         fontNameCB.setFont(verdana11);
         fontNameCB.setBounds(new Rectangle(171, 100, 147, 21));
         gapSymbolCB.setFont(verdana11);
-        gapSymbolCB.setBounds(new Rectangle(172, 153, 69, 21));
+        gapSymbolCB.setBounds(new Rectangle(171, 153, 69, 21));
         startupCheckbox.setText("Open file");
     startupCheckbox.setFont(verdana11);
         startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
         startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
         startupCheckbox.setSelected(true);
         startupFileTextfield.setFont(verdana11);
-        startupFileTextfield.setBounds(new Rectangle(170, 236, 271, 20));
+        startupFileTextfield.setBounds(new Rectangle(171, 236, 270, 20));
         startupFileTextfield.addMouseListener(new MouseAdapter()
             {
                 public void mouseClicked(MouseEvent e)
@@ -308,7 +312,7 @@ public class GPreferences extends JPanel
     sortLabel.setFont(verdana11);
     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     sortLabel.setText("Sort by ");
-    jPanel2.setBounds(new Rectangle(7, 17, 158, 246));
+    jPanel2.setBounds(new Rectangle(7, 17, 158, 245));
     jPanel2.setLayout(gridLayout2);
     gridLayout2.setRows(9);
     jPanel3.setBounds(new Rectangle(167, 41, 274, 26));
@@ -350,13 +354,23 @@ public class GPreferences extends JPanel
     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
     seqLimit.setFont(verdana11);
     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
-    seqLimit.setHorizontalTextPosition(SwingConstants.LEADING);
+    seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
     seqLimit.setText("Full Sequence Id");
     gridLayout3.setRows(8);
     smoothFont.setFont(verdana11);
     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
     smoothFont.setText("Smooth Font");
+    calcTab.setLayout(null);
+    autoCalculateConsCheck.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    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.setBounds(new Rectangle(22, 94, 168, 23));
+    modellerOutput.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    modellerOutput.setText("Use Modeller Output");
+    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
     jPanel2.add(fullScreen);
 
     jPanel2.add(annotations);
@@ -367,10 +381,10 @@ public class GPreferences extends JPanel
     jPanel2.add(colourLabel);
     jPanel2.add(sortLabel);
     jPanel2.add(startupCheckbox);
-    visualTab.add(startupFileTextfield);
-    visualTab.add(sortby);
     visualTab.add(colour);
     visualTab.add(gapSymbolCB);
+    visualTab.add(startupFileTextfield);
+    visualTab.add(sortby);
     visualTab.add(fontNameCB);
     visualTab.add(fontSizeCB);
     visualTab.add(fontStyleCB);
@@ -428,7 +442,7 @@ public class GPreferences extends JPanel
         dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
         gapSymbolCB.setRenderer(dlcr);
 
-    tabbedPane.add(visualTab, "visualTab");
+    tabbedPane.add(visualTab, "Visual");
     tabbedPane.add(connectTab,"Connections");
     tabbedPane.add(exportTab, "Output");
     jPanel11.add(jLabel1);
@@ -439,6 +453,10 @@ public class GPreferences extends JPanel
     jPanel11.add(pfamjv);
     jPanel11.add(pileupjv);
     jPanel11.add(pirjv);
+    exportTab.add(modellerOutput);
+    tabbedPane.add(calcTab, "Editing");
+    calcTab.add(autoCalculateConsCheck);
+    calcTab.add(padGaps);
 
     exportTab.add(epsLabel);
     exportTab.add(epsRendering);