remove new line in alquality

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 74859c1..1cbe15c 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -110,7 +110,7 @@ public class GAlignFrame
   protected JMenu sort = new JMenu();\r
   JMenu calculate = new JMenu();\r
   JMenu jMenu2 = new JMenu();\r
-  JMenuItem padGapsMenuitem = new JMenuItem();\r
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();\r
   protected ButtonGroup colours = new ButtonGroup();\r
   JMenuItem vamsasStore = new JMenuItem();\r
   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
@@ -121,6 +121,10 @@ public class GAlignFrame
   JMenuItem annotationColour = new JMenuItem();\r
   JMenuItem fetchSeqFeatures = new JMenuItem();\r
 \r
+\r
+\r
+  JMenuItem associatedData = new JMenuItem();\r
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();\r
   public GAlignFrame()\r
   {\r
 \r
@@ -966,6 +970,23 @@ public class GAlignFrame
         fetchSeqFeatures_actionPerformed(e);\r
       }\r
     });\r
+    associatedData.setText("Load Features / Annotations");\r
+    associatedData.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        associatedData_actionPerformed(e);\r
+      }\r
+    });\r
+    autoCalculate.setText("Autocalculate Consensus");\r
+    autoCalculate.setState(true);\r
+    autoCalculate.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        autoCalculate_actionPerformed(e);\r
+      }\r
+    });\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -974,6 +995,7 @@ public class GAlignFrame
     alignFrameMenuBar.add(calculateMenu);\r
     alignFrameMenuBar.add(webService);\r
     fileMenu.add(fetchSequence);\r
+    fileMenu.addSeparator();\r
     fileMenu.add(vamsasStore);\r
     fileMenu.add(saveAlignmentMenu);\r
     fileMenu.add(jMenu2);\r
@@ -981,6 +1003,7 @@ public class GAlignFrame
     fileMenu.add(printMenuItem);\r
     fileMenu.addSeparator();\r
     fileMenu.add(LoadtreeMenuItem);\r
+    fileMenu.add(associatedData);\r
     fileMenu.addSeparator();\r
     fileMenu.add(closeMenuItem);\r
     editMenu.add(undoMenuItem);\r
@@ -1038,11 +1061,11 @@ public class GAlignFrame
     colourMenu.add(nucleotideColour);\r
     colourMenu.add(userDefinedColour);\r
     colourMenu.addSeparator();\r
-    colourMenu.add(annotationColour);\r
     colourMenu.add(conservationMenuItem);\r
     colourMenu.add(modifyConservation);\r
     colourMenu.add(abovePIDThreshold);\r
     colourMenu.add(modifyPID);\r
+    colourMenu.add(annotationColour);\r
     calculateMenu.add(sort);\r
     calculateMenu.add(calculate);\r
     calculateMenu.addSeparator();\r
@@ -1050,6 +1073,7 @@ public class GAlignFrame
     calculateMenu.add(PCAMenuItem);\r
     calculateMenu.addSeparator();\r
     calculateMenu.add(showTranslation);\r
+    calculateMenu.add(autoCalculate);\r
     webServiceNoServices=new JMenuItem("<No Services>");\r
     webService.add(webServiceNoServices);\r
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
@@ -1360,11 +1384,6 @@ public class GAlignFrame
 \r
   }\r
 \r
-  public void tabSelected()\r
-  {\r
-\r
-  }\r
-\r
   public void featureSettings_actionPerformed(ActionEvent e)\r
   {\r
 \r
@@ -1389,4 +1408,14 @@ public class GAlignFrame
   {\r
 \r
   }\r
+\r
+  public void associatedData_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void autoCalculate_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
 }\r