Disable featuresettings

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 7d09f1b..5a0357e 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -36,6 +36,7 @@ public class GAlignFrame
   protected JMenu colourMenu = new JMenu();\r
   protected JMenu calculateMenu = new JMenu();\r
   protected JMenu webService = new JMenu();\r
+  protected JMenuItem webServiceNoServices;\r
   protected JMenuItem selectAllSequenceMenuItem = new JMenuItem();\r
   protected JMenuItem deselectAllSequenceMenuItem = new JMenuItem();\r
   protected JMenuItem invertSequenceMenuItem = new JMenuItem();\r
@@ -101,20 +102,21 @@ public class GAlignFrame
   public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
   JMenuItem epsFile = new JMenuItem();\r
   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
-  JMenuItem jnet = new JMenuItem();\r
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
   public JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();\r
   public JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();\r
-  JMenuItem modifyPID = new JMenuItem();\r
-  JMenuItem modifyConservation = new JMenuItem();\r
+  protected JMenuItem modifyPID = new JMenuItem();\r
+  protected JMenuItem modifyConservation = new JMenuItem();\r
   protected JMenu sortByTreeMenu = new JMenu();\r
   protected JMenu sort = new JMenu();\r
   JMenu calculate = new JMenu();\r
-  JMenuItem msaAlignMenuItem = new JMenuItem();\r
   JMenu jMenu2 = new JMenu();\r
   JMenuItem padGapsMenuitem = new JMenuItem();\r
-  JMenuItem ClustalRealign = new JMenuItem();\r
   protected ButtonGroup colours = new ButtonGroup();\r
+  JMenuItem vamsasStore = new JMenuItem();\r
+  protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();\r
+  protected JTabbedPane tabbedPane = new JTabbedPane();\r
+  protected JMenuItem featureSettings = new JMenuItem();\r
 \r
   public GAlignFrame()\r
   {\r
@@ -471,14 +473,6 @@ public class GAlignFrame
         neighbourTreeMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    clustalAlignMenuItem.setText("Clustal Alignment");\r
-    clustalAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        clustalAlignMenuItem_actionPerformed(e);\r
-      }\r
-    });\r
     this.getContentPane().setLayout(borderLayout1);\r
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
     alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
@@ -833,7 +827,7 @@ public class GAlignFrame
       }\r
     });\r
     fullSeqId.setText("Show Full Sequence ID");\r
-    fullSeqId.setState(true);\r
+    fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",true));\r
     fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -858,14 +852,6 @@ public class GAlignFrame
         LoadtreeMenuItem_actionPerformed(e);\r
       }\r
     });\r
-    jnet.setText("JNet");\r
-    jnet.addActionListener(new java.awt.event.ActionListener()\r
-    {\r
-      public void actionPerformed(ActionEvent e)\r
-      {\r
-        jpred_actionPerformed(e);\r
-      }\r
-    });\r
     scaleAbove.setVisible(false);\r
     scaleAbove.setText("Scale Above");\r
     scaleAbove.addActionListener(new java.awt.event.ActionListener()\r
@@ -914,29 +900,48 @@ public class GAlignFrame
     sortByTreeMenu.setText("By Tree Order");\r
     sort.setText("Sort");\r
     calculate.setText("Calculate Tree");\r
-    msaAlignMenuItem.setText("Muscle Alignment");\r
-    msaAlignMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+\r
+    jMenu2.setText("Export");\r
+    padGapsMenuitem.setText("Pad Gaps");\r
+    padGapsMenuitem.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        msaAlignMenuItem_actionPerformed(e);\r
+        padGapsMenuitem_actionPerformed(e);\r
       }\r
     });\r
-    jMenu2.setText("Export");\r
-    padGapsMenuitem.setText("Pad Gaps");\r
-    padGapsMenuitem.addActionListener(new ActionListener()\r
+    vamsasStore.setText("VAMSAS store");\r
+    vamsasStore.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        padGapsMenuitem_actionPerformed(e);\r
+        vamsasStore_actionPerformed(e);\r
       }\r
     });\r
-    ClustalRealign.setText("Clustal Realign");\r
-    ClustalRealign.addActionListener(new ActionListener()\r
+    showTranslation.setText("Translate cDNA");\r
+    showTranslation.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        ClustalRealign_actionPerformed(e);\r
+        showTranslation_actionPerformed(e);\r
+      }\r
+    });\r
+\r
+    tabbedPane.addChangeListener(new ChangeListener()\r
+        {\r
+          public void stateChanged(ChangeEvent ece)\r
+          {\r
+\r
+            tabSelected();\r
+          }\r
+        });\r
+    featureSettings.setEnabled(false);\r
+    featureSettings.setText("Feature Settings...");\r
+    featureSettings.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        featureSettings_actionPerformed(e);\r
       }\r
     });\r
     alignFrameMenuBar.add(fileMenu);\r
@@ -945,6 +950,8 @@ public class GAlignFrame
     alignFrameMenuBar.add(viewMenu);\r
     alignFrameMenuBar.add(colourMenu);\r
     alignFrameMenuBar.add(calculateMenu);\r
+    alignFrameMenuBar.add(webService);\r
+    fileMenu.add(vamsasStore);\r
     fileMenu.add(saveAlignmentMenu);\r
     fileMenu.add(jMenu2);\r
     fileMenu.add(outputTextboxMenu);\r
@@ -985,7 +992,9 @@ public class GAlignFrame
     viewMenu.add(colourTextMenuItem);\r
     viewMenu.add(renderGapsMenuItem);\r
     viewMenu.add(annotationPanelMenuItem);\r
+    viewMenu.addSeparator();\r
     viewMenu.add(sequenceFeatures);\r
+    viewMenu.add(featureSettings);\r
     viewMenu.addSeparator();\r
     viewMenu.add(overviewMenuItem);\r
     colourMenu.add(applyToAllGroups);\r
@@ -1014,12 +1023,11 @@ public class GAlignFrame
     calculateMenu.add(pairwiseAlignmentMenuItem);\r
     calculateMenu.add(PCAMenuItem);\r
     calculateMenu.addSeparator();\r
-    calculateMenu.add(webService);\r
-    webService.add(clustalAlignMenuItem);\r
-    webService.add(msaAlignMenuItem);\r
-    webService.add(jnet);\r
-    webService.add(ClustalRealign);\r
+    calculateMenu.add(showTranslation);\r
+    webServiceNoServices=new JMenuItem("<No Services>");\r
+    webService.add(webServiceNoServices);\r
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);\r
+    this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);\r
     jMenu1.add(pasteNew);\r
     jMenu1.add(pasteThis);\r
     sort.add(sortIDMenuItem);\r
@@ -1321,4 +1329,29 @@ public class GAlignFrame
   protected void ClustalRealign_actionPerformed(ActionEvent e)\r
   {\r
   }\r
+\r
+  public void vamsasStore_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void vamsasLoad_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void showTranslation_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void tabSelected()\r
+  {\r
+\r
+  }\r
+\r
+  public void featureSettings_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
 }\r