after merge

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index ddb2bcd..bb69a54 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -21,7 +21,6 @@ package jalview.jbgui;
 import java.awt.*;\r
 import java.awt.event.*;\r
 import javax.swing.*;\r
-import javax.swing.event.*;\r
 \r
 import jalview.schemes.*;\r
 \r
@@ -99,7 +98,7 @@ public class GAlignFrame
   public JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();\r
   JMenuItem createPNG = new JMenuItem();\r
   protected JMenuItem font = new JMenuItem();\r
-  public JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();\r
+  public JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();\r
   JMenuItem epsFile = new JMenuItem();\r
   JMenuItem LoadtreeMenuItem = new JMenuItem();\r
   public JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();\r
@@ -113,6 +112,11 @@ public class GAlignFrame
   JMenu jMenu2 = new JMenu();\r
   JMenuItem padGapsMenuitem = 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
+  public JMenuItem featureSettings = new JMenuItem();\r
+  JMenuItem fetchSequence = new JMenuItem();\r
 \r
   public GAlignFrame()\r
   {\r
@@ -471,21 +475,6 @@ public class GAlignFrame
     });\r
     this.getContentPane().setLayout(borderLayout1);\r
     alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
-    alignFrameMenuBar.addAncestorListener(new AncestorListener()\r
-    {\r
-      public void ancestorAdded(AncestorEvent event)\r
-      {\r
-        alignFrameMenuBar_ancestorAdded(event);\r
-      }\r
-\r
-      public void ancestorRemoved(AncestorEvent event)\r
-      {\r
-      }\r
-\r
-      public void ancestorMoved(AncestorEvent event)\r
-      {\r
-      }\r
-    });\r
     statusBar.setBackground(Color.white);\r
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
     statusBar.setBorder(BorderFactory.createLineBorder(Color.black));\r
@@ -822,13 +811,14 @@ public class GAlignFrame
         font_actionPerformed(e);\r
       }\r
     });\r
-    fullSeqId.setText("Show Full Sequence ID");\r
-    fullSeqId.setState( jalview.bin.Cache.getDefault("SHOW_FULL_ID",true));\r
-    fullSeqId.addActionListener(new java.awt.event.ActionListener()\r
+\r
+    seqLimits.setText("Show Sequence Limits");\r
+    seqLimits.setState( jalview.bin.Cache.getDefault("SHOW_JVSUFFIX",true));\r
+    seqLimits.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
       {\r
-        fullSeqId_actionPerformed(e);\r
+        seqLimit_actionPerformed(e);\r
       }\r
     });\r
     epsFile.setText("EPS");\r
@@ -906,6 +896,49 @@ public class GAlignFrame
         padGapsMenuitem_actionPerformed(e);\r
       }\r
     });\r
+    vamsasStore.setVisible(false);\r
+    vamsasStore.setText("VAMSAS store");\r
+    vamsasStore.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        vamsasStore_actionPerformed(e);\r
+      }\r
+    });\r
+    showTranslation.setText("Translate cDNA");\r
+    showTranslation.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\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
+    fetchSequence.setText("Fetch Sequence...");\r
+    fetchSequence.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        fetchSequence_actionPerformed(e);\r
+      }\r
+    });\r
     alignFrameMenuBar.add(fileMenu);\r
     alignFrameMenuBar.add(editMenu);\r
     alignFrameMenuBar.add(searchMenu);\r
@@ -913,6 +946,8 @@ public class GAlignFrame
     alignFrameMenuBar.add(colourMenu);\r
     alignFrameMenuBar.add(calculateMenu);\r
     alignFrameMenuBar.add(webService);\r
+    fileMenu.add(fetchSequence);\r
+    fileMenu.add(vamsasStore);\r
     fileMenu.add(saveAlignmentMenu);\r
     fileMenu.add(jMenu2);\r
     fileMenu.add(outputTextboxMenu);\r
@@ -944,7 +979,7 @@ public class GAlignFrame
     viewMenu.add(font);\r
     viewMenu.addSeparator();\r
     viewMenu.add(wrapMenuItem);\r
-    viewMenu.add(fullSeqId);\r
+    viewMenu.add(seqLimits);\r
     viewMenu.add(scaleAbove);\r
     viewMenu.add(scaleLeft);\r
     viewMenu.add(scaleRight);\r
@@ -953,7 +988,9 @@ 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
@@ -981,9 +1018,12 @@ public class GAlignFrame
     calculateMenu.addSeparator();\r
     calculateMenu.add(pairwiseAlignmentMenuItem);\r
     calculateMenu.add(PCAMenuItem);\r
+    calculateMenu.addSeparator();\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
@@ -1110,10 +1150,6 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  protected void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-  }\r
-\r
   protected void clustalColour_actionPerformed(ActionEvent e)\r
   {\r
   }\r
@@ -1226,10 +1262,16 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  protected void fullSeqId_actionPerformed(ActionEvent e)\r
+  protected void seqLimit_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
+  public void seqDBRef_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+\r
   public void createEPS(java.io.File f)\r
   {\r
   }\r
@@ -1262,27 +1304,44 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  protected void preferences_actionPerformed(ActionEvent e)\r
+\r
+\r
+  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+  {\r
+  }\r
+\r
+  protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
   {\r
   }\r
 \r
-  protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
+\r
+  public void vamsasStore_actionPerformed(ActionEvent e)\r
   {\r
+\r
   }\r
 \r
-  protected void alignFrameMenuBar_ancestorAdded(AncestorEvent event)\r
+  public void vamsasLoad_actionPerformed(ActionEvent e)\r
   {\r
+\r
   }\r
 \r
-  protected void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
+  public void showTranslation_actionPerformed(ActionEvent e)\r
   {\r
+\r
   }\r
 \r
-  protected void padGapsMenuitem_actionPerformed(ActionEvent e)\r
+  public void tabSelected()\r
+  {\r
+\r
+  }\r
+\r
+  public void featureSettings_actionPerformed(ActionEvent e)\r
   {\r
+\r
   }\r
 \r
-  protected void ClustalRealign_actionPerformed(ActionEvent e)\r
+  public void fetchSequence_actionPerformed(ActionEvent e)\r
   {\r
+\r
   }\r
 }\r