X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=44cb8b7b874ef9d64321c25a5dda0e27503151b3;hb=71154bd332b2c1487a0bd67e5afbeb0a25423a28;hp=11d1ff3ea212fd11402e1f58d16c4a3cb2f71baa;hpb=a291866e1f09688953bd4eb49a0ab1c9d325d8d6;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 11d1ff3..44cb8b7 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -18,7 +18,6 @@ public class GAlignFrame extends JInternalFrame
   protected JMenu fileMenu = new JMenu();
   protected JMenuItem closeMenuItem = new JMenuItem();
   protected JMenu editMenu = new JMenu();
-  protected JMenu fontMenu = new JMenu();
   protected JMenu viewMenu = new JMenu();
   protected JMenu colourMenu = new JMenu();
   protected JMenu calculateMenu = new JMenu();
@@ -33,9 +32,6 @@ public class GAlignFrame extends JInternalFrame
   protected JMenuItem removeGappedColumnMenuItem = new JMenuItem();
   protected JMenuItem removeAllGapsMenuItem = new JMenuItem();
   protected JMenuItem setGapCharMenuItem = new JMenuItem();
-  protected JMenuItem fontNameMenuItem = new JMenuItem();
-  protected JMenuItem fontSizeMenuItem = new JMenuItem();
-  protected JMenuItem fontStyleMenuItem = new JMenuItem();
   protected JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
   protected JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
   protected JMenuItem sortPairwiseMenuItem = new JMenuItem();
@@ -74,7 +70,6 @@ public class GAlignFrame extends JInternalFrame
   protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
   JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
-  JMenuItem pdbTest = new JMenuItem();
   JMenuItem printMenuItem = new JMenuItem();
   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
   JMenuItem findMenuItem = new JMenuItem();
@@ -89,6 +84,11 @@ public class GAlignFrame extends JInternalFrame
   JMenu jMenu1 = new JMenu();
   JMenuItem pasteNew = new JMenuItem();
   JMenuItem pasteThis = new JMenuItem();
+  protected JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
+  JMenuItem createPNG = new JMenuItem();
+  protected JMenuItem font = new JMenuItem();
+  protected JCheckBoxMenuItem fullSeqId = new JCheckBoxMenuItem();
+  JMenuItem epsFile = new JMenuItem();
   public GAlignFrame()
   {
 
@@ -160,11 +160,11 @@ public class GAlignFrame extends JInternalFrame
       }
     });
     editMenu.setText("Edit");
-    fontMenu.setText("Font");
     viewMenu.setText("View");
     colourMenu.setText("Colour");
     calculateMenu.setText("Calculate");
     alignMenu.setText("Web Service");
+    groupsMenuItem.setVisible(false);
     groupsMenuItem.setText("Groups");
     groupsMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -245,29 +245,6 @@ public class GAlignFrame extends JInternalFrame
         setGapCharMenuItem_actionPerformed(e);
       }
     });
-    fontNameMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fontNameMenuItem_actionPerformed(e);
-      }
-    });
-    fontSizeMenuItem.setText("10");
-    fontSizeMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fontSizeMenuItem_actionPerformed(e);
-      }
-    });
-    fontStyleMenuItem.setText("Plain");
-    fontStyleMenuItem.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        fontStyleMenuItem_actionPerformed(e);
-      }
-    });
     viewBoxesMenuItem.setText("Boxes");
     viewBoxesMenuItem.setState(true);
     viewBoxesMenuItem.addActionListener(new java.awt.event.ActionListener()
@@ -558,14 +535,6 @@ public class GAlignFrame extends JInternalFrame
         wrapMenuItem_actionPerformed(e);
       }
     });
-    pdbTest.setText("PDB Test Viewer");
-    pdbTest.addActionListener(new java.awt.event.ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        pdbTest_actionPerformed(e);
-      }
-    });
     printMenuItem.setText("Print");
     printMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -599,7 +568,6 @@ public class GAlignFrame extends JInternalFrame
         abovePIDThreshold_actionPerformed(e);
       }
     });
-    sequenceFeatures.setSelected(true);
     sequenceFeatures.setText("Sequence Features");
     sequenceFeatures.addActionListener(new ActionListener()
     {
@@ -670,10 +638,51 @@ public class GAlignFrame extends JInternalFrame
         pasteThis_actionPerformed(e);
       }
     });
+    applyToAllGroups.setText("Apply colour to all groups");
+    applyToAllGroups.setState(true);
+    applyToAllGroups.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        applyToAllGroups_actionPerformed(e);
+      }
+    });
+    createPNG.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        createPNG_actionPerformed(e);
+      }
+    });
+    createPNG.setActionCommand("Save as PNG Image");
+    createPNG.setText("Save as PNG Image");
+    font.setText("Change Font");
+    font.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        font_actionPerformed(e);
+      }
+    });
+    fullSeqId.setText("Show full sequence id");
+    fullSeqId.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fullSeqId_actionPerformed(e);
+      }
+    });
+    epsFile.setText("Save as EPS file");
+    epsFile.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        epsFile_actionPerformed(e);
+      }
+    });
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
-    alignFrameMenuBar.add(fontMenu);
     alignFrameMenuBar.add(viewMenu);
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
@@ -681,6 +690,8 @@ public class GAlignFrame extends JInternalFrame
     fileMenu.add(saveAlignmentMenu);
     fileMenu.add(outputTextboxMenu);
     fileMenu.add(htmlMenuItem);
+    fileMenu.add(epsFile);
+    fileMenu.add(createPNG);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
@@ -706,9 +717,8 @@ public class GAlignFrame extends JInternalFrame
     editMenu.add(removeAllGapsMenuItem);
     editMenu.add(setGapCharMenuItem);
     searchMenu.add(findMenuItem);
-    fontMenu.add(fontNameMenuItem);
-    fontMenu.add(fontSizeMenuItem);
-    fontMenu.add(fontStyleMenuItem);
+    viewMenu.add(font);
+    viewMenu.add(fullSeqId);
     viewMenu.add(wrapMenuItem);
     viewMenu.add(viewBoxesMenuItem);
     viewMenu.add(viewTextMenuItem);
@@ -717,6 +727,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(consensusGraphMenuItem);
     viewMenu.add(overviewMenuItem);
     viewMenu.add(sequenceFeatures);
+    colourMenu.add(applyToAllGroups);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(zappoColour);
@@ -747,7 +758,6 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(avDistanceTreeBlosumMenuItem);
     calculateMenu.add(njTreeBlosumMenuItem);
     alignMenu.add(clustalAlignMenuItem);
-    alignMenu.add(pdbTest);
     this.getContentPane().add(statusBar, BorderLayout.SOUTH);
     jMenu1.add(pasteNew);
     jMenu1.add(pasteThis);
@@ -841,20 +851,8 @@ public class GAlignFrame extends JInternalFrame
   }
 
 
-  protected void fontNameMenuItem_actionPerformed(ActionEvent e)
-  {
 
-  }
 
-  protected void fontSizeMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
-
-  protected void fontStyleMenuItem_actionPerformed(ActionEvent e)
-  {
-
-  }
 
   protected void wrapMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1025,10 +1023,6 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  protected void pdbTest_actionPerformed(ActionEvent e)
-  {
-
-  }
 
   protected void printMenuItem_actionPerformed(ActionEvent e)
   {
@@ -1091,6 +1085,31 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
+  protected void applyToAllGroups_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void createPNG_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void font_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void fullSeqId_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  protected void epsFile_actionPerformed(ActionEvent e)
+  {
+
+  }
+
 
 
 }