X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGAlignFrame.java;h=eafbf12f097e6a0a2615081a8026170140b75f17;hb=a6708aa208f1380c980dc51282b5380d9eda5470;hp=bb69a54dba0d2ed06b16a5c5dfc07176f43b68c2;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index bb69a54..eafbf12 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -23,6 +23,7 @@ import java.awt.event.*;
 import javax.swing.*;
 
 import jalview.schemes.*;
+import java.awt.BorderLayout;
 
 public class GAlignFrame
     extends JInternalFrame
@@ -86,7 +87,7 @@ public class GAlignFrame
   JMenuItem findMenuItem = new JMenuItem();
   JMenu searchMenu = new JMenu();
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-  public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
   JMenuItem deleteGroups = new JMenuItem();
   JMenuItem delete = new JMenuItem();
@@ -110,14 +111,29 @@ public class GAlignFrame
   protected JMenu sort = new JMenu();
   JMenu calculate = new JMenu();
   JMenu jMenu2 = new JMenu();
-  JMenuItem padGapsMenuitem = new JMenuItem();
+  protected JCheckBoxMenuItem padGapsMenuitem = new JCheckBoxMenuItem();
   protected ButtonGroup colours = new ButtonGroup();
   JMenuItem vamsasStore = new JMenuItem();
   protected JCheckBoxMenuItem showTranslation = new JCheckBoxMenuItem();
-  //protected JTabbedPane tabbedPane = new JTabbedPane();
   public JMenuItem featureSettings = new JMenuItem();
   JMenuItem fetchSequence = new JMenuItem();
-
+  protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();
+  JMenuItem annotationColour = new JMenuItem();
+  JMenuItem fetchSeqFeatures = new JMenuItem();
+
+
+
+  JMenuItem associatedData = new JMenuItem();
+  protected JCheckBoxMenuItem autoCalculate = new JCheckBoxMenuItem();
+  JMenu addSequenceMenu = new JMenu();
+  JMenuItem addFromFile = new JMenuItem();
+  JMenuItem addFromText = new JMenuItem();
+  JMenuItem addFromURL = new JMenuItem();
+  JMenuItem exportAnnotations = new JMenuItem();
+  JMenuItem exportFeatures = new JMenuItem();
+  JMenuItem dbRefs = new JMenuItem();
+  protected JPanel statusPanel = new JPanel();
+  GridLayout gridLayout1 = new GridLayout();
   public GAlignFrame()
   {
 
@@ -707,12 +723,12 @@ public class GAlignFrame
         abovePIDThreshold_actionPerformed(e);
       }
     });
-    sequenceFeatures.setText("Sequence Features");
-    sequenceFeatures.addActionListener(new ActionListener()
+    showSeqFeatures.setText("Show Sequence Features");
+    showSeqFeatures.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
       {
-        sequenceFeatures_actionPerformed(actionEvent);
+        showSeqFeatures_actionPerformed(actionEvent);
       }
     });
     nucleotideColour.setText("Nucleotide");
@@ -830,7 +846,7 @@ public class GAlignFrame
       }
     });
     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");
-    LoadtreeMenuItem.setText("Load Assocated Tree");
+    LoadtreeMenuItem.setText("Load Associated Tree");
     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -889,6 +905,7 @@ public class GAlignFrame
 
     jMenu2.setText("Export");
     padGapsMenuitem.setText("Pad Gaps");
+    padGapsMenuitem.setState( jalview.bin.Cache.getDefault("PAD_GAPS", false));
     padGapsMenuitem.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -922,7 +939,6 @@ public class GAlignFrame
             tabSelected();
           }
         });*/
-    featureSettings.setEnabled(false);
     featureSettings.setText("Feature Settings...");
     featureSettings.addActionListener(new ActionListener()
     {
@@ -931,7 +947,7 @@ public class GAlignFrame
         featureSettings_actionPerformed(e);
       }
     });
-    fetchSequence.setText("Fetch Sequence...");
+    fetchSequence.setText("Fetch Sequence(s)...");
     fetchSequence.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -939,6 +955,98 @@ public class GAlignFrame
         fetchSequence_actionPerformed(e);
       }
     });
+    smoothFont.setText("Smooth Fonts");
+    smoothFont.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        smoothFont_actionPerformed(e);
+      }
+    });
+    smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));
+    annotationColour.setText("By Annotation...");
+    annotationColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotationColour_actionPerformed(e);
+      }
+    });
+    fetchSeqFeatures.setText("Fetch Sequence Features");
+    fetchSeqFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        fetchSeqFeatures_actionPerformed(e);
+      }
+    });
+    associatedData.setText("Load Features / Annotations");
+    associatedData.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        associatedData_actionPerformed(e);
+      }
+    });
+    autoCalculate.setText("Autocalculate Consensus");
+    autoCalculate.setState( jalview.bin.Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+    autoCalculate.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        autoCalculate_actionPerformed(e);
+      }
+    });
+    addSequenceMenu.setText("Add Sequences");
+    addFromFile.setText("From File");
+    addFromFile.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromFile_actionPerformed(e);
+      }
+    });
+    addFromText.setText("From Textbox");
+    addFromText.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromText_actionPerformed(e);
+      }
+    });
+    addFromURL.setText("From URL");
+    addFromURL.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        addFromURL_actionPerformed(e);
+      }
+    });
+    exportFeatures.setText("Export Features...");
+    exportFeatures.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportFeatures_actionPerformed(e);
+      }
+    });
+    exportAnnotations.setText("Export Annotations...");
+    exportAnnotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        exportAnnotations_actionPerformed(e);
+      }
+    });
+    dbRefs.setText("Fetch DB Refs");
+    dbRefs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        dbRefs_actionPerformed(e);
+      }
+    });
+    statusPanel.setLayout(gridLayout1);
     alignFrameMenuBar.add(fileMenu);
     alignFrameMenuBar.add(editMenu);
     alignFrameMenuBar.add(searchMenu);
@@ -946,14 +1054,19 @@ public class GAlignFrame
     alignFrameMenuBar.add(colourMenu);
     alignFrameMenuBar.add(calculateMenu);
     alignFrameMenuBar.add(webService);
+    fileMenu.add(addSequenceMenu);
     fileMenu.add(fetchSequence);
+    fileMenu.addSeparator();
     fileMenu.add(vamsasStore);
     fileMenu.add(saveAlignmentMenu);
     fileMenu.add(jMenu2);
     fileMenu.add(outputTextboxMenu);
     fileMenu.add(printMenuItem);
     fileMenu.addSeparator();
+    fileMenu.add(exportFeatures);
+    fileMenu.add(exportAnnotations);
     fileMenu.add(LoadtreeMenuItem);
+    fileMenu.add(associatedData);
     fileMenu.addSeparator();
     fileMenu.add(closeMenuItem);
     editMenu.add(undoMenuItem);
@@ -977,6 +1090,7 @@ public class GAlignFrame
     editMenu.add(padGapsMenuitem);
     searchMenu.add(findMenuItem);
     viewMenu.add(font);
+    viewMenu.add(smoothFont);
     viewMenu.addSeparator();
     viewMenu.add(wrapMenuItem);
     viewMenu.add(seqLimits);
@@ -989,7 +1103,9 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(annotationPanelMenuItem);
     viewMenu.addSeparator();
-    viewMenu.add(sequenceFeatures);
+    viewMenu.add(dbRefs);
+    viewMenu.add(fetchSeqFeatures);
+    viewMenu.add(showSeqFeatures);
     viewMenu.add(featureSettings);
     viewMenu.addSeparator();
     viewMenu.add(overviewMenuItem);
@@ -1013,6 +1129,7 @@ public class GAlignFrame
     colourMenu.add(modifyConservation);
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
+    colourMenu.add(annotationColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculate);
     calculateMenu.addSeparator();
@@ -1020,11 +1137,9 @@ public class GAlignFrame
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
+    calculateMenu.add(autoCalculate);
     webServiceNoServices=new JMenuItem("<No Services>");
-    webService.add(webServiceNoServices);
-    this.getContentPane().add(statusBar, BorderLayout.SOUTH);
-  //  this.getContentPane().add(tabbedPane, java.awt.BorderLayout.CENTER);
-    jMenu1.add(pasteNew);
+    webService.add(webServiceNoServices);jMenu1.add(pasteNew);
     jMenu1.add(pasteThis);
     sort.add(sortIDMenuItem);
     sort.add(sortGroupMenuItem);
@@ -1036,12 +1151,42 @@ public class GAlignFrame
     jMenu2.add(htmlMenuItem);
     jMenu2.add(epsFile);
     jMenu2.add(createPNG);
+    addSequenceMenu.add(addFromFile);
+    addSequenceMenu.add(addFromText);
+    addSequenceMenu.add(addFromURL);
+    this.getContentPane().add(statusPanel, java.awt.BorderLayout.SOUTH);
+    statusPanel.add(statusBar, null);
   }
 
   protected void outputText_actionPerformed(ActionEvent e)
   {
   }
 
+  public void addFromFile_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromText_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void addFromURL_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void exportFeatures_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void exportAnnotations_actionPerformed(ActionEvent e)
+  {
+
+  }
+
   protected void htmlMenuItem_actionPerformed(ActionEvent e)
   {
   }
@@ -1218,7 +1363,7 @@ public class GAlignFrame
   {
   }
 
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)
   {
   }
 
@@ -1330,17 +1475,42 @@ public class GAlignFrame
 
   }
 
-  public void tabSelected()
+  public void featureSettings_actionPerformed(ActionEvent e)
   {
 
   }
 
-  public void featureSettings_actionPerformed(ActionEvent e)
+  public void fetchSequence_actionPerformed(ActionEvent e)
   {
 
   }
 
-  public void fetchSequence_actionPerformed(ActionEvent e)
+  public void smoothFont_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void annotationColour_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void fetchSeqFeatures_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void associatedData_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void autoCalculate_actionPerformed(ActionEvent e)
+  {
+
+  }
+
+  public void dbRefs_actionPerformed(ActionEvent e)
   {
 
   }