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 bb69a54..1cbe15c 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -86,7 +86,7 @@ public class GAlignFrame
   JMenuItem findMenuItem = new JMenuItem();\r
   JMenu searchMenu = new JMenu();\r
   public JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();\r
-  public JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();\r
+  public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();\r
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();\r
   JMenuItem deleteGroups = new JMenuItem();\r
   JMenuItem delete = new JMenuItem();\r
@@ -110,14 +110,21 @@ 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
   //protected JTabbedPane tabbedPane = new JTabbedPane();\r
   public JMenuItem featureSettings = new JMenuItem();\r
   JMenuItem fetchSequence = new JMenuItem();\r
+  protected JCheckBoxMenuItem smoothFont = new JCheckBoxMenuItem();\r
+  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
@@ -707,12 +714,12 @@ public class GAlignFrame
         abovePIDThreshold_actionPerformed(e);\r
       }\r
     });\r
-    sequenceFeatures.setText("Sequence Features");\r
-    sequenceFeatures.addActionListener(new ActionListener()\r
+    showSeqFeatures.setText("Show Sequence Features");\r
+    showSeqFeatures.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent actionEvent)\r
       {\r
-        sequenceFeatures_actionPerformed(actionEvent);\r
+        showSeqFeatures_actionPerformed(actionEvent);\r
       }\r
     });\r
     nucleotideColour.setText("Nucleotide");\r
@@ -830,7 +837,7 @@ public class GAlignFrame
       }\r
     });\r
     LoadtreeMenuItem.setActionCommand("Load a tree for this sequence set");\r
-    LoadtreeMenuItem.setText("Load Assocated Tree");\r
+    LoadtreeMenuItem.setText("Load Associated Tree");\r
     LoadtreeMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -922,7 +929,6 @@ public class GAlignFrame
             tabSelected();\r
           }\r
         });*/\r
-    featureSettings.setEnabled(false);\r
     featureSettings.setText("Feature Settings...");\r
     featureSettings.addActionListener(new ActionListener()\r
     {\r
@@ -931,7 +937,7 @@ public class GAlignFrame
         featureSettings_actionPerformed(e);\r
       }\r
     });\r
-    fetchSequence.setText("Fetch Sequence...");\r
+    fetchSequence.setText("Fetch Sequence(s)...");\r
     fetchSequence.addActionListener(new ActionListener()\r
     {\r
       public void actionPerformed(ActionEvent e)\r
@@ -939,6 +945,48 @@ public class GAlignFrame
         fetchSequence_actionPerformed(e);\r
       }\r
     });\r
+    smoothFont.setText("Smooth Fonts");\r
+    smoothFont.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        smoothFont_actionPerformed(e);\r
+      }\r
+    });\r
+    smoothFont.setState( jalview.bin.Cache.getDefault("ANTI_ALIAS",false));\r
+    annotationColour.setText("By Annotation...");\r
+    annotationColour.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        annotationColour_actionPerformed(e);\r
+      }\r
+    });\r
+    fetchSeqFeatures.setText("Fetch Sequence Features");\r
+    fetchSeqFeatures.addActionListener(new ActionListener()\r
+    {\r
+      public void actionPerformed(ActionEvent e)\r
+      {\r
+        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
@@ -947,6 +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
@@ -954,6 +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
@@ -977,6 +1027,7 @@ public class GAlignFrame
     editMenu.add(padGapsMenuitem);\r
     searchMenu.add(findMenuItem);\r
     viewMenu.add(font);\r
+    viewMenu.add(smoothFont);\r
     viewMenu.addSeparator();\r
     viewMenu.add(wrapMenuItem);\r
     viewMenu.add(seqLimits);\r
@@ -989,7 +1040,8 @@ public class GAlignFrame
     viewMenu.add(renderGapsMenuItem);\r
     viewMenu.add(annotationPanelMenuItem);\r
     viewMenu.addSeparator();\r
-    viewMenu.add(sequenceFeatures);\r
+    viewMenu.add(fetchSeqFeatures);\r
+    viewMenu.add(showSeqFeatures);\r
     viewMenu.add(featureSettings);\r
     viewMenu.addSeparator();\r
     viewMenu.add(overviewMenuItem);\r
@@ -1013,6 +1065,7 @@ public class GAlignFrame
     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
@@ -1020,6 +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
@@ -1218,7 +1272,7 @@ public class GAlignFrame
   {\r
   }\r
 \r
-  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)\r
+  public void showSeqFeatures_actionPerformed(ActionEvent actionEvent)\r
   {\r
   }\r
 \r
@@ -1330,17 +1384,37 @@ public class GAlignFrame
 \r
   }\r
 \r
-  public void tabSelected()\r
+  public void featureSettings_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
 \r
-  public void featureSettings_actionPerformed(ActionEvent e)\r
+  public void fetchSequence_actionPerformed(ActionEvent e)\r
   {\r
 \r
   }\r
 \r
-  public void fetchSequence_actionPerformed(ActionEvent e)\r
+  public void smoothFont_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void annotationColour_actionPerformed(ActionEvent e)\r
+  {\r
+\r
+  }\r
+\r
+  public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
+  {\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