Preferences panel added

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1b9ee91..a21aabe 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -38,31 +38,20 @@ public class AlignFrame extends GAlignFrame
     try{\r
       String ip = java.net.InetAddress.getLocalHost().getHostAddress();\r
       if( !ip.startsWith("10."))\r
-        alignMenu.setVisible(false);\r
+        webService.setVisible(false);\r
     }\r
     catch(java.net.UnknownHostException e){}\r
-    viewport = new AlignViewport(al,true,true,false);\r
-\r
-    String fontName = jalview.bin.Cache.getProperty("FONT_NAME");\r
-    String fontStyle= jalview.bin.Cache.getProperty("FONT_STYLE");\r
-    String fontSize = jalview.bin.Cache.getProperty("FONT_SIZE");\r
-    if(fontName!=null && fontStyle!=null && fontSize!=null)\r
-      viewport.setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );\r
-\r
-    // add conservation graph to alignment\r
-    viewport.updateConservation();\r
-    viewport.updateConsensus();\r
+    viewport = new AlignViewport(al);\r
 \r
 \r
     alignPanel = new AlignmentPanel(this, viewport);\r
-\r
     alignPanel.annotationPanel.adjustPanelHeight();\r
     alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
     alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.getPreferredSize());\r
+    alignPanel.setAnnotationVisible( viewport.getShowAnnotation() );\r
 \r
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
 \r
-\r
     addInternalFrameListener(new InternalFrameAdapter()\r
    {\r
      public void internalFrameActivated(InternalFrameEvent evt)\r
@@ -184,7 +173,6 @@ public class AlignFrame extends GAlignFrame
 \r
   Stack historyList = new Stack();\r
   Stack redoList = new Stack();\r
-  JMenuBar jMenuBar1 = new JMenuBar();\r
 \r
   void updateEditMenuBar()\r
   {\r
@@ -448,6 +436,8 @@ public class AlignFrame extends GAlignFrame
   public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     viewport.setSelectionGroup(null);\r
+    viewport.getColumnSelection().clear();\r
+    viewport.setSelectionGroup(null);\r
     PaintRefresher.Refresh(null);\r
   }\r
 \r
@@ -460,13 +450,6 @@ public class AlignFrame extends GAlignFrame
     PaintRefresher.Refresh(null);\r
   }\r
 \r
-\r
-  public void deselectAllColumnsMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-    viewport.getColumnSelection().clear();\r
-    repaint();\r
-  }\r
-\r
   public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
   {\r
     addHistoryItem("delete columns");\r
@@ -549,19 +532,12 @@ public class AlignFrame extends GAlignFrame
     alignPanel.repaint();\r
   }\r
 \r
-  public void setGapCharMenuItem_actionPerformed(ActionEvent e)\r
-  {\r
-    char thisChar = '-';\r
-    char nextChar = '.';\r
-    if(viewport.getGapCharacter()=='-')\r
-    {\r
-      thisChar = '.';\r
-      nextChar = '-';\r
-    }\r
-    setGapCharMenuItem.setText("Set gap character to \""+nextChar+"\"");\r
-    viewport.setGapCharacter(thisChar);\r
-    alignPanel.repaint();\r
-  }\r
+\r
+  protected void preferences_actionPerformed(ActionEvent e)\r
+{\r
+    Preferences pref = new Preferences(viewport);\r
+}\r
+\r
 \r
   public void findMenuItem_actionPerformed(ActionEvent e)\r
   {\r
@@ -576,13 +552,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void font_actionPerformed(ActionEvent e)\r
   {\r
-    JInternalFrame frame = new JInternalFrame();\r
-    FontChooser fc = new FontChooser( alignPanel, frame );\r
-    frame.setContentPane(fc);\r
-    Desktop.addInternalFrame(frame, "Change Font", 480,100, false);\r
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
-    if(alignPanel.getOverviewPanel()!=null)\r
-      alignPanel.getOverviewPanel().updateOverviewImage();\r
+    FontChooser fc = new FontChooser( alignPanel );\r
   }\r
 \r
   protected void fullSeqId_actionPerformed(ActionEvent e)\r
@@ -928,10 +898,7 @@ public class AlignFrame extends GAlignFrame
 \r
   public void userDefinedColour_actionPerformed(ActionEvent e)\r
   {\r
-    JInternalFrame frame = new JInternalFrame();\r
-    UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
-    frame.setContentPane(chooser);\r
-    Desktop.addInternalFrame(frame,"User defined colours", 450,540, false );\r
+    UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);\r
   }\r
 \r
   public void PIDColour_actionPerformed(ActionEvent e)\r