From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 28 Apr 2005 15:33:56 +0000 (+0000)
Subject: Preferences panel added
X-Git-Tag: Release_2_0~358
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=affd24332b831acf0ffe4697dc1efafe8e414b31;p=jalview.git

Preferences panel added
---

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