X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=001c2d58b7872d8cd5dde81188bc0cdb1600ad2a;hb=a4780f236ded1ae07824254bca59b2aa0ea539ba;hp=80838e2ce6826b82c8bba19e9563448bea42147b;hpb=8c6722b27ff92e3610376295e2b4363f942d9969;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 80838e2..001c2d5 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,57 +20,6 @@
  */
 package jalview.gui;
 
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.GridLayout;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.StringSelection;
-import java.awt.datatransfer.Transferable;
-import java.awt.dnd.DnDConstants;
-import java.awt.dnd.DropTargetDragEvent;
-import java.awt.dnd.DropTargetDropEvent;
-import java.awt.dnd.DropTargetEvent;
-import java.awt.dnd.DropTargetListener;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyAdapter;
-import java.awt.event.KeyEvent;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.print.PageFormat;
-import java.awt.print.PrinterJob;
-import java.beans.PropertyChangeEvent;
-import java.io.File;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Set;
-import java.util.Vector;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
-import javax.swing.JLayeredPane;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-import javax.swing.JRadioButtonMenuItem;
-import javax.swing.JScrollPane;
-import javax.swing.SwingUtilities;
-
 import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
@@ -148,6 +97,57 @@ import jalview.ws.jws2.Jws2Discoverer;
 import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
 /**
  * DOCUMENT ME!
  * 
@@ -1212,7 +1212,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           omitHidden = viewport.getViewAsString(false);
         }
       }
-      FormatAdapter f = new FormatAdapter();
+      FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
+      viewport.setFeatureRenderer(fr);
+      FormatAdapter f = new FormatAdapter(viewport);
       String output = f.formatSequences(format,
               viewport.getAlignment(), // class cast exceptions will
               // occur in the distant future
@@ -1282,7 +1284,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   protected void outputText_actionPerformed(ActionEvent e)
   {
     String[] omitHidden = null;
-
+    FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
+    viewport.setFeatureRenderer(fr);
     if (viewport.hasHiddenColumns())
     {
       int reply = JOptionPane
@@ -1306,7 +1309,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     try
     {
-      cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
+      cap.setText(new FormatAdapter(viewport).formatSequences(
+              e.getActionCommand(),
               viewport.getAlignment(), omitHidden,
               viewport.getColumnSelection()));
       Desktop.addInternalFrame(cap, MessageManager.formatMessage(
@@ -5787,8 +5791,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   public void setShowSeqFeatures(boolean b)
   {
-    showSeqFeatures.setSelected(true);
-    viewport.setShowSequenceFeatures(true);
+    showSeqFeatures.setSelected(b);
+    viewport.setShowSequenceFeatures(b);
   }
 
   /*
@@ -5960,6 +5964,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     for (AlignmentAnnotation aa : alignPanel.getAlignment()
             .getAlignmentAnnotation())
     {
+      /*
+       * don't display non-positional annotations on an alignment
+       */
+      if (aa.annotations == null)
+      {
+        continue;
+      }
       boolean apply = (aa.sequenceRef == null && forAlignment)
               || (aa.sequenceRef != null && forSequences);
       if (apply)