*/
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;
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!
*
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
protected void outputText_actionPerformed(ActionEvent e)
{
String[] omitHidden = null;
-
+ FeatureRenderer fr = new FeatureRenderer(this.alignPanel);
+ viewport.setFeatureRenderer(fr);
if (viewport.hasHiddenColumns())
{
int reply = JOptionPane
try
{
- Desktop.setCurrentAlignFrame(this);
- 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(
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)