JAL-1780 more support for export setting for flatfile output

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 478aa09..4f7e2b9 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -20,6 +20,40 @@
  */
 package jalview.appletgui;
 
+import java.awt.BorderLayout;
+import java.awt.Canvas;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Label;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.io.IOException;
+import java.net.URL;
+import java.net.URLEncoder;
+import java.util.Arrays;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.AlignViewControllerGuiI;
@@ -71,40 +105,6 @@ import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
-import java.awt.BorderLayout;
-import java.awt.Canvas;
-import java.awt.CheckboxMenuItem;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Frame;
-import java.awt.Graphics;
-import java.awt.Label;
-import java.awt.Menu;
-import java.awt.MenuBar;
-import java.awt.MenuItem;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.io.IOException;
-import java.net.URL;
-import java.net.URLEncoder;
-import java.util.Arrays;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
 public class AlignFrame extends EmbmenuFrame implements ActionListener,
         ItemListener, KeyListener, AlignViewControllerGuiI
 {
@@ -156,6 +156,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public AlignFrame(AlignmentI al, JalviewLite applet,
           String title, boolean embedded, boolean addToDisplay)
   {
+    this(al, null, null, applet, title, embedded, addToDisplay);
+  }
+
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection columnSelection, JalviewLite applet,
+          String title, boolean embedded)
+  {
+    this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
+  }
+
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection columnSelection, JalviewLite applet,
+          String title, boolean embedded, boolean addToDisplay)
+  {
     if (applet != null)
     {
       jalviewServletURL = applet.getParameter("APPLICATION_URL");
@@ -191,6 +205,17 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
     }
     viewport = new AlignViewport(al, applet);
+
+    if (hiddenSeqs != null && hiddenSeqs.length > 0)
+    {
+      viewport.hideSequence(hiddenSeqs);
+      viewport.setHasHiddenRows(true);
+    }
+    if (columnSelection != null)
+    {
+      viewport.setColumnSelection(columnSelection);
+    }
+
     alignPanel = new AlignmentPanel(this, viewport);
     avc = new jalview.controller.AlignViewController(this, viewport,
             alignPanel);
@@ -1313,7 +1338,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.alignment_output_command", new Object[]
             { e.getActionCommand() }), 600, 500);
-    cap.setText(new AppletFormatAdapter().formatSequences(
+
+    FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+    viewport.setFeatureRenderer(fr);
+    cap.setText(new AppletFormatAdapter(viewport).formatSequences(
             e.getActionCommand(), viewport.getAlignment(),
             viewport.getShowJVSuffix()));
   }
@@ -4178,19 +4206,4 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     this.splitFrame = sf;
   }
-
-  @Override
-  public void setShowSeqFeatures(boolean b)
-  {
-    // showSeqFeatures.setSelected(b);
-    viewport.setShowSequenceFeatures(b);
-
-  }
-
-  @Override
-  public void setMenusForViewport()
-  {
-    // setMenusFromViewport(viewport);
-
-  }
 }