JAL-2838 JAL-2872 added sorting from the Aptx frame (still misbehaving

[jalview.git] / src / jalview / ext / archaeopteryx / AptxFrame.java

diff --git a/src/jalview/ext/archaeopteryx/AptxFrame.java b/src/jalview/ext/archaeopteryx/AptxFrame.java
index c105c25..79798d3 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxFrame.java
+++ b/src/jalview/ext/archaeopteryx/AptxFrame.java
@@ -1,10 +1,17 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.ext.treeviewer.ExternalTreeControlsI;
-import jalview.ext.treeviewer.ExternalTreeFrame;
-import jalview.ext.treeviewer.ExternalTreeI;
-import jalview.ext.treeviewer.ExternalTreePanel;
+import jalview.bin.Cache;
+import jalview.ext.treeviewer.TreeControlsI;
+import jalview.ext.treeviewer.TreeFrameI;
+import jalview.ext.treeviewer.TreeI;
+import jalview.ext.treeviewer.TreePanelI;
+import jalview.ext.treeviewer.TreeViewerUtils;
 import jalview.gui.Desktop;
+import jalview.gui.EPSOptions;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
 
 import java.awt.Component;
 import java.awt.Container;
@@ -15,6 +22,7 @@ import java.awt.Image;
 import java.awt.MenuComponent;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.io.FileOutputStream;
 
 import javax.accessibility.AccessibleContext;
 import javax.swing.JLayeredPane;
@@ -25,18 +33,34 @@ import javax.swing.JRootPane;
 import javax.swing.JSeparator;
 import javax.swing.event.InternalFrameListener;
 
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.archaeopteryx.Configuration;
 import org.forester.archaeopteryx.MainFrame;
+import org.forester.phylogeny.Phylogeny;
+import org.jibble.epsgraphics.EpsGraphics2D;
 
-public class AptxFrame implements ExternalTreeFrame
+public class AptxFrame implements TreeFrameI
 {
   private final MainFrame aptxFrame;
 
-  private ExternalTreePanel aptxPanel;
+  private TreePanelI aptxPanel;
+
+  private TreeControlsI aptxControls;
+
+
+  public AptxFrame(Phylogeny tree, Configuration aptxConfig,
+          String treeTitle)
+  {
+    this(Archaeopteryx.createApplication(tree,
+            aptxConfig,
+            treeTitle));
+
+  }
 
-  private ExternalTreeControlsI aptxControls;
 
   public AptxFrame(MainFrame aptx)
   {
+
     aptxFrame = aptx;
     aptxPanel = new AptxTreePanel(
             aptxFrame.getMainPanel().getCurrentTreePanel());
@@ -45,15 +69,16 @@ public class AptxFrame implements ExternalTreeFrame
     adaptAptxGui(aptxFrame);
 
   }
+  
   /**
    * Hides certain redundant Archaeopteryx GUI elements such as the menu items
    * for reading in trees and adds extra items related to Jalview such as the
-   * tree sorting item.
+   * tree sorting menu item.
    * 
    * 
    * @param aptxFrame
    */
-  private void adaptAptxGui(MainFrame aptxFrame)
+  protected void adaptAptxGui(MainFrame aptxFrame)
   {
     JMenuBar frameBar = aptxFrame.getJMenuBar();
     boolean epsAdded = false;
@@ -98,7 +123,7 @@ public class AptxFrame implements ExternalTreeFrame
                 @Override
                 public void actionPerformed(ActionEvent e)
                 {
-                  // TODO Auto-generated method stub
+                  epsTree_actionPerformed(e);
 
                 }
                 
@@ -122,38 +147,108 @@ public class AptxFrame implements ExternalTreeFrame
                 "Filter alignment to show only currently visible sequences");
 
         refreshJalview.setFont(menu.getFont());
-
-        menu.add(sortByTree);
-        menu.add(refreshJalview);
-
-        sortByTree.setFont(menu.getFont());
-        refreshJalview.addActionListener(new ActionListener()
+        refreshJalview.addActionListener(
+                TreeViewerUtils.getActiveTreeViews().get(this));
+        sortByTree.addActionListener(new ActionListener()
         {
 
           @Override
           public void actionPerformed(ActionEvent e)
           {
-            // TODO Auto-generated method stub
+            TreeViewerUtils.getActiveTreeViews().get(AptxFrame.this)
+                    .sortByTree_actionPerformed();
 
           }
 
         });
 
+        menu.add(sortByTree);
+        menu.add(refreshJalview);
+
+        sortByTree.setFont(menu.getFont());
+
+
 
       }
 
     }
-    aptxFrame.validate();
+    // aptxFrame.validate();
   }
 
+  public void epsTree_actionPerformed(ActionEvent e)
+  {
+    boolean accurateText = true;
+
+    String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+            "Prompt each time");
+
+    // If we need to prompt, and if the GUI is visible then
+    // Prompt for EPS rendering style
+    if (renderStyle.equalsIgnoreCase("Prompt each time")
+            && !(System.getProperty("java.awt.headless") != null && System
+                    .getProperty("java.awt.headless").equals("true")))
+    {
+      EPSOptions eps = new EPSOptions();
+      renderStyle = eps.getValue();
+
+      if (renderStyle == null || eps.cancelled)
+      {
+        return;
+      }
+
+    }
+
+    if (renderStyle.equalsIgnoreCase("text"))
+    {
+      accurateText = false;
+    }
+
+    int width = getTreePanel().getWidth();
+    int height = getTreePanel().getHeight();
+
+    try
+    {
+      JalviewFileChooser chooser = new JalviewFileChooser(
+              ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
+      chooser.setFileView(new JalviewFileView());
+      chooser.setDialogTitle(
+              MessageManager.getString("label.create_eps_from_tree"));
+      chooser.setToolTipText(MessageManager.getString("action.save"));
+
+      int value = chooser.showSaveDialog(aptxFrame);
+
+      if (value != JalviewFileChooser.APPROVE_OPTION)
+      {
+        return;
+      }
+
+      Cache.setProperty("LAST_DIRECTORY",
+              chooser.getSelectedFile().getParent());
+
+      FileOutputStream out = new FileOutputStream(
+              chooser.getSelectedFile());
+      EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+              height);
+
+      pg.setAccurateTextMode(accurateText);
+
+      getTreePanel().paintToFile(pg, width, height);
+
+      pg.flush();
+      pg.close();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
   @Override
-  public ExternalTreePanel getTreePanel()
+  public TreePanelI getTreePanel()
   {
     return aptxPanel;
   }
 
   @Override
-  public ExternalTreeI getTree()
+  public TreeI getTree()
   {
     return aptxPanel.getTree();
   }
@@ -172,7 +267,7 @@ public class AptxFrame implements ExternalTreeFrame
   }
 
   @Override
-  public ExternalTreeControlsI getTreeControls()
+  public TreeControlsI getTreeControls()
   {
     return aptxControls;
   }