X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=1c70c240b08b0d2f4a3810594e226dd400429b4d;hb=975c24894c5cd28f756f3ef695bb5c8d6d43d7dc;hp=603a80faf44ce79b5fc59267cf2731d1b99cda03;hpb=0039639a8b6fa7a9bfc131c83a493b5a696f0104;p=jalview.git

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 603a80f..1c70c24 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -26,19 +26,14 @@ import jalview.io.*;
 
 import jalview.jbgui.*;
 
-import org.jibble.epsgraphics.*;
 
 import java.awt.*;
 import java.awt.event.*;
-import java.awt.image.*;
 
 import java.io.*;
 
 import java.util.*;
 
-import javax.imageio.*;
-
-import javax.swing.*;
 import java.beans.PropertyChangeEvent;
 
 
@@ -75,7 +70,7 @@ public class TreePanel extends GTreePanel
       initTreePanel(av, seqVector, type, pwtype, s, e, null);
 
       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
-      treeCanvas.setShowDistances(true);
+      showDistances(true);
     }
 
     /**
@@ -94,6 +89,11 @@ public class TreePanel extends GTreePanel
       initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
     }
 
+    public AlignmentI getAlignment()
+    {
+      return treeCanvas.av.getAlignment();
+    }
+
 
     void initTreePanel(AlignViewport av, Vector seqVector, String type,
                        String pwtype, int s, int e, NewickFile newTree)
@@ -143,6 +143,14 @@ public class TreePanel extends GTreePanel
       public TreeLoader(NewickFile newtree)
       {
         this.newtree = newtree;
+        if (newtree != null)
+        {
+          // Must be outside run(), as Jalview2XML tries to
+          // update distance/bootstrap visibility at the same time
+          showBootstrap(newtree.HasBootstrap());
+          showDistances(newtree.HasDistances());
+          showPlaceholders(true);
+        }
       }
 
       public void run()
@@ -155,56 +163,51 @@ public class TreePanel extends GTreePanel
         tree.reCount(tree.getTopNode());
         tree.findHeight(tree.getTopNode());
         treeCanvas.setTree(tree);
-        if(newtree!=null)
-        {
-          treeCanvas.setShowBootstrap(newtree.HasBootstrap());
-          treeCanvas.setShowDistances(newtree.HasDistances());
-        }
-
-        setViewStateFromTreeCanvas(treeCanvas);
 
         treeCanvas.repaint();
 
+
+        fullid.setState(treeCanvas.av.showDBPrefix);
+        if(!treeCanvas.av.showDBPrefix)
+        {
+          fullid_actionPerformed(null);
+        }
       }
+
     }
 
+    public void showDistances(boolean b)
+    {
+      treeCanvas.setShowDistances(b);
+      distanceMenu.setSelected(b);
+    }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public NJTree getTree()
+    public void showBootstrap(boolean b)
     {
-        return tree;
+      treeCanvas.setShowBootstrap(b);
+      bootstrapMenu.setSelected(b);
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param tree DOCUMENT ME!
-     */
-    private void setViewStateFromTreeCanvas(TreeCanvas tree)
+    public void showPlaceholders(boolean b)
     {
-        // update view menu state from treeCanvas render state
-        distanceMenu.setSelected(tree.showDistances);
-        bootstrapMenu.setSelected(tree.showBootstrap);
-        placeholdersMenu.setSelected(tree.markPlaceholders);
+      placeholdersMenu.setState(b);
+      treeCanvas.setMarkPlaceholders(b);
     }
 
+
+
+
     /**
      * DOCUMENT ME!
      *
-     * @param tree DOCUMENT ME!
+     * @return DOCUMENT ME!
      */
-    private void setTreeCanvasFromViewState(TreeCanvas tree)
+    public NJTree getTree()
     {
-        // update view menu state from treeCanvas render state
-        tree.showDistances = distanceMenu.isSelected();
-        tree.showBootstrap = bootstrapMenu.isSelected();
-        tree.markPlaceholders = placeholdersMenu.isSelected();
+        return tree;
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -311,15 +314,15 @@ public class TreePanel extends GTreePanel
             return;
         }
 
-        FontChooser fontchooser = new FontChooser(this);
+        new FontChooser(this);
     }
 
-    public Font getFont()
+    public Font getTreeFont()
     {
-      return treeCanvas.font;
+        return treeCanvas.font;
     }
 
-    public void setFont(Font font)
+    public void setTreeFont(Font font)
     {
       if(treeCanvas!=null)
       treeCanvas.setFont(font);
@@ -355,77 +358,36 @@ public class TreePanel extends GTreePanel
         treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    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;
 
+    public void fullid_actionPerformed(ActionEvent e)
+    {
+      tree.findHeight(tree.getTopNode());
 
-      }
+      // Now have to calculate longest name based on the leaves
+      Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
 
-      if (renderStyle.equalsIgnoreCase("text"))
+      treeCanvas.longestName="";
+      for (int i = 0; i < leaves.size(); i++)
       {
-        accurateText = false;
+        SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+        Sequence seq = (Sequence) lf.element();
+        lf.setName(seq.getDisplayId(fullid.getState(), false));
+        if(lf.getName().length() > treeCanvas.longestName.length())
+          treeCanvas.longestName = lf.getName();
       }
 
-        int width = treeCanvas.getWidth();
-        int height = treeCanvas.getHeight();
-
-        try
-        {
-            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-                        "LAST_DIRECTORY"), new String[] { "eps" },
-                    new String[] { "Encapsulated Postscript" },
-                    "Encapsulated Postscript");
-            chooser.setFileView(new jalview.io.JalviewFileView());
-            chooser.setDialogTitle("Create EPS file from tree");
-            chooser.setToolTipText("Save");
-
-            int value = chooser.showSaveDialog(this);
-
-            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-            {
-                return;
-            }
-
-            jalview.bin.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);
+      treeCanvas.repaint();
+    }
 
-            treeCanvas.draw(pg, width, height);
 
-            pg.flush();
-            pg.close();
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void epsTree_actionPerformed(ActionEvent e)
+    {
+      makeTreeImage(jalview.util.ImageMaker.EPS);
     }
 
     /**
@@ -435,44 +397,34 @@ public class TreePanel extends GTreePanel
      */
     public void pngTree_actionPerformed(ActionEvent e)
     {
-        int width = treeCanvas.getWidth();
-        int height = treeCanvas.getHeight();
-
-        try
-        {
-            jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
-                        "LAST_DIRECTORY"), new String[] { "png" },
-                    new String[] { "Portable network graphics" },
-                    "Portable network graphics");
-
-            chooser.setFileView(new jalview.io.JalviewFileView());
-            chooser.setDialogTitle("Create PNG image from tree");
-            chooser.setToolTipText("Save");
-
-            int value = chooser.showSaveDialog(this);
-
-            if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
-            {
-                return;
-            }
-
-            jalview.bin.Cache.setProperty("LAST_DIRECTORY",
-                chooser.getSelectedFile().getParent());
+       makeTreeImage(jalview.util.ImageMaker.PNG);
+    }
 
-            FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+    void makeTreeImage(int type)
+    {
+      int width = treeCanvas.getWidth();
+      int height = treeCanvas.getHeight();
 
-            BufferedImage bi = new BufferedImage(width, height,
-                    BufferedImage.TYPE_INT_RGB);
-            Graphics png = bi.getGraphics();
+      jalview.util.ImageMaker im;
 
-            treeCanvas.draw(png, width, height);
+      if(type == jalview.util.ImageMaker.PNG)
+        im = new jalview.util.ImageMaker(this,
+                                         jalview.util.ImageMaker.PNG,
+                                         "Make PNG image from tree",
+                                         width, height,
+                                         null, null);
+        else
+          im = new jalview.util.ImageMaker(this,
+                                 jalview.util.ImageMaker.EPS,
+                                 "Make EPS file from tree",
+                                 width, height,
+                                 null, this.getTitle());
 
-            ImageIO.write(bi, "png", out);
-            out.close();
-        }
-        catch (Exception ex)
-        {
-            ex.printStackTrace();
-        }
+      if(im.getGraphics()!=null)
+      {
+        treeCanvas.draw(im.getGraphics(), width, height);
+        im.writeImage();
+      }
     }
+
 }