X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=eea181f476701e4d2a58abcf7b5068100d337692;hb=246746e55bd02c66746d5cd872f49890cbae206a;hp=f0d63c4dcb6fbdeda12cb91d269712b8cb750c34;hpb=ef23c17739a6fba3a8d455b725782bce4607ac9f;p=jalview.git

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index f0d63c4..eea181f 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -50,7 +50,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     JScrollPane scrollPane;
     AlignViewport av;
     Font font;
-    int fontSize = 12;
+    int fontSize;
     boolean fitToWindow = true;
     boolean showDistances = false;
     boolean showBootstrap = false;
@@ -74,19 +74,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
      * @param scroller DOCUMENT ME!
      * @param label DOCUMENT ME!
      */
-    public TreeCanvas(AlignViewport av, NJTree tree, JScrollPane scroller,
-        String label)
+    public TreeCanvas(AlignViewport av, JScrollPane scroller)
     {
         this.av = av;
-        this.tree = tree;
+        font = av.getFont();
         scrollPane = scroller;
         addMouseListener(this);
-        tree.findHeight(tree.getTopNode());
-        longestName = label;
-
         PaintRefresher.Register(this, av.alignment);
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -102,7 +99,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
             av.setSelectionGroup(selected);
         }
 
-        selected.setEndRes(av.alignment.getWidth());
+        selected.setEndRes(av.alignment.getWidth()-1);
         selected.addOrRemove(sequence, true);
 
         PaintRefresher.Refresh(this, av.alignment);
@@ -118,6 +115,30 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     {
         this.tree = tree;
         tree.findHeight(tree.getTopNode());
+
+        // Now have to calculate longest name based on the leaves
+        Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+        boolean has_placeholders = false;
+        longestName = "";
+
+        for (int i = 0; i < leaves.size(); i++)
+        {
+          SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+
+          if (lf.isPlaceholder())
+          {
+            has_placeholders = true;
+          }
+
+          if (longestName.length() < ( (Sequence) lf.element()).getName()
+              .length())
+          {
+            longestName = TreeCanvas.PLACEHOLDER +
+                ( (Sequence) lf.element()).getName();
+          }
+        }
+
+        setMarkPlaceholders(has_placeholders);
     }
 
     /**
@@ -503,32 +524,38 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     public void paintComponent(Graphics g)
     {
         super.paintComponent(g);
-        font = new Font("Verdana", Font.PLAIN, fontSize);
         g.setFont(font);
 
-        FontMetrics fm = g.getFontMetrics(font);
-
-        if (nameHash.size() == 0)
+        if(tree==null)
         {
-            repaint();
+          g.drawString("Calculating tree....", 20, getHeight()/2);
         }
-
-        if (fitToWindow ||
-                (!fitToWindow &&
-                (scrollPane.getHeight() > ((fm.getHeight() * nameHash.size()) +
-                offy))))
+        else
         {
+          FontMetrics fm = g.getFontMetrics(font);
+
+          if (nameHash.size() == 0)
+          {
+            repaint();
+          }
+
+          if (fitToWindow ||
+              (!fitToWindow &&
+               (scrollPane.getHeight() > ( (fm.getHeight() * nameHash.size()) +
+                                          offy))))
+          {
             draw(g, scrollPane.getWidth(), scrollPane.getHeight());
             setPreferredSize(null);
-        }
-        else
-        {
+          }
+          else
+          {
             setPreferredSize(new Dimension(scrollPane.getWidth(),
-                    fm.getHeight() * nameHash.size()));
+                                           fm.getHeight() * nameHash.size()));
             draw(g, scrollPane.getWidth(), fm.getHeight() * nameHash.size());
-        }
+          }
 
-        scrollPane.revalidate();
+          scrollPane.revalidate();
+        }
     }
 
     /**
@@ -549,6 +576,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     public void setFontSize(int fontSize)
     {
         this.fontSize = fontSize;
+        font = new Font(font.getName(), font.getStyle(), fontSize);
         repaint();
     }
 
@@ -567,6 +595,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         g2.setColor(Color.white);
         g2.fillRect(0, 0, width, height);
 
+        g2.setFont(font);
+
         labelLength = g2.getFontMetrics(font).stringWidth(longestName) + 20; //20 allows for scrollbar
 
         float wscale = (float) (width - labelLength - (offx * 2)) / tree.getMaxHeight();
@@ -704,19 +734,31 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
                         }
                     }
 
-                    ColourSchemeI cs = ColourSchemeProperty.getColour(sequences,
-                            av.alignment.getWidth(),
-                            ColourSchemeProperty.getColourName(
-                                av.getGlobalColourScheme()));
+                    ColourSchemeI cs = null;
+
+                    if (av.getGlobalColourScheme() != null)
+                    {
+                      if (av.getGlobalColourScheme() instanceof UserColourScheme)
+                      {
+                        cs = new UserColourScheme(
+                            ( (UserColourScheme) av.getGlobalColourScheme()).getColours());
+
+                      }
+                      else
+                        cs = ColourSchemeProperty.getColour(sequences,
+                                                            av.alignment.getWidth(),
+                                                            ColourSchemeProperty.getColourName(
+                                                                av.getGlobalColourScheme()));
+
+                        cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+                                                             av.getIgnoreGapsConsensus());
+                    }
+
 
                     SequenceGroup sg = new SequenceGroup(sequences,
                             "TreeGroup", cs, true, true, false, 0,
                             av.alignment.getWidth());
 
-                    if (sg.cs != null)
-                    {
-                        sg.cs.setThreshold(25, av.getIgnoreGapsConsensus());
-                    }
 
                     if (  av.getGlobalColourScheme()!=null
                        && av.getGlobalColourScheme().conservationApplied())