From: jprocter <Jim Procter>
Date: Fri, 20 May 2005 14:54:29 +0000 (+0000)
Subject: sequence place holder reveal menu item.
X-Git-Tag: Release_2_0~247
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8d1b94fdb228e81f3deb79bff3c34f5f68db5f07;p=jalview.git

sequence place holder reveal menu item.
---

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index d4c88de..f9cb39c 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -16,13 +16,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
   NJTree tree;
   JScrollPane scrollPane;
   AlignViewport av;
-
+  public static final String PLACEHOLDER=" * ";
   Font font;
   int  fontSize = 12;
 
   boolean fitToWindow = true;
   boolean showDistances = false;
   boolean showBootstrap = false;
+  boolean markPlaceholders = false;
 
   int offx = 20;
   int offy = 20;
@@ -122,10 +123,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
       g.drawString(nodeLabel,xstart,ypos - 10);
       }
 
-      // Colour selected leaves differently
-      String name    = node.getName();
+      String name    = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER+node.getName()) : node.getName();
       FontMetrics fm = g.getFontMetrics(font);
-      int charWidth  = fm.stringWidth(node.getName()) + 3;
+      int charWidth  = fm.stringWidth(name) + 3;
       int charHeight = fm.getHeight();
 
       Rectangle rect = new Rectangle(xend+20,ypos-charHeight,
@@ -133,6 +133,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
 
       nameHash.put((SequenceI)node.element(),rect);
 
+      // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
       if (selected!=null && selected.sequences.contains((SequenceI)node.element())) {
         g.setColor(Color.gray);
@@ -140,7 +141,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
         g.fillRect(xend + 10, ypos - charHeight + 3,charWidth,charHeight);
         g.setColor(Color.white);
       }
-      g.drawString(node.getName(),xend+10,ypos);
+      g.drawString(name,xend+10,ypos);
       g.setColor(Color.black);
     } else {
       drawNode(g,(SequenceNode)node.left(), chunk,scale,width,offx,offy);
@@ -496,6 +497,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Print
       this.showBootstrap = state;
       repaint();
     }
+    public void setMarkPlaceholders(boolean state) {
+            this.markPlaceholders = state;
+            repaint();
+    }
 
 }
 
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index c458638..3c571f8 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -78,11 +78,15 @@ public class TreePanel extends GTreePanel
       for (int i=0;i < seqVector.size();i++)
       {
         seq[i] = (Sequence) seqVector.elementAt(i);
-        if(seq[i].getName().length()>longestName.length())
-          longestName = seq[i].getName();
       }
       // This constructor matches sequence names to treenodes and sets up the tree layouts.
       tree = new NJTree(seq, newtree);
+      // Now have to calculate longest name based on the leaves
+      Vector leaves = tree.findLeaves(tree.getTopNode(),new Vector());
+
+      for (int i=0;i < leaves.size();i++)
+        if (longestName.length()<((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName().length())
+          longestName = TreeCanvas.PLACEHOLDER+((Sequence) ((SequenceNode) leaves.elementAt(i)).element()).getName();
 
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
@@ -91,6 +95,10 @@ public class TreePanel extends GTreePanel
       treeCanvas.setShowBootstrap(newtree.HasBootstrap());
       treeCanvas.setShowDistances(newtree.HasDistances());
       scrollPane.setViewportView(treeCanvas);
+      distanceMenu.setSelected(newtree.HasDistances());
+      bootstrapMenu.setSelected(newtree.HasBootstrap());
+      if (true) // JBPNote TODO: preference for always marking placeholders in new associated tree
+        placeholdersMenu.setSelected(treeCanvas.markPlaceholders);
 
     }
 
@@ -172,6 +180,10 @@ public class TreePanel extends GTreePanel
     treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
   }
 
+  protected void placeholdersMenu_actionPerformed(ActionEvent e)
+    {
+      treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+  }
 
   protected void epsTree_actionPerformed(ActionEvent e)
   {