X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=c38b1a5d5a1aa0564c401169e4f8a3a33c5646d2;hb=ad52f1ddcaefa09c6a3e85329b28dad155613f49;hp=5f707d59294389bb66febe7bc255eec94c45e130;hpb=3e6b14950a06bb87c147493e4dfff0c4491ea25b;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 5f707d5..c38b1a5 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -55,7 +55,6 @@ public class TreeCanvas
 
   SequenceNode highlightNode;
 
-
   public TreeCanvas(AlignViewport av, ScrollPane scroller)
   {
     this.av = av;
@@ -77,7 +76,7 @@ public class TreeCanvas
       av.setSelectionGroup(selected);
     }
 
-    selected.setEndRes(av.alignment.getWidth()-1);
+    selected.setEndRes(av.alignment.getWidth() - 1);
     selected.addOrRemove(sequence, true);
   }
 
@@ -168,7 +167,7 @@ public class TreeCanvas
       }
       if (!nodeLabel.equals(""))
       {
-        g.drawString(nodeLabel, xstart+2, ypos - 2);
+        g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
       String name = (markPlaceholders && node.isPlaceholder()) ?
@@ -212,9 +211,13 @@ public class TreeCanvas
       // Draw horizontal line
       g.drawLine(xstart, ypos, xend, ypos);
       if (node == highlightNode)
+      {
         g.fillRect(xend - 3, ypos - 3, 6, 6);
+      }
       else
+      {
         g.fillRect(xend - 2, ypos - 2, 4, 4);
+      }
 
       int ystart = (int) ( ( (SequenceNode) node.left()).ycount * chunk) + offy;
       int yend = (int) ( ( (SequenceNode) node.right()).ycount * chunk) + offy;
@@ -227,7 +230,7 @@ public class TreeCanvas
 
       if (showDistances && node.dist > 0)
       {
-        g.drawString(new Format("%-.2f").form(node.dist), xstart+2, ypos - 2);
+        g.drawString(new Format("%-.2f").form(node.dist), xstart + 2, ypos - 2);
       }
 
     }
@@ -337,7 +340,7 @@ public class TreeCanvas
 
       if (node.element() instanceof SequenceI)
       {
-        av.setSequenceColour((SequenceI) node.element(), c);
+        av.setSequenceColour( (SequenceI) node.element(), c);
       }
     }
     else
@@ -355,8 +358,10 @@ public class TreeCanvas
 
   public void paint(Graphics g)
   {
-    if(tree==null)
+    if (tree == null)
+    {
       return;
+    }
 
     if (nameHash.size() == 0)
     {
@@ -365,20 +370,19 @@ public class TreeCanvas
 
     int width = scrollPane.getSize().width;
     int height = scrollPane.getSize().height;
-    if(!fitToWindow)
+    if (!fitToWindow)
     {
       height = g.getFontMetrics(font).getHeight() * nameHash.size();
     }
 
-    if(getSize().width>width)
+    if (getSize().width > width)
     {
-      setSize(new Dimension(width,height));
+      setSize(new Dimension(width, height));
       scrollPane.validate();
       return;
     }
 
-    setSize(new Dimension(width,height));
-
+    setSize(new Dimension(width, height));
 
     g.setFont(font);
 
@@ -386,10 +390,9 @@ public class TreeCanvas
 
   }
 
-
   public void draw(Graphics g, int width, int height)
   {
-    offy = font.getSize()+10;
+    offy = font.getSize() + 10;
 
     g.setColor(Color.white);
     g.fillRect(0, 0, width, height);
@@ -468,7 +471,6 @@ public class TreeCanvas
   public void mouseDragged(MouseEvent ect)
   {}
 
-
   public void mouseMoved(MouseEvent evt)
   {
     av.setCurrentTree(tree);
@@ -506,7 +508,7 @@ public class TreeCanvas
       repaint();
       return;
     }
-    else if ( !(ob instanceof SequenceNode))
+    else if (! (ob instanceof SequenceNode))
     {
       // Find threshold
 
@@ -521,7 +523,7 @@ public class TreeCanvas
 
         av.setSelectionGroup(null);
         av.alignment.deleteAllGroups();
-        av.sequenceColours=null;
+        av.sequenceColours = null;
 
         colourGroups();
 
@@ -536,71 +538,76 @@ public class TreeCanvas
   void colourGroups()
   {
     for (int i = 0; i < tree.getGroups().size(); i++)
-        {
+    {
 
-          Color col = new Color( (int) (Math.random() * 255),
-                                (int) (Math.random() * 255),
-                                (int) (Math.random() * 255));
-          setColor( (SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+      Color col = new Color( (int) (Math.random() * 255),
+                            (int) (Math.random() * 255),
+                            (int) (Math.random() * 255));
+      setColor( (SequenceNode) tree.getGroups().elementAt(i), col.brighter());
 
-          Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(
-              i), new Vector());
+      Vector l = tree.findLeaves( (SequenceNode) tree.getGroups().elementAt(
+          i), new Vector());
 
-          Vector sequences = new Vector();
-          for (int j = 0; j < l.size(); j++)
-          {
-            SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
-            if(!sequences.contains(s1))
-              sequences.addElement(s1);
-          }
+      Vector sequences = new Vector();
+      for (int j = 0; j < l.size(); j++)
+      {
+        SequenceI s1 = (SequenceI) ( (SequenceNode) l.elementAt(j)).element();
+        if (!sequences.contains(s1))
+        {
+          sequences.addElement(s1);
+        }
+      }
 
-          ColourSchemeI cs = null;
+      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());
-          }
+      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()));
+        }
 
-          SequenceGroup sg = new SequenceGroup(sequences, "",
-                                               cs, true, true,
-                                               false, 0, av.alignment.getWidth()-1);
+        cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
+                        av.getIgnoreGapsConsensus());
+      }
 
-          sg.setName("JTreeGroup:"+sg.hashCode());
+      SequenceGroup sg = new SequenceGroup(sequences, "",
+                                           cs, true, true,
+                                           false, 0,
+                                           av.alignment.getWidth() - 1);
 
+      sg.setName("JTreeGroup:" + sg.hashCode());
 
-          if (  av.getGlobalColourScheme()!=null
-             && av.getGlobalColourScheme().conservationApplied())
-            {
-            Conservation c = new Conservation("Group",
-                                              ResidueProperties.propHash, 3,
-                                              sg.getSequences(null),
-                                              sg.getStartRes(),
-                                              sg.getEndRes());
+      if (av.getGlobalColourScheme() != null
+          && av.getGlobalColourScheme().conservationApplied())
+      {
+        Conservation c = new Conservation("Group",
+                                          ResidueProperties.propHash, 3,
+                                          sg.getSequences(null),
+                                          sg.getStartRes(),
+                                          sg.getEndRes());
 
-            c.calculate();
-            c.verdict(false, av.ConsPercGaps);
-            cs.setConservation(c);
+        c.calculate();
+        c.verdict(false, av.ConsPercGaps);
+        cs.setConservation(c);
 
-            sg.cs = cs;
+        sg.cs = cs;
 
-          }
+      }
 
-          av.alignment.addGroup(sg);
+      av.alignment.addGroup(sg);
 
-        }
+    }
 
   }