From 101b7144584f697b0381873fe40296020eec62b6 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 23 Jul 2010 14:21:57 +0200
Subject: code cleanup

---
 public/java/Structure.java | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/public/java/Structure.java b/public/java/Structure.java
index e1b229d..c46ea05 100644
--- a/public/java/Structure.java
+++ b/public/java/Structure.java
@@ -54,11 +54,11 @@ public class Structure{
     generators.add(new RingGenerator());
     generators.add(new BasicBondGenerator());
     generators.add(new BasicAtomGenerator());
-    //generators.add(new AtomNumberGenerator());
     generators.add(new SelectBondGenerator());
     generators.add(new SelectAtomGenerator());
 
     renderer = new Renderer(generators, new AWTFontManager());
+    renderer.getRenderer2DModel().set( SelectBondGenerator.SelectionBondColor.class,Color.RED);
 
     try { molecule = sp.parseSmiles(smiles); }
     catch (Exception ex) { ex.printStackTrace(); }
@@ -74,10 +74,15 @@ public class Structure{
     g2.fillRect(0, 0, size, size);
 
     layout();
+
   }
 
   public byte[] show() {
     try {
+      // create a fake ChemModel to make the LogicalSelection happy
+      selectionChemModel.setMoleculeSet(selectionMoleculeSet);
+      selection.select(selectionChemModel);
+      renderer.getRenderer2DModel().setSelection(selection);
       renderer.paintMoleculeSet(moleculeSet, new AWTDrawVisitor(g2), drawArea, true);
       ImageIO.write(image, "png", out);
     }
@@ -104,20 +109,19 @@ public class Structure{
   }
 
   public void match_activating(String[] smarts) {
-    Color color = Color.RED;
     for (int i = 0; i < smarts.length; i++) {
-      match(smarts[i], color);
+      match(smarts[i]);
     }
   }
 
   public void match_deactivating(String[] smarts) {
-    Color color = Color.GREEN;
+    renderer.getRenderer2DModel().set( SelectBondGenerator.SelectionBondColor.class,Color.GREEN);
     for (int i = 0; i < smarts.length; i++) {
-      match(smarts[i], color);
+      match(smarts[i]);
     }
   }
 
-  public void match(String smarts, Color color) {
+  public void match(String smarts) {
 
     try {
       SMARTSQueryTool querytool = new SMARTSQueryTool(smarts);
@@ -152,12 +156,6 @@ public class Structure{
         }
       }
 
-      // create a fake ChemModel to make the LogicalSelection happy
-      selectionChemModel.setMoleculeSet(selectionMoleculeSet);
-      selection.select(selectionChemModel);
-      renderer.getRenderer2DModel().setSelection(selection);
-      renderer.getRenderer2DModel().set( SelectBondGenerator.SelectionBondColor.class,color);
-
     }
     catch (Exception exc) { exc.printStackTrace(); }
 
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