From 25284ea792e7cc73b507028d8bab71e0f17d0e3e Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 19 Jul 2010 12:20:37 +0200
Subject: opentox-api-wrapper bumped to 1.6.0

---
 application.rb           | 2 +-
 public/java/Display.java | 5 ++---
 public/java/Makefile     | 9 +++++++++
 3 files changed, 12 insertions(+), 4 deletions(-)
 create mode 100644 public/java/Makefile

diff --git a/application.rb b/application.rb
index cc0279b..967a29d 100644
--- a/application.rb
+++ b/application.rb
@@ -7,7 +7,7 @@ ENV["CLASSPATH"] = "#{ENV["CLASSPATH"]}:#{java_dir}:#{cdk}:#{jchempaint}"
 
 require 'rubygems'
 require 'rjb'
-gem "opentox-ruby-api-wrapper", "= 1.5.7"
+gem "opentox-ruby-api-wrapper", "= 1.6.0"
 require 'opentox-ruby-api-wrapper'
 
 #set :lock, true
diff --git a/public/java/Display.java b/public/java/Display.java
index 4a3e221..2950ca7 100644
--- a/public/java/Display.java
+++ b/public/java/Display.java
@@ -56,7 +56,7 @@ public class Display{
 		drawArea = new Rectangle(size, size);
 		image = new BufferedImage(size, size , BufferedImage.TYPE_INT_RGB);
 		g2 = (Graphics2D)image.getGraphics();
-		g2.setColor(Color.yellow);
+		g2.setColor(Color.WHITE);
 		g2.fillRect(0, 0, size, size);
 	}
 
@@ -69,14 +69,13 @@ public class Display{
 				sdg.generateCoordinates();
 				mol = sdg.getMolecule();
 				GeometryTools.translateAllPositive(mol);
-				
 				// get size of previous mol and shift
 				last = GeometryTools.shiftContainer(mol, GeometryTools.getRectangle2D(mol), last,2);
 				coordinated_mols[i] = (IMolecule) mol;
 			}
 			moleculeSet.setMolecules(coordinated_mols);
 			renderer.paintMoleculeSet(moleculeSet, new AWTDrawVisitor(g2), drawArea, true);
-			//matchSmarts("NN",Color.green);
+			matchSmarts("NN",Color.green);
 			ImageIO.write(image, "png", out);
 		} catch (Exception ex) {
 				ex.printStackTrace();
diff --git a/public/java/Makefile b/public/java/Makefile
new file mode 100644
index 0000000..bcae6ec
--- /dev/null
+++ b/public/java/Makefile
@@ -0,0 +1,9 @@
+#all: DisplayStructure.class
+all: Display.class
+
+#%.class: %.java
+#	javac -Xlint:deprecation -Xlint:unchecked -classpath ./:./cdk-1.0.1.jar $<
+
+%.class: %.java
+	javac -classpath ./:./cdk-1.3.5.jar:./cdk-jchempaint-15.jar $<
+	#javac -Xlint:deprecation -Xlint:unchecked -classpath ./:./cdk-1.3.5.jar:./cdk-jchempaint-15.jar $<
-- 
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