CONFIG reverted to @@config

3 files changed, 20 insertions, 135 deletions

diff --git a/application.rb b/application.rb
index e1c6214..b8b1d04 100644
--- a/application.rb
+++ b/application.rb
@@ -1,25 +1,37 @@
 # Java environment
-=begin
 ENV["JAVA_HOME"] = "/usr/lib/jvm/java-6-sun" unless ENV["JAVA_HOME"]
 java_dir = File.join File.expand_path(File.dirname(__FILE__)),"public/java"
 cdk = File.join java_dir, "cdk-1.3.5.jar"
 jchempaint = File.join java_dir, "cdk-jchempaint-15.jar"
 ENV["CLASSPATH"] = "#{ENV["CLASSPATH"]}:#{java_dir}:#{cdk}:#{jchempaint}"
-=end
 
 require 'rubygems'
-#require 'rjb'
+require 'rjb'
 gem "opentox-ruby-api-wrapper", "= 1.6.0"
 require 'opentox-ruby-api-wrapper'
 
-#set :lock, true
+get %r{/smiles/(.+)/smarts/(.*)} do |smiles,smarts| 
+		content_type "image/png"
+		attachment "#{smiles}.png"
+    #LOGGER.debug "SMILES: #{smiles}, SMARTS: #{smarts}"
+    s = Rjb::import('Structure').new(smiles,200)
+    s.match(smarts)
+    s.show
+end
+
+
+get %r{/smiles/(.+)} do |smiles| 
+		content_type "image/png"
+		attachment "#{smiles}.png"
+    Rjb::import('Structure').new(smiles,200).show
+end
 
 get %r{/(.+)/image} do |inchi| # catches all remaining get requests
 
 		smiles = OpenTox::Compound.new(:inchi => inchi).smiles
 		content_type "image/png"
 		attachment "#{smiles}.png"
-    Rjb::import('Display').new(smiles,600).image
+    Rjb::import('Structure').new(smiles,200).show
 
 end
 
diff --git a/public/java/Display.java b/public/java/Display.java
deleted file mode 100644
index 2950ca7..0000000
--- a/public/java/Display.java
+++ /dev/null
@@ -1,124 +0,0 @@
-import java.util.List;
-import java.util.Arrays;
-import java.util.*;
-import java.io.*;
-
-import java.awt.*;
-import java.awt.image.*;
-import java.awt.geom.*;
-
-import javax.imageio.*;
-
-import org.openscience.cdk.*;
-import org.openscience.cdk.interfaces.*;
-import org.openscience.cdk.layout.*;
-import org.openscience.cdk.renderer.*;
-import org.openscience.cdk.renderer.font.*;
-import org.openscience.cdk.renderer.generators.*;
-import org.openscience.cdk.renderer.visitor.*;
-import org.openscience.cdk.templates.*;
-import org.openscience.cdk.smiles.*;
-import org.openscience.cdk.smiles.smarts.*;
-import org.openscience.cdk.graph.*;
-import org.openscience.cdk.geometry.*;
-
-public class Display{
-
-	int size;
-	Rectangle drawArea;
-	IMolecule molecule = new Molecule();
-	IMoleculeSet moleculeSet;
-	IMolecule[] coordinated_mols;
-	StructureDiagramGenerator sdg = new StructureDiagramGenerator();
-	SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
-	AtomContainer matches = new AtomContainer();
-	Vector<Integer> idlist = new Vector<Integer>();
-	List generators = new ArrayList();
-	Renderer renderer;
-	BufferedImage image;
-	Graphics2D g2;
-
-	ByteArrayOutputStream out = new ByteArrayOutputStream();
-
-	public Display (String smiles, int s) {
-
-		size = s; 
-		// generators make the image elements
-		generators.add(new BasicSceneGenerator());
-		generators.add(new BasicBondGenerator());
-		generators.add(new RingGenerator());
-		generators.add(new BasicAtomGenerator());
-		renderer = new Renderer(generators, new AWTFontManager());
-		try { molecule = sp.parseSmiles(smiles); }
-		catch (Exception ex) { ex.printStackTrace(); }
-		moleculeSet = ConnectivityChecker.partitionIntoMolecules(molecule);
-		coordinated_mols = new IMolecule[moleculeSet.getMoleculeCount()];
-		drawArea = new Rectangle(size, size);
-		image = new BufferedImage(size, size , BufferedImage.TYPE_INT_RGB);
-		g2 = (Graphics2D)image.getGraphics();
-		g2.setColor(Color.WHITE);
-		g2.fillRect(0, 0, size, size);
-	}
-
-	public byte[] image() {
-		try {
-			Rectangle2D last = new Rectangle(0,0);
-			for (int i = 0; i < moleculeSet.getMoleculeCount(); i++) {
-				IAtomContainer mol = moleculeSet.getMolecule(i);
-				sdg.setMolecule((IMolecule) mol);
-				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);
-			ImageIO.write(image, "png", out);
-		} catch (Exception ex) {
-				ex.printStackTrace();
-		}
-		return out.toByteArray();
-	}
-
-//	public Image match(String smiles, String smarts) {
-//	}
-	private void matchSmarts(String smarts, Color color) {
-		try {
-			// map smarts
-				SMARTSQueryTool querytool = new SMARTSQueryTool(smarts);
-				boolean status = querytool.matches(molecule);
-				if (status) {
-					List<List<java.lang.Integer>>	mappings = querytool.getMatchingAtoms();
-					int nmatch = querytool.countMatches();
-					for (int i = 0; i < nmatch; i++) {
-						List atomIndices = (List) mappings.get(i);
-						for (int n = 0; n < atomIndices.size(); n++) {
-							Integer atomID = (Integer) atomIndices.get(n);
-							idlist.add(atomID);
-						}
-					}
-				}
-
-				// get a unique list of bond ID's and add them to an AtomContainer
-				HashSet<Integer> hs = new HashSet<Integer>(idlist);
-				for (Integer h : hs) {
-					IAtom a = molecule.getAtom(h);
-					List bond_list = molecule.getConnectedBondsList(a);
-					for (int i = 0; i < bond_list.size(); i++) {
-						IBond b = (IBond) bond_list.get(i);
-						Integer connectedNr = molecule.getAtomNumber(b.getConnectedAtom(a));
-						//if (hs.contains(connectedNr)) renderer.getRenderer2DModel().getColorHash().put(b, color);
-					}
-				}
-
-		} catch (Exception exc) {
-				exc.printStackTrace();
-		}
-
-	}
-
-}
-
diff --git a/public/java/Makefile b/public/java/Makefile
index bcae6ec..bffc3d8 100644
--- a/public/java/Makefile
+++ b/public/java/Makefile
@@ -1,9 +1,6 @@
-#all: DisplayStructure.class
-all: Display.class
-
-#%.class: %.java
-#	javac -Xlint:deprecation -Xlint:unchecked -classpath ./:./cdk-1.0.1.jar $<
+all: Structure.class
 
 %.class: %.java
-	javac -classpath ./:./cdk-1.3.5.jar:./cdk-jchempaint-15.jar $<
+	javac  -classpath ./:./cdk-1.3.5.jar:./cdk-jchempaint-15.jar $<
+	#javac -classpath ./:./cdk-1.2.5.jar $<
 	#javac -Xlint:deprecation -Xlint:unchecked -classpath ./:./cdk-1.3.5.jar:./cdk-jchempaint-15.jar $<