java libs moved from public to root

6 files changed, 107 insertions, 190 deletions

diff --git a/application.rb b/application.rb
index e0e469d..09e447a 100644
--- a/application.rb
+++ b/application.rb
@@ -1,6 +1,6 @@
 # Java environment
 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"
+java_dir = File.join File.expand_path(File.dirname(__FILE__)),"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}"
@@ -10,19 +10,78 @@ require 'rjb'
 gem "opentox-ruby-api-wrapper", "= 1.6.0"
 require 'opentox-ruby-api-wrapper'
 
-post "/display" do
+#set :lock, true # avoid JVM memory allocation problems
+# -Xmx64m
+
+get "/display/activating/(.+)$" do
   content_type "image/png"
   attachment "#{params["smiles"]}.png"
-  s = Rjb::import('Structure').new(params["smiles"],200)
+  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
+  s = Rjb::import('Structure').new(params["smiles"],150)
   s.match_activating(params["smarts"])
-  s.match_deactivating(["CC"])
   s.show
 end
 
-get %r{/smiles/(.+)/smarts/(.*)} do |smiles,smarts| 
+post "/display/deactivating" do
+  content_type "image/png"
+  attachment "#{params["smiles"]}.png"
+  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
+  s = Rjb::import('Structure').new(params["smiles"],150)
+  s.match_deactivating(params["smarts"])
+  s.show
+end
+
+get %r{/smiles/(.+)/smarts/activating/(.*)/deactivating/(.*)/highlight/(.*)$} do |smiles,activating,deactivating,smarts| 
+  activating = activating.to_s.split(/\//).collect{|s| s.gsub(/"/,'')}
+  deactivating = deactivating.to_s.split(/\//).collect{|s| s.gsub(/"/,'')}
+  content_type "image/png"
+  attachment "#{smiles}.png"
+  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
+  s = Rjb::import('Structure').new(smiles,150)
+  s.match_deactivating(deactivating) unless deactivating.empty?
+  s.match_activating(activating) unless activating.empty?
+  s.match(smarts)
+  s.show
+  #s = nil
+end
+
+get %r{/smiles/(.+)/smarts/activating/(.*)/deactivating/(.*)$} do |smiles,activating,deactivating| 
+  activating = activating.to_s.split(/\//).collect{|s| s.gsub(/"/,'')}
+  deactivating = deactivating.to_s.split(/\//).collect{|s| s.gsub(/"/,'')}
+  content_type "image/png"
+  attachment "#{smiles}.png"
+  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
+  s = Rjb::import('Structure').new(smiles,150)
+  s.match_deactivating(deactivating)
+  s.match_activating(activating)
+  s.show
+  #s = nil
+end
+
+get %r{/smiles/(.+)/smarts/(.*)/(.*activating)$} do |smiles,allsmarts,effect| 
+  LOGGER.debug "String:"
+  LOGGER.debug allsmarts
+  smarts = allsmarts.to_s.split(/\//)
+  smarts.collect!{|s| s.gsub(/"/,'')}
+  LOGGER.debug "Smarts:"
+  LOGGER.debug smarts.to_yaml
+  content_type "image/png"
+  attachment "#{smiles}.png"
+  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
+  s = Rjb::import('Structure').new(smiles,150)
+  if effect == "activating"
+    s.match_activating(smarts)
+  elsif effect == "deactivating"
+    s.match_deactivating(smarts)
+  end
+  s.show
+end
+
+get %r{/smiles/(.+)/smarts/(.*)$} do |smiles,smarts| 
   content_type "image/png"
   attachment "#{smiles}.png"
-  s = Rjb::import('Structure').new(smiles,200)
+  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
+  s = Rjb::import('Structure').new(smiles,150)
   s.match(smarts)
   s.show
 end
@@ -30,14 +89,16 @@ end
 get %r{/smiles/(.+)} do |smiles| 
   content_type "image/png"
   attachment "#{smiles}.png"
-  Rjb::import('Structure').new(smiles,200).show
+  Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
+  Rjb::import('Structure').new(smiles,150).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('Structure').new(smiles,200).show
+   Rjb.load(nil,["-Xmx64m"])# avoid JVM memory allocation problems
+   Rjb::import('Structure').new(smiles,150).show
 end
 
 get %r{/(.+)} do |inchi| # catches all remaining get requests
diff --git a/public/java/Makefile b/java/Makefile
index bffc3d8..bffc3d8 100644
--- a/public/java/Makefile
+++ b/java/Makefile
diff --git a/java/Structure.java b/java/Structure.java
index d1ac188..af0f3b4 100644
--- a/java/Structure.java
+++ b/java/Structure.java
@@ -2,6 +2,7 @@ import java.util.List;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.*;
+import java.lang.Math;
 import java.io.*;
 
 import java.awt.*;
@@ -35,6 +36,11 @@ public class Structure{
 
   StructureDiagramGenerator sdg = new StructureDiagramGenerator();
   SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
+
+  List<IChemObject> matchingBonds = new ArrayList<IChemObject>();
+  List<IChemObject> activatingBonds = new ArrayList<IChemObject>();
+  List<IChemObject> deactivatingBonds = new ArrayList<IChemObject>();
+
   Map<IChemObject,Color> coloredMatches = new HashMap<IChemObject,Color>();
   Renderer renderer;
 
@@ -75,7 +81,17 @@ public class Structure{
 
   public byte[] show() {
     try {
+      // set colors
+      for (int i = 0; i < matchingBonds.size(); i++) {
+        float red = 0;
+        float green = 0;
+        IChemObject bond = (IChemObject) matchingBonds.get(i);
+        if (activatingBonds.contains(bond)) { red = 1; };
+        if (deactivatingBonds.contains(bond)) { green = 1; };
+        coloredMatches.put((IChemObject) bond , new Color(red,green,0));
+      }
       renderer.getRenderer2DModel().set( RendererModel.ColorHash.class, coloredMatches );
+      // render and write
       renderer.paintMoleculeSet(moleculeSet, new AWTDrawVisitor(g2), drawArea, true);
       ImageIO.write(image, "png", out);
     }
@@ -86,14 +102,16 @@ public class Structure{
   private void layout() {
     try {
       Rectangle2D last = new Rectangle(0,0);
-      for (int i = 0; i < moleculeSet.getMoleculeCount(); i++) {
+      //for (int i = 0; i < moleculeSet.getMoleculeCount(); i++) {
+      // reverse iteration to show small molecules at the right side
+      for (int i = moleculeSet.getMoleculeCount()-1; i >= 0 ; 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 to the right
-        last = GeometryTools.shiftContainer(mol, GeometryTools.getRectangle2D(mol), last, 5);
+        // gives nasty results for single atom molecules, but works otherwise
+        last = GeometryTools.shiftContainer(mol, GeometryTools.getRectangle2D(mol), last, 0);
         coordinated_mols[i] = (IMolecule) mol;
       }
       moleculeSet.setMolecules(coordinated_mols);
@@ -103,25 +121,22 @@ public class Structure{
 
   public void match_activating(String[] smarts) {
     for (int i = 0; i < smarts.length; i++) {
-      match(smarts[i],Color.RED);
+      match(smarts[i],true);
     }
   }
 
   public void match_deactivating(String[] smarts) {
     for (int i = 0; i < smarts.length; i++) {
-      match(smarts[i],Color.GREEN);
+      match(smarts[i],false);
     }
   }
 
-  public void match(String smarts) { match(smarts, Color.BLUE); }
-
-  public void match(String smarts, Color color) {
+  public void match(String smarts) { match(smarts, true); }
 
-    IAtom a1 = new Atom();
-    IAtom a2 = new Atom();
-    IBond bond = new Bond();
+  public void match(String smarts, Boolean active) {
 
     try {
+      int count;
       SMARTSQueryTool querytool = new SMARTSQueryTool(smarts);
       // iterate over molecule set
       for (int i = 0; i < moleculeSet.getMoleculeCount(); i++) {
@@ -131,19 +146,25 @@ public class Structure{
         boolean status = querytool.matches(mol);
         if (status) {
           List matches = querytool.getUniqueMatchingAtoms();
-          //System.out.print("Matches: ");
-          //System.out.println(matches);
           // iterate over all matches
           for (int j = 0; j < matches.size(); j++) {
             List atomIndices = (List) matches.get(j);
             // itrate over all atoms
             for (int k = 0; k < atomIndices.size(); k++) {
-              a1 = mol.getAtom( (Integer) atomIndices.get(k));
+              IAtom a1 = mol.getAtom( (Integer) atomIndices.get(k));
               // find bonds
               for (int l = k + 1; l < atomIndices.size(); l++) {
-                a2 = mol.getAtom( (Integer) atomIndices.get(l));
-                bond = mol.getBond(a1,a2);
-                if (bond != null) { coloredMatches.put((IChemObject) bond , color); }
+                IAtom a2 = mol.getAtom( (Integer) atomIndices.get(l));
+                IChemObject bond = (IChemObject) mol.getBond(a1,a2);
+                if (bond != null) {
+                  // collect all/active/inactive bonds
+                  if (!matchingBonds.contains(bond)) { matchingBonds.add(bond); }
+                  if (active) {
+                    if (!activatingBonds.contains(bond)) { activatingBonds.add(bond); }
+                  } else {
+                    if (!deactivatingBonds.contains(bond)) { deactivatingBonds.add(bond); }
+                  }
+                }
               }
             }
           }
@@ -152,7 +173,6 @@ public class Structure{
 
     }
     catch (Exception exc) { exc.printStackTrace(); }
-
   }
 
 }
diff --git a/java/cdk-1.3.5.jar b/java/cdk-1.3.5.jar
new file mode 100644
index 0000000..7d80934
--- /dev/null
+++ b/java/cdk-1.3.5.jar
diff --git a/java/cdk-jchempaint-15.jar b/java/cdk-jchempaint-15.jar
new file mode 100644
index 0000000..7078c2b
--- /dev/null
+++ b/java/cdk-jchempaint-15.jar
diff --git a/public/java/Structure.java b/public/java/Structure.java
deleted file mode 100644
index c46ea05..0000000
--- a/public/java/Structure.java
+++ /dev/null
@@ -1,164 +0,0 @@
-import java.util.List;
-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.renderer.selection.*;
-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 Structure{
-
-  int size;
-  List generators = new ArrayList();
-
-  IMolecule molecule = new Molecule();
-  IMoleculeSet moleculeSet;
-  IMolecule[] coordinated_mols;
-
-  StructureDiagramGenerator sdg = new StructureDiagramGenerator();
-  SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
-  Renderer renderer;
-
-  BufferedImage image;
-  Rectangle drawArea;
-  Graphics2D g2;
-
-  LogicalSelection selection = new LogicalSelection(LogicalSelection.Type.ALL);
-  MoleculeSet selectionMoleculeSet = new MoleculeSet();
-  ChemModel selectionChemModel = new ChemModel();
-
-  ByteArrayOutputStream out = new ByteArrayOutputStream();
-
-  public Structure (String smiles, int imageSize) {
-
-    size = imageSize; 
-
-    // generators make the image elements
-    generators.add(new BasicSceneGenerator());
-    generators.add(new RingGenerator());
-    generators.add(new BasicBondGenerator());
-    generators.add(new BasicAtomGenerator());
-    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(); }
-
-    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);
-
-    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);
-    }
-    catch (Exception ex) { ex.printStackTrace(); }
-    return out.toByteArray();
-  }
-
-  private void layout() {
-    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 to the right
-        last = GeometryTools.shiftContainer(mol, GeometryTools.getRectangle2D(mol), last,2);
-        coordinated_mols[i] = (IMolecule) mol;
-      }
-      moleculeSet.setMolecules(coordinated_mols);
-    }
-    catch (Exception ex) { ex.printStackTrace(); }
-  }
-
-  public void match_activating(String[] smarts) {
-    for (int i = 0; i < smarts.length; i++) {
-      match(smarts[i]);
-    }
-  }
-
-  public void match_deactivating(String[] smarts) {
-    renderer.getRenderer2DModel().set( SelectBondGenerator.SelectionBondColor.class,Color.GREEN);
-    for (int i = 0; i < smarts.length; i++) {
-      match(smarts[i]);
-    }
-  }
-
-  public void match(String smarts) {
-
-    try {
-      SMARTSQueryTool querytool = new SMARTSQueryTool(smarts);
-      // iterate over molecule set
-      for (int i = 0; i < moleculeSet.getMoleculeCount(); i++) {
-        IAtomContainer mol = moleculeSet.getMolecule(i);
-        ChemModel fragment = new ChemModel();
-        // match smarts
-        boolean status = querytool.matches(mol);
-        if (status) {
-          List matches = querytool.getUniqueMatchingAtoms();
-          //System.out.print("Matches: ");
-          //System.out.println(matches);
-          // iterate over all matches
-          for (int j = 0; j < matches.size(); j++) {
-            IAtomContainer selectionContainer = new AtomContainer();
-            List atomIndices = (List) matches.get(j);
-            // itrate over all atoms
-            for (int k = 0; k < atomIndices.size(); k++) {
-              IAtom a1 = mol.getAtom( (Integer) atomIndices.get(k));
-              if (!selectionContainer.contains(a1)) {  selectionContainer.addAtom(a1); }
-              // find bonds
-              for (int l = k + 1; l < atomIndices.size(); l++) {
-                IAtom a2 = mol.getAtom( (Integer) atomIndices.get(l));
-                IBond bond = mol.getBond(a1,a2);
-                if (bond != null) { selectionContainer.addBond(bond); }
-              }
-            }
-            // create a fake MoleculeSet to make the LogicalSelection happy
-            selectionMoleculeSet.addMolecule(new Molecule(selectionContainer));
-          }
-        }
-      }
-
-    }
-    catch (Exception exc) { exc.printStackTrace(); }
-
-  }
-
-}