toxtree 0.0.1

data/Toxtree-v2.6.13/src/toxtree/data/ToxTreeModule.java

@@ -0,0 +1,265 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2007 
+
+Contact: nina@acad.bg
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU General Public License
+as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+*/
+/**
+ * <b>Filename</b> toxTreeData.java 
+ * @author Nina Jeliazkova nina@acad.bg
+ * <b>Created</b> 2005-8-1
+ * <b>Project</b> toxTree
+ */
+package toxtree.data;
+
+import java.awt.Frame;
+import java.io.File;
+import java.util.Observable;
+import java.util.logging.Level;
+
+import javax.swing.JFrame;
+import javax.swing.SwingWorker;
+
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomContainerSet;
+
+import toxTree.core.IDecisionMethod;
+import toxTree.core.IMetaboliteGenerator;
+import toxTree.io.batch.BatchProcessing;
+import toxTree.io.batch.BatchProcessingException;
+import toxTree.io.batch.ToxTreeBatchProcessing;
+import toxTree.query.metabolite.MetabolyteRecycler;
+import toxTree.tree.DecisionMethodsList;
+import toxTree.tree.RuleResult;
+import toxtree.ui.metabolites.MetabolitesFrame;
+import toxtree.ui.tree.TreeFrame;
+import ambit2.base.data.Property;
+
+/**
+ * Contains data essential for {@link toxTree.apps.ToxTreeApp} application
+ * <ul>
+ * <li>the current method {@link toxTree.core.IDecisionMethod}
+ * <li>the result {@link toxTree.core.IDecisionResult}
+ * <li>the list of available methods {@link toxTree.core.IDecisionMethodsList}
+ * <li>the data {@link toxtree.data.DecisionMethodData}
+ * <li>the tree data {@link toxtree.data.DecisionMethodData}
+ * <li>the batch processing object {@link toxTree.io.batch.ToxTreeBatchProcessing}
+ * </ul>
+ * Also contains some UI frames :
+ * <ul>
+ * <li> a Frame to view a decision tree {@link toxtree.ui.tree.TreeFrame}
+ * <li> a Frame to edit a decision tree {@link toxTree.ui.tree.EditTreeFrame}
+ * <li> a dialog with structure diagram editor {@link ambit2.jchempaint.editor.JChemPaintDialog}
+ * <li> and a {@link org.openscience.cdk.applications.jchempaint.JChemPaintModel}
+ * </ul>  
+ * @author Nina Jeliazkova <br>
+ * <b>Modified</b> 2005-8-1
+ */
+public class ToxTreeModule extends DecisionMethodsDataModule {
+
+    /**
+     * Comment for <code>serialVersionUID</code>
+     */
+    private static final long serialVersionUID = 8292481405980136292L;
+    
+    protected MetabolyteRecycler listener;
+	private TreeFrame treeFrame = null;
+	private MetabolitesFrame metabolitesFrame = null;
+
+//	protected IDecisionRule currentRule = null;
+	//protected EditTreeFrame editMethodFrame = null;
+
+	ToxTreeActions actions;
+	
+    /**
+     * 
+     */
+    public ToxTreeModule(JFrame frame, File inputFile, DecisionMethodsList methods) {
+        super(frame,inputFile,methods);
+        if (methods.size()>0)
+        	setRules(methods.getMethod(0));
+        
+        actions = new ToxTreeActions(frame,this);
+        listener = new MetabolyteRecycler() {
+        	protected void handleproduct(IAtomContainer product) {
+        		int found = -1;
+        		try {
+        			dataContainer.setEnabled(false);
+        			found =dataContainer.lookup(Property.opentox_InChI_std,product.getProperty(Property.opentox_InChI_std),true);
+
+        		} catch (Exception x) { found = -1;
+        		} 
+        		finally {
+        			dataContainer.setEnabled(true);
+        		}
+        		if (found>=0) {
+        			dataContainer.gotoRecord(found+1);
+        		}  else 
+        			dataContainer.addMolecule(product);        		
+
+        	};
+        };
+
+    }
+    @Override
+	protected DataContainer createDataContainer(File inputFile) {
+    	DecisionMethodData dc = new DecisionMethodData(inputFile);
+        dc.addObserver(this);
+        return dc;
+    }
+  
+
+    /* (non-Javadoc)
+     * @see java.util.Observer#update(java.util.Observable, java.lang.Object)
+     */
+    @Override
+	public void update(Observable o, Object arg) {
+        if (treeResult.isEstimating()) return; //can't change compound during estimation
+        if (o instanceof DecisionMethodData) {
+            treeResult.clear();
+            if (metabolitesFrame!=null) {
+            	metabolitesFrame.setVisible(false);
+            	metabolitesFrame.setProducts("Metabolites",null);
+            }
+            setChanged();
+            notifyObservers();
+        }
+
+    }
+
+
+    @Override
+	public void batch(BatchProcessing bp) {
+    	this.batch = bp;
+    	if (bp instanceof ToxTreeBatchProcessing)
+    	((ToxTreeBatchProcessing) this.batch).setDecisionMethod(rules);
+    	
+    	new SwingWorker<BatchProcessing, Object>() {
+			 
+  	       @Override
+  	       public BatchProcessing doInBackground() {
+	           	try {
+	        		batch.start();
+	        	} catch (BatchProcessingException x) {
+	        		logger.log(Level.SEVERE,x.getMessage(),x);
+	        		ToxTreeActions.showMsg("Error on batch processing",x.getMessage());
+	        	} catch (Throwable x) {
+	        		logger.log(Level.SEVERE,x.getMessage(),x);
+	        	}
+	            return batch;
+  	       }
+  	       @Override
+  	       protected void done() {
+                setChanged();
+                notifyObservers();
+  	       }
+  	   }.execute(); 	
+  
+    }	
+
+    
+    @Override
+	public ActionList getActions() {
+        return actions;
+    }
+
+    
+    public void viewMethod(boolean editable) {
+        if (treeFrame == null) 
+            treeFrame = new TreeFrame(rules);
+        else 
+            treeFrame.setDecisionMethod(rules);
+
+        treeFrame.setVisible(true);
+    }
+
+    
+
+    @Override
+	public void setRules(IDecisionMethod rules) {
+
+    	super.setRules(rules);
+
+        if (treeFrame != null) { 
+            treeFrame.dispose();
+            treeFrame = null;
+        }    
+        
+        synchronized (this) {
+			
+		if (metabolitesFrame !=null) {
+        	metabolitesFrame.removePropertyChangeListener(listener);
+        	metabolitesFrame.dispose();
+        	metabolitesFrame = null;
+        }
+        }
+    }
+
+    /*
+    public void launchEditFrame(IDecisionMethod tree) {
+        if (editMethodFrame == null)  {
+        	
+        	editMethodFrame = new EditTreeFrame(tree);
+        	editMethodFrame.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
+        	editMethodFrame.setVisible(true);
+        	editMethodFrame.addWindowListener(new WindowAdapter() {
+        		public void windowClosing(WindowEvent arg0) {
+        			boolean doClose =  (!editMethodFrame.isModified()) || (
+        				editMethodFrame.isModified() &&
+        	        	 (JOptionPane.showConfirmDialog(null,"The decision tree is not saved. \nAre you sure to exit without saving the decision tree?","Please confirm",JOptionPane.YES_NO_OPTION)
+        	        		==JOptionPane.YES_OPTION));
+        			if (doClose) {
+        			editMethodFrame.setVisible(false);
+        			editMethodFrame.dispose();
+        			editMethodFrame = null;
+        	        }
+        		}
+        	});
+        }
+
+    }
+      */  
+    public String showMetabolites(RuleResult ruleResult) throws Exception {
+		if (getRules() instanceof IMetaboliteGenerator) {
+			
+			if (!treeResult.isEstimated()) 
+				treeResult.classify(getDataContainer().getMolecule());
+
+			IAtomContainerSet products = ((IMetaboliteGenerator)getRules()).getProducts(
+							getDataContainer().getMolecule(),
+							ruleResult);
+			
+	        if (metabolitesFrame == null)  {
+	        	metabolitesFrame = new MetabolitesFrame();
+	        	metabolitesFrame.addPropertyChangeListener("metabolite",listener);
+	        }
+ 
+	        metabolitesFrame.setProducts(((IMetaboliteGenerator)getRules()).getHelp(ruleResult),products);
+	        metabolitesFrame.setVisible(true);
+
+	        metabolitesFrame.setState ( Frame.NORMAL );
+
+		}
+		return null;
+    }    
+
+}
+

data/Toxtree-v2.6.13/src/toxtree/lookup/RemoteLookup.java

@@ -0,0 +1,108 @@
+package toxtree.lookup;
+
+import java.io.InputStream;
+import java.util.Hashtable;
+
+import org.opentox.aa.IOpenToxUser;
+import org.opentox.aa.OpenToxUser;
+import org.opentox.aa.cli.InvalidCredentials;
+import org.opentox.aa.opensso.AAServicesConfig;
+import org.opentox.aa.opensso.OpenSSOToken;
+import org.opentox.rest.HTTPClient;
+
+public abstract class RemoteLookup<RESULT> {
+	//protected static final String defaultLookup = "https://apps.ideaconsult.net/ambit2/query/compound/search/all?search=%s&max=1&media=chemical%%2Fx-mdl-sdfile";;
+	protected static String lookupService = null;
+	protected String authService;
+	protected String policyService;
+	protected OpenSSOToken ssotoken;
+	protected IOpenToxUser user;
+	
+	
+	public RemoteLookup() throws Exception {
+		super();
+		user = new OpenToxUser();
+		authService = AAServicesConfig.getSingleton().getOpenSSOService();
+		policyService = AAServicesConfig.getSingleton().getPolicyService();
+
+		
+
+
+	}
+	protected String init() {
+		HTTPClient cli = null;
+		try {
+			cli = new HTTPClient("http://toxtree.sf.net/lookup.txt");
+			cli.get();
+			return cli.getText();
+		} catch (Exception x) {
+			try { cli.release();} catch (Exception xx) {}
+			return null;
+		}
+	}
+	public void login() throws Exception {
+		login(AAServicesConfig.getSingleton().getTestUser(),AAServicesConfig.getSingleton().getTestUserPass());
+	}
+	public void login(String uname,String pass) throws Exception {
+		user.setUserName(uname);
+		user.setPassword(pass);		
+		Hashtable<String, String> results = new Hashtable<String, String>();
+		
+		if (ssotoken==null) ssotoken = new OpenSSOToken(authService);
+		if (ssotoken.getToken()==null) {
+			ssotoken.login(user);
+			if (ssotoken.getToken()==null) {
+				throw new InvalidCredentials(authService);
+			} //else
+			//System.out.println(String.format("Logged as %s token %s",user.getUsername(),ssotoken.getToken()));
+		} else {
+			//System.out.println(String.format("Using provided token %s",ssotoken.getToken()));
+			if (!ssotoken.isTokenValid()) {
+				throw new InvalidCredentials("Invalid token submited to ");
+			}
+		}
+//		ssotoken.getAttributes(new String[] {"uid"},results);
+		
+	}
+	public void logout() throws Exception {
+
+		if ((ssotoken!=null) && (ssotoken.getToken()!=null)) {
+			//System.out.println("Invalidating the token ...");
+			ssotoken.logout();
+			//System.out.println("Logout completed. The token is no longer valid.");
+		}
+		
+	}
+	public abstract RESULT processStream(String uri,String input,InputStream in) throws Exception;
+	
+	public RESULT lookup(String input) throws Exception {
+		
+		if (lookupService==null)
+		synchronized (this) {
+			
+			String uri = init();
+			if ((uri!=null) && !"".equals(uri.trim())) lookupService = uri;
+			//else lookupService = defaultLookup;
+		}
+		
+		HTTPClient cli = null;
+		InputStream in = null;
+		try {
+			try { login(); } catch (Exception x) {}
+			cli = new HTTPClient(String.format(lookupService,input));
+			cli.get();
+			if (cli.getStatus()==200) {
+				in = cli.getInputStream();
+				return processStream(lookupService,input,in);
+				
+			}
+			return null;
+		} catch (Exception x) {
+			return null;
+		} finally {
+			try { if (in != null) in.close();} catch (Exception x) {}
+			try { if (cli != null) cli.release();} catch (Exception x) {}
+			try { logout();} catch (Exception x) {}
+		}
+	}	
+}

data/Toxtree-v2.6.13/src/toxtree/plugins/ames/AmesMutagenicityRules.java

@@ -0,0 +1,432 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2008  
+
+Contact: nina@acad.bg
+
+This program is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public License
+as published by the Free Software Foundation; either version 2.1
+of the License, or (at your option) any later version.
+All we ask is that proper credit is given for our work, which includes
+- but is not limited to - adding the above copyright notice to the beginning
+of your source code files, and to any copyright notice that you may distribute
+with programs based on this work.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public License
+along with this program; if not, write to the Free Software
+Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA
+*/
+
+package toxtree.plugins.ames;
+
+import java.beans.PropertyChangeListener;
+import java.beans.PropertyChangeSupport;
+
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.qsar.DescriptorSpecification;
+
+import toxTree.core.IDecisionInteractive;
+import toxTree.core.IDecisionResult;
+import toxTree.exceptions.DecisionMethodException;
+import toxTree.exceptions.DecisionResultException;
+import toxTree.tree.CategoriesList;
+import toxTree.tree.DecisionNodesFactory;
+import toxTree.tree.UserDefinedTree;
+import toxtree.plugins.ames.categories.CategoryError;
+import toxtree.plugins.ames.categories.CategoryMutagenTA100;
+import toxtree.plugins.ames.categories.CategoryNoAlertAmes;
+import toxtree.plugins.ames.categories.CategoryNonMutagen;
+import toxtree.plugins.ames.categories.CategoryPositiveAlertAmes;
+import toxtree.plugins.ames.categories.QSARApplicable;
+import toxtree.plugins.ames.rules.AmesMutagenicityTreeResult;
+import toxtree.plugins.ames.rules.RuleABUnsaturatedAldehyde;
+import toxtree.plugins.ames.rules.RuleAlertsForAmesMutagenicity;
+import toxtree.plugins.ames.rules.RuleAlertsForNewAmesMutagenicity;
+import toxtree.plugins.ames.rules.RuleAromaticAmineNoSulfonicGroup;
+import toxtree.plugins.ames.rules.RuleAromaticDiazo;
+import toxtree.plugins.ames.rules.RuleDAMutagenicityABUnsaturatedAldehydes;
+import toxtree.plugins.ames.rules.RuleDAMutagenicityAromaticAmines;
+import toxtree.plugins.ames.rules.RuleDerivedAromaticAmines;
+import toxtree.plugins.ames.rules.SA10_gen;
+import toxtree.plugins.ames.rules.SA11_gen;
+import toxtree.plugins.ames.rules.SA12_gen;
+import toxtree.plugins.ames.rules.SA13_gen;
+import toxtree.plugins.ames.rules.SA14_gen;
+import toxtree.plugins.ames.rules.SA15_gen;
+import toxtree.plugins.ames.rules.SA16_gen;
+import toxtree.plugins.ames.rules.SA18_gen;
+import toxtree.plugins.ames.rules.SA19_gen;
+import toxtree.plugins.ames.rules.SA1_gen;
+import toxtree.plugins.ames.rules.SA21_gen;
+import toxtree.plugins.ames.rules.SA22_gen;
+import toxtree.plugins.ames.rules.SA23_gen;
+import toxtree.plugins.ames.rules.SA24_gen;
+import toxtree.plugins.ames.rules.SA25_gen;
+import toxtree.plugins.ames.rules.SA26_gen;
+import toxtree.plugins.ames.rules.SA27_gen;
+import toxtree.plugins.ames.rules.SA28_gen;
+import toxtree.plugins.ames.rules.SA28bis_gen;
+import toxtree.plugins.ames.rules.SA28ter_gen;
+import toxtree.plugins.ames.rules.SA29_gen;
+import toxtree.plugins.ames.rules.SA2_gen;
+import toxtree.plugins.ames.rules.SA30_gen;
+import toxtree.plugins.ames.rules.SA37_gen;
+import toxtree.plugins.ames.rules.SA38_gen;
+import toxtree.plugins.ames.rules.SA39_gen_and_nogen;
+import toxtree.plugins.ames.rules.SA3_gen;
+import toxtree.plugins.ames.rules.SA4_gen;
+import toxtree.plugins.ames.rules.SA57_Ames;
+import toxtree.plugins.ames.rules.SA58_Ames;
+import toxtree.plugins.ames.rules.SA59_Ames;
+import toxtree.plugins.ames.rules.SA5_gen;
+import toxtree.plugins.ames.rules.SA60_Ames;
+import toxtree.plugins.ames.rules.SA61_Ames;
+import toxtree.plugins.ames.rules.SA62_Ames;
+import toxtree.plugins.ames.rules.SA63_Ames;
+import toxtree.plugins.ames.rules.SA64_Ames;
+import toxtree.plugins.ames.rules.SA65_Ames;
+import toxtree.plugins.ames.rules.SA66_Ames;
+import toxtree.plugins.ames.rules.SA67_Ames;
+import toxtree.plugins.ames.rules.SA68_Ames;
+import toxtree.plugins.ames.rules.SA69_Ames;
+import toxtree.plugins.ames.rules.SA6_gen;
+import toxtree.plugins.ames.rules.SA7_gen;
+import toxtree.plugins.ames.rules.SA8_gen;
+import toxtree.plugins.ames.rules.SA9_gen;
+import toxtree.plugins.ames.rules.UserInputABUnsaturatedAldehyde;
+import toxtree.plugins.ames.rules.UserInputAromaticAmine;
+import toxtree.plugins.ames.rules.VerifyAlertsAmes;
+import toxtree.plugins.ames.rules.VerifyAlertsNewAmes;
+
+/**
+ * 
+
+ * @author nina
+ * @modified 04/07/2007
+ *
+ */
+public class AmesMutagenicityRules extends UserDefinedTree implements IDecisionInteractive{
+	/**
+     * Comment for <code>serialVersionUID</code>
+     */
+    private static final long serialVersionUID = 0;
+    protected boolean residuesIDVisible;
+ 
+
+        public final static transient String[] c_rules = { 
+            RuleAlertsForAmesMutagenicity.class.getName(), // Rule  1         
+            SA1_gen.class.getName(), //2
+            SA2_gen.class.getName(), //3
+            SA3_gen.class.getName(), //4
+            SA4_gen.class.getName(), //5
+            SA5_gen.class.getName(), //6
+            SA6_gen.class.getName(), //7
+            SA7_gen.class.getName(), //8
+            SA8_gen.class.getName(), //9
+            SA9_gen.class.getName(), //10
+            SA11_gen.class.getName(), //11
+            SA12_gen.class.getName(), //12
+            SA13_gen.class.getName(), //13
+            SA14_gen.class.getName(), //14
+            SA15_gen.class.getName(), //15
+            SA16_gen.class.getName(), //16
+            SA18_gen.class.getName(), //17
+            SA19_gen.class.getName(), //18 
+            SA21_gen.class.getName(), //29
+            SA22_gen.class.getName(), //20
+            SA23_gen.class.getName(), //21
+            SA24_gen.class.getName(), //22
+            SA25_gen.class.getName(), //23
+            SA26_gen.class.getName(), //24
+            SA27_gen.class.getName(), //25
+            SA28_gen.class.getName(), //26
+            SA28bis_gen.class.getName(), //27
+            SA28ter_gen.class.getName(), //28   
+            SA29_gen.class.getName(),    //29
+            SA30_gen.class.getName(), //30
+            SA37_gen.class.getName(), //28//31   
+            SA38_gen.class.getName(),    //32
+            SA39_gen_and_nogen.class.getName(), //33
+                                       
+            VerifyAlertsAmes.class.getName(), //31//34 no go to qsar 13, no go to sa10, cat 8 neg and 1 pos
+            
+            RuleABUnsaturatedAldehyde.class.getName(), //is a,b unsaturated aldehyde Rule 54//35 app13? no go to sa10, yes go to proceed next?
+            UserInputABUnsaturatedAldehyde.class.getName(), //56//36 proceed qsar13? no go to sa 10, yes to to qsar 13, no cat 0 yes cat 7
+            RuleDAMutagenicityABUnsaturatedAldehydes.class.getName(), //QSAR13 Rule 57// 37 both go to sa 10, cat. 4 neg 3 pos
+            
+            SA10_gen.class.getName(), //39// 38  sa10 yes no go next, cat no 0 pos 1 
+            
+            RuleAromaticDiazo.class.getName(), //40//39
+            RuleDerivedAromaticAmines.class.getName(), //41//40
+            RuleAromaticAmineNoSulfonicGroup.class.getName(), //is aromatic amine Rule  42/app 8 and 6//41 no go to nongen sa 45, yes go next
+            UserInputAromaticAmine.class.getName(), //43//42  roceed qsar8 and 6? no go to sa nongen 45, yes to to next, no cat 0 yes cat 7
+            //RuleDACancerogenicityAromaticAmines.class.getName(), //QSAR8  Rule 44// 43 rules next, cat. 6 neg 5 pos
+            RuleDAMutagenicityAromaticAmines.class.getName(), //QSAR6 Rule 46// 44 rules next, cat. 4 neg 3 pos
+            //get here by No alerts for genotoxic carc. branch /43
+            
+  
+            RuleAlertsForNewAmesMutagenicity.class.getName(), //32//45/44
+            //SA17_nogen.class.getName(), //33 nongenotoxic//46
+            //SA20_nogen.class.getName(), //34 nongenotoxic//47
+            //SA31a_nogen.class.getName(), //35 nongenotoxic//48
+            //SA31b_nogen.class.getName(), //36 nongenotoxic//49
+            //SA31c_nogen.class.getName(), //37 nongenotoxic//50
+            
+            //SA39_gen_and_nogen.class.getName(), //51
+            
+            SA57_Ames.class.getName(), //33 nongenotoxic//52/45
+            SA58_Ames.class.getName(), //33 nongenotoxic//53/46
+            SA59_Ames.class.getName(), //34 nongenotoxic//54/47
+            SA60_Ames.class.getName(), //33 nongenotoxic//55/48/
+            SA61_Ames.class.getName(), //34 nongenotoxic//56/49
+            SA62_Ames.class.getName(), //33 nongenotoxic//57/50
+            SA63_Ames.class.getName(), //34 nongenotoxic//58/51
+            SA64_Ames.class.getName(), //33 nongenotoxic//59/52
+            SA65_Ames.class.getName(), //34 nongenotoxic//60/53
+            SA66_Ames.class.getName(), //33 nongenotoxic//61/54
+            SA67_Ames.class.getName(), //34 nongenotoxic//62/55/
+            SA68_Ames.class.getName(), //34 nongenotoxic//63/56
+            SA69_Ames.class.getName(), //34 nongenotoxic//64/57
+            
+            //SA53_nogen.class.getName(), //34 nongenotoxic//65
+            //SA54_nogen.class.getName(), //34 nongenotoxic//66
+           // SA55_nogen.class.getName(), //34 nongenotoxic//67
+            //SA56_nogen.class.getName(), //34 nongenotoxic//68
+            
+            VerifyAlertsNewAmes.class.getName(), //38//69 rules 0 0  cat neg 9 pos 2/58
+        
+        
+         
+            
+            };
+        private final static transient int c_transitions[][] ={
+            //{if no go to, if yes go to, assign if no, assign if yes}
+        	
+            {2,2,0,0}, //Rule 1  1
+            
+            {3,3,0,0}, //sa1 2
+            {4,4,0,0}, //sa2 3
+            {5,5,0,0}, //sa3  4
+            {6,6,0,0}, //sa4 5
+            {7,7,0,0}, //sa5 6
+            {8,8,0,0}, //sa6 7
+            {9,9,0,0}, //sa7 8
+            {10,10,0,0}, //sa8 9
+            {11,11,0,0}, //sa9 10
+            {12,12,0,0}, //sa11 11
+            {13,13,0,0}, //sa12 12
+            {14,14,0,0}, //sa13 13 
+            {15,15,0,0}, //sa14 14
+            {16,16,0,0}, //sa15 15
+            {17,17,0,0}, //sa16 16 
+            {18,18,0,0}, //sa18 17
+            {19,19,0,0}, //sa19 18
+            {20,20,0,0}, //sa21 19
+            {21,21,0,0}, //sa22 20
+            {22,22,0,0}, //sa23 21
+            {23,23,0,0}, //sa24 22
+            {24,24,0,0}, //sa25 23
+            {25,25,0,0}, //sa26 24
+            {26,26,0,0}, //sa27 25
+            {27,27,0,0}, //sa28 26
+            {28,28,0,0}, //sa28bis 27
+            {29,29,0,0}, //sa28ter 28
+            {30,30,0,0}, //sa29 29
+            {31,31,0,0}, //sa30 30
+            {32,32,0,0}, //sa37 31
+            {33,33,0,0}, //sa38 32
+            {34,34,0,0}, //sa39mix 33
+                        
+            {35,38,2,1}, //counter non gen alert senza sa10 34
+            //no go to qsar 13 next, yes go to sa10 38, cat 8 neg and 1 pos
+            
+                        
+            {38,36,0,0}, //app Q13? 35
+            //no go to sa10, yes go to proceed next
+            
+            {38,37,5,0}, //proceed Q13? 36
+            //no go to sa 10, yes to to qsar 13, no cat 0 yes cat 7
+                        
+            {38,38,4,3}, //Q13 37
+            //both go to sa 10, cat. 4 neg 3 pos
+            
+            {39,39,0,1}, //sa110 38
+            //yes no go next, cat no 0 pos 1 
+            
+            
+            {40,40,0,0}, // 39   aN=Na  - if yes will be split into ar amines, otherwise will work with the original compound 41
+            {41,41,0,0}, //40  Rule  (ii)    
+            
+            {44,42,0,0}, //41  qsar 8 and 6 app? ar amine? 
+            //no go to nongen sa 46, yes go next
+            
+            {44,43,5,0}, // 42 user input proceed?
+            //no go to sa nongen 46, yes to to next, no cat 0 yes cat 7?
+            
+           // {44,44,6,5}, //43 QSAR8 //Yes (>threshold)- carcinogen,No - not a carcinogen/next, cat. 6 neg 5 pos
+            
+            {44,44,4,3}, //44 QSAR6 //rules next, cat. 4 neg 3 pos
+            
+            
+            
+            {45,45,0,0}, //nongenotoxic alerts 45/counter new Ames 44
+            {46,46,0,0}, //sa17 46/45 ames 57
+            {47,47,0,0}, //sa17 46/45 ames 58
+            {48,48,0,0}, //sa20 47/46 ames 59
+            {49,49,0,0}, //sa31a 48/47 ames 60
+            
+            
+            {50,50,0,0}, //sa31b 49/48 ames 61
+            {51,51,0,0}, //sa31c 50/49 ames 62
+            {52,52,0,0}, //sa39mixed 51/50 ames 63
+            
+            {53,53,0,0}, //sa40 52/51 ames 64
+            {54,54,0,0}, //sa41 53/52 ames 65
+            {55,55,0,0}, //sa42 54/53 ames 66
+            {56,56,0,0}, //sa43 55/54 ames 67
+            {57,57,0,0}, //sa44 56/55 ames 68
+            {58,58,0,0}, //sa45 57/56 ames 69
+           
+            
+            
+            {0,0,0,1}, //any new Ames alert? 69/58
+            
+          
+
+            
+        };	
+	
+		private final static transient String c_categories[] ={
+			CategoryPositiveAlertAmes.class.getName(), //1 -1
+			CategoryNoAlertAmes.class.getName(), //2 -2
+			//CategoryNoAlert",		//3 
+			CategoryMutagenTA100.class.getName(),	//4 -3
+			CategoryNonMutagen.class.getName(),	//5 -4
+			//CategoryCarcinogen.class.getName(),		//6  -5
+			//CategoryNotCarcinogen.class.getName(), //7 -6
+			QSARApplicable.class.getName(),	//8 -7/5
+			//CategoryNoGenotoxicAlert.class.getName(), //9 -8
+			//CategoryNoNongenotoxicAlert.class.getName(), //10 -9
+			CategoryError.class.getName()//10 -10/6
+		};
+	/**
+	 * 
+	 */
+	public AmesMutagenicityRules() throws DecisionMethodException {
+		super(new CategoriesList(c_categories,true),c_rules,c_transitions,new DecisionNodesFactory(true));
+        //getRule(53).setID("SA10a");
+		setChanged();
+		notifyObservers();
+		setTitle("In vitro mutagenicity (Ames test) alerts by ISS");
+        setPriority(6);
+        setFalseIfRuleNotImplemented(false);
+        
+        //setFalseIfRuleNotImplemented(false); //this will cause exception if an error occurs in a rule
+	}
+
+
+	/* (non-Javadoc)
+     * @see toxTree.core.IDecisionMethod#addPropertyChangeListener(java.beans.PropertyChangeListener)
+     */
+    public void addPropertyChangeListener(PropertyChangeListener l) {
+        if (changes == null) 		changes = new PropertyChangeSupport(this);        
+        changes.addPropertyChangeListener(l);
+		for (int i=0; i < rules.size(); i++) 
+			if (rules.getRule(i) != null)
+				rules.getRule(i).addPropertyChangeListener(l);
+    }
+    /* (non-Javadoc)
+     * @see toxTree.core.IDecisionMethod#removePropertyChangeListener(java.beans.PropertyChangeListener)
+     */
+    public void removePropertyChangeListener(PropertyChangeListener l) {
+        if (changes == null) {
+	        changes.removePropertyChangeListener(l);
+	        for (int i=0; i < rules.size(); i++) 
+	        	if (rules.getRule(i) != null)
+	        		rules.getRule(i).removePropertyChangeListener(l);
+        }	
+    }	
+    /* (non-Javadoc)
+     * @see java.lang.Object#toString()
+     */
+    public String toString() {
+        return getName();
+    }
+	
+
+
+	/* (non-Javadoc)
+     * @see toxTree.core.IDecisionMethod#getName()
+     */
+    public String getName() {
+        return name;
+    }
+    /* (non-Javadoc)
+     * @see toxTree.core.IDecisionMethod#setName(java.lang.String)
+     */
+    public void setName(String value) {
+       name = value;
+
+    }
+    
+	public DescriptorSpecification getSpecification() {
+        return new DescriptorSpecification(
+                "http://toxtree.sourceforge.net/ames.html",
+                getTitle(),
+                this.getClass().getName(),                
+                "Toxtree plugin");
+	}    
+	public StringBuffer explainRules(IDecisionResult result,boolean verbose) throws DecisionMethodException{
+		try {
+			StringBuffer b = result.explain(verbose);
+			return b;
+		} catch (DecisionResultException x) {
+			throw new DecisionMethodException(x);
+		}
+	}
+
+
+	@Override
+	public IDecisionResult createDecisionResult() {
+		IDecisionResult result =  new AmesMutagenicityTreeResult();
+		result.setDecisionMethod(this);
+		return result;
+	}
+
+	public boolean isResiduesIDVisible() {
+		return residuesIDVisible;
+	}
+
+
+	public void setResiduesIDVisible(boolean residuesIDVisible) {
+		this.residuesIDVisible = residuesIDVisible;
+		for (int i=0;i< rules.size(); i++) {
+			rules.getRule(i).hideResiduesID(!residuesIDVisible);
+		}
+	}
+	public void setEditable(boolean value) {
+		editable = value;
+		for (int i=0;i<rules.size();i++)
+			rules.getRule(i).setEditable(value);
+	}
+
+
+    @Override
+    public void setParameters(IAtomContainer mol) {
+        if (getInteractive()) {
+            JComponent c = optionsPanel(mol);
+            if (c != null)
+                JOptionPane.showMessageDialog(null,c,getTitle(),JOptionPane.PLAIN_MESSAGE);
+        } 
+    }
+}
+
+