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toxtree 0.0.1

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Files changed (1384) hide show

data/Toxtree-v2.6.13/src/toxTree/core/XMLSerializable.java ADDED

@@ -0,0 +1,53 @@
+/*
+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.
+*/
+package toxTree.core;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import toxTree.exceptions.XMLDecisionMethodException;
+public interface XMLSerializable {
+	public static String xmltag_NAME = "name";
+	public static String xmltag_ID = "id";
+	public static String xmltag_EXPLANATION = "explanation";
+	public static String xmltag_METHODS = "methods";
+	public static String xmltag_METHOD = "method";
+	public static String xmltag_CLASS = "class";
+	public static String xmltag_METHODPARAMETER = "parameter";
+	public static String xmltag_TREEROOT = "root";
+	public static String xmltag_RULES = "rules";
+	public static String xmltag_RULE = "rule";
+	public static String xmltag_RULEEXAMPLE = "example";
+	public static String xmltag_CATEGORIES = "categories";
+	public static String xmltag_CATEGORY = "category";
+	public static String xmltag_CATEGORYTHRESHOLD = "threshold";
+	public Element toXML(Document document) throws XMLDecisionMethodException;
+	public void fromXML(Element xml)  throws XMLDecisionMethodException ;
+	public Element toShallowXML(Document document)  throws XMLDecisionMethodException;
+}

data/Toxtree-v2.6.13/src/toxTree/core/package.html ADDED

@@ -0,0 +1,46 @@
+<HTML><HEAD><TITLE>toxTree interfaces</TITLE>
+<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
+</SCRIPT>
+<META NAME="Description" CONTENT="toxTree application">
+<META NAME="Keywords" CONTENT="source,decision tree,TTC,java">
+<!--  -->
+<body bgColor="#FFFFFF" link="#428EFF">
+This packages contains only interface definitions, defining essential classes in toxTree application.
+<UL>
+<LI>A decision tree should implement interface {@link toxTree.core.IDecisionMethod}
+<LI>A decision rule should implement interface {@link toxTree.core.IDecisionRule}
+<LI>The application of a decision tree on a query molecule
+assigns it to a category {@link toxTree.core.IDecisionCategory}
+<LI>The path followed through the decision tree should be provided by  {@link toxTree.core.IDecisionResult}
+</UL>
+The existence of these interfaces allows various implementation of decision rules, trees and categories,
+which can nevertheless be used interdependently.
+<P>
+A set of classes implementing these interfaces can be found in package {@link toxTree.tree}
+<p>
+<h3>Plugins</h3>
+Plugins are .jar files, containing any one or all of the following:
+<ul>
+<li>Decision tree(s), i.e. classes implementing {@link toxTree.core.IDecisionMethod}
+<li>Rule(s), i.e. classes implementing {@link toxTree.core.IDecisionRule}
+<li>Categories, i.e. classes implementing {@link toxTree.core.IDecisionCategory}
+</ul>
+Plugins are searched at run-time in the following directories:
+<ul>
+<li>The directory where toxTree.jar resides (current directory).
+<li>The directory "ext" below the current directory.
+</ul>
+Plugins containing decision trees are searched when presenting a list of available trees.
+Plugins containing rules are searched when presenting a list of available rules.
+Plugins containing categories are searched when presenting a list of available categories.
+<br>
+The Cramer tree {@link toxTree.tree.cramer.CramerRules} is used by default, but relies on the same mechanism. It is distributed in toxCramer.jar.
+A demo decision tree is available at {@link toxTree.tree.demo.SubstructureTree} and distributed in toxDemo.jar.
+</body></HTML>

data/Toxtree-v2.6.13/src/toxTree/data/AbstractFilter.java ADDED

@@ -0,0 +1,135 @@
+/*
+Copyright Ideaconsult (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.
+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.
+*/
+package toxTree.data;
+import java.awt.BorderLayout;
+import java.awt.LayoutManager;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.util.Hashtable;
+import java.util.Map;
+import javax.swing.JComponent;
+import javax.swing.JPanel;
+import org.openscience.cdk.interfaces.IChemObject;
+public abstract class AbstractFilter implements IObjectFilter {
+	protected Hashtable parameters;
+	public AbstractFilter() {
+		super();
+		parameters = new Hashtable();
+	}
+    public void preprocess(IChemObject object) {
+    }
+	public void setProperty(String key, Object value) {
+		parameters.put(key,value);
+	}
+	public Object getProperty(String key) {
+		return parameters.get(key);
+	}
+	public Object removeProperty(String key) {
+		return parameters.remove(key);
+	}
+	public void setProperties(Map properties) {
+		parameters.clear();
+		parameters.putAll(properties);
+	}
+	public Map getProperties() {
+		return parameters;
+	}
+	public JComponent getEditor() {
+		return new AbstractFilterEditor(toString(),this);
+	}
+    public int hashCode() {
+    	return parameters.hashCode();
+    }
+    @Override
+    public boolean equals(Object obj) {
+    	if (obj instanceof AbstractFilter) {
+    		return parameters.equals(((AbstractFilter)obj).parameters);
+    	} else return false;
+    }
+    public int compareTo(Object obj) {
+    	if (obj instanceof AbstractFilter) {
+    		return parameters.toString().compareTo(((AbstractFilter)obj).parameters.toString());
+    	} else return -1;
+    }
+}
+class AbstractFilterEditor extends JPanel implements  ActionListener,  FocusListener {
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = -5047904516589635601L;
+	protected String title;
+	protected Object object;
+	protected boolean editable;
+	public AbstractFilterEditor(LayoutManager layout ,String title,IObjectFilter object) {
+		super(layout);
+		this.object = object;
+		this.title = title;
+	    setName(object.toString());
+	}
+	public AbstractFilterEditor(String title,IObjectFilter object) {
+		this(new BorderLayout(),title,object);
+	}
+	public AbstractFilterEditor() {
+		this("",null);
+	}
+	public void actionPerformed(ActionEvent e) {
+		// TODO Auto-generated method stub
+	}
+	public boolean isEditable() {
+		return editable;
+	}
+	public void setEditable(boolean editable) {
+		this.editable = editable;
+	}
+	public void focusGained(FocusEvent e) {
+		// TODO Auto-generated method stub
+	}
+	public void focusLost(FocusEvent e) {
+		// TODO Auto-generated method stub
+	}
+}

data/Toxtree-v2.6.13/src/toxTree/data/CategoryFilter.java ADDED

@@ -0,0 +1,41 @@
+/*
+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.
+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.
+*/
+package toxTree.data;
+import toxTree.core.IDecisionCategory;
+import toxTree.exceptions.FilterException;
+public class CategoryFilter extends ObjectPropertyFilter {
+	public CategoryFilter(Object property, IDecisionCategory category) throws FilterException {
+		super(property,category.toString());
+	}
+	public CategoryFilter(Object property, String category) throws FilterException {
+		super(property,category);
+	}
+	@Override
+	public String toString() {
+		return getTag() + " = " + getValue().toString();
+	}
+}

data/Toxtree-v2.6.13/src/toxTree/data/IMoleculeLookup.java ADDED

@@ -0,0 +1,36 @@
+/*
+Copyright (C) 2005-2006
+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.data;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import toxTree.exceptions.DecisionMethodException;
+public interface IMoleculeLookup {
+	public boolean find(IAtomContainer mol ) throws DecisionMethodException;
+	public int find(Object property,Object value) throws DecisionMethodException;
+}

data/Toxtree-v2.6.13/src/toxTree/data/IObjectFilter.java ADDED

@@ -0,0 +1,38 @@
+/*
+Copyright Ideaconsult (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.
+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.
+*/
+package toxTree.data;
+import java.util.Map;
+import javax.swing.JComponent;
+import org.openscience.cdk.interfaces.IChemObject;
+public interface IObjectFilter extends Comparable {
+    public void preprocess(IChemObject object);
+    public boolean accept(IChemObject object);
+    public void setProperty(String key, Object value);
+    public Object getProperty(String key);
+    public Object removeProperty(String key);
+    public void setProperties(Map properties);
+    public Map getProperties();
+    public JComponent getEditor();
+}

data/Toxtree-v2.6.13/src/toxTree/data/IPropertyFilter.java ADDED

@@ -0,0 +1,34 @@
+/*
+Copyright Ideaconsult Ltd. (C) 2005-2006
+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.data;
+public interface IPropertyFilter  extends IObjectFilter {
+	public abstract boolean acceptProperty(Object value);
+	public abstract void setTag(Object property);
+	public abstract Object getTag();
+}

data/Toxtree-v2.6.13/src/toxTree/data/ListOfAtomContainers.java ADDED

@@ -0,0 +1,248 @@
+/*
+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.
+*/
+package toxTree.data;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomContainerSet;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
+import org.openscience.cdk.interfaces.IChemObjectListener;
+import org.openscience.cdk.silent.SilentChemObjectBuilder;
+/**
+ * An attempt to implement {@link org.openscience.cdk.interfaces.SetOfAtomContainers} interface
+ * as a {@link java.util.List}
+ * @author Nina Jeliazkova
+ *
+ */
+public class ListOfAtomContainers extends ArrayList<IAtomContainer> implements	IAtomContainerSet {
+	protected transient static Logger logger = Logger.getLogger(ListOfAtomContainers.class.getName());
+	protected String id = "";
+	protected Map properties = null;
+	/**
+	 *
+	 */
+	private static final long serialVersionUID = 7586214506838048913L;
+	public ListOfAtomContainers() {
+		super();
+	}
+	public ListOfAtomContainers(int arg0) {
+		super(arg0);
+	}
+	public ListOfAtomContainers(Collection arg0) {
+		super(arg0);
+	}
+	public void addAtomContainer(IAtomContainer atomContainer) {
+		add(atomContainer);
+	}
+	public void removeAtomContainer(IAtomContainer atomContainer) {
+		remove(atomContainer);
+	}
+	public void removeAllAtomContainers() {
+		clear();
+	}
+	public void removeAtomContainer(int pos) {
+		remove(pos);
+	}
+	public void setMultiplier(int position, Double multiplier) {
+		// TODO Auto-generated method stub
+	}
+	public Double getMultiplier(int arg0) {
+		return null;
+	}
+	public Double[] getMultipliers() {
+		return null;
+	}
+	public boolean setMultipliers(Double[] newMultipliers) {
+		return false;
+	}
+	public void addAtomContainer(IAtomContainer atomContainer, double multiplier) {
+		addAtomContainer(atomContainer);
+	}
+	public void add(IAtomContainerSet atomContainerSet) {
+		for (int i=0; i< atomContainerSet.getAtomContainerCount(); i++)
+			addAtomContainer(atomContainerSet.getAtomContainer(i));
+	}
+	public IAtomContainer[] getAtomContainers() {
+		try {
+			IAtomContainer[] m = new IAtomContainer[getAtomContainerCount()];
+			for (int i=0; i<size();i++)
+				m[i] = (IAtomContainer) get(i);
+			return m;
+		} catch (Exception x) {
+			logger.log(Level.SEVERE,x.getMessage(),x);
+			return null;
+		}
+	}
+	public IAtomContainer getAtomContainer(int number) {
+		return (IAtomContainer)get(number);
+	}
+	public Double getMultiplier(IAtomContainer arg0) {
+		return 1.0;
+	}
+	public boolean setMultiplier(IAtomContainer arg0, Double arg1) {
+		return false;
+	}
+	public int getAtomContainerCount() {
+		return size();
+	}
+	public void addListener(IChemObjectListener col) {
+		// TODO Auto-generated method stub
+	}
+	public int getListenerCount() {
+		// TODO Auto-generated method stub
+		return 0;
+	}
+	public void removeListener(IChemObjectListener col) {
+		// TODO Auto-generated method stub
+	}
+	public void notifyChanged() {
+		// TODO Auto-generated method stub
+	}
+	public void setProperty(Object description, Object property) {
+		properties.put(description,property);
+	}
+	public void removeProperty(Object description) {
+		properties.remove(description);
+	}
+	public Object getProperty(Object description) {
+		// TODO Auto-generated method stub
+		return null;
+	}
+	public Map getProperties() {
+		return properties;
+	}
+	public String getID() {
+		return id;
+	}
+	public void setID(String identifier) {
+		this.id = identifier;
+	}
+	public void setFlag(int flag_type, boolean flag_value) {
+		// TODO Auto-generated method stub
+	}
+	public boolean getFlag(int flag_type) {
+		// TODO Auto-generated method stub
+		return false;
+	}
+	public void setProperties(Map<Object, Object> properties) {
+        this.properties = properties;
+	}
+	public void setFlags(boolean[] flagsNew) {
+		// TODO Auto-generated method stub
+	}
+	public boolean[] getFlags() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+	public IChemObjectBuilder getBuilder() {
+		return SilentChemObjectBuilder.getInstance();
+	}
+	/* (non-Javadoc)
+     * @see org.openscience.cdk.interfaces.IChemObject#setNotification(boolean)
+     */
+    public void setNotification(boolean arg0) {
+        // TODO Auto-generated method stub
+    }
+    /* (non-Javadoc)
+     * @see org.openscience.cdk.interfaces.IChemObject#getNotification()
+     */
+    public boolean getNotification() {
+        // TODO Auto-generated method stub
+        return false;
+    }
+    /* (non-Javadoc)
+     * @see org.openscience.cdk.interfaces.IChemObject#notifyChanged(org.openscience.cdk.interfaces.IChemObjectChangeEvent)
+     */
+    public void notifyChanged(IChemObjectChangeEvent arg0) {
+        // TODO Auto-generated method stub
+    }
+    public Iterable<IAtomContainer> atomContainers() {
+    	return this;
+    }
+    public void sortAtomContainers(Comparator<IAtomContainer> comparator) {
+    	Collections.sort(this,comparator);
+    }
+	public void replaceAtomContainer(int position, IAtomContainer container) {
+		set(position,container);
+	}
+}