toxtree 0.0.1

data/Toxtree-v2.6.13/src/toxtree/ui/tree/QueryAtomContainersModel.java

@@ -0,0 +1,77 @@
+/*
+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.ui.tree;
+
+import java.util.List;
+import java.util.Observable;
+import java.util.Observer;
+
+import org.openscience.cdk.interfaces.IAtomContainer;
+
+import toxTree.core.IDecisionRule;
+import toxTree.query.QueryAtomContainers;
+
+/**
+ * 
+ * Table model for {@link QueryAtomContainers}.
+ * @author Nina Jeliazkova nina@acad.bg
+ * <b>Modified</b> Dec 17, 2006
+ */
+public class QueryAtomContainersModel extends ListTableModel implements Observer {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 3277542698124116055L;
+
+    public QueryAtomContainersModel(List list,IDecisionRule rule) {
+        super(list);
+        if (rule instanceof Observable) ((Observable) rule).addObserver(this);
+    }
+	public QueryAtomContainersModel(QueryAtomContainers list, IDecisionRule rule) {
+		super(list);
+		if (rule instanceof Observable) ((Observable) rule).addObserver(this);
+	}	
+	@Override
+	public Object getValueAt(int rowIndex, int columnIndex) {
+		switch (columnIndex) {
+		case 0: {
+			try {
+			IAtomContainer a = (IAtomContainer)((QueryAtomContainers) list).get(rowIndex);
+			return a.getID();
+			} catch (Exception x) {
+				return super.getValueAt(rowIndex,columnIndex);
+			}
+		}
+		default: return "NA";
+		}
+	}
+	@Override
+	public void update(Observable arg0, Object arg1) {
+		fireTableDataChanged();
+		
+	}
+
+}

data/Toxtree-v2.6.13/src/toxtree/ui/tree/SelectListDialog.java

@@ -0,0 +1,350 @@
+/*
+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.ui.tree;
+
+import java.awt.Component;
+import java.awt.Desktop;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.AbstractAction;
+import javax.swing.ActionMap;
+import javax.swing.JDialog;
+import javax.swing.JOptionPane;
+import javax.swing.JScrollPane;
+import javax.swing.JSplitPane;
+import javax.swing.JTabbedPane;
+import javax.swing.JTextPane;
+import javax.swing.ListSelectionModel;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.text.html.HTMLEditorKit;
+
+import toxTree.core.IDecisionCategory;
+import toxTree.core.IDecisionMethod;
+import toxTree.core.IDecisionRule;
+import toxTree.core.Introspection;
+import toxTree.core.ToxTreePackageEntries;
+import toxTree.core.ToxTreePackageEntry;
+import toxTree.io.Tools;
+import toxTree.tree.DecisionNode;
+
+/**
+ * A singleton class, providing several methods to select an object from a {@link java.util.List}.
+ * <br>
+ * Launches a modal dialogs with optional buttons on the right. Buttons are created from an optional 
+ * {@link javax.swing.ActionMap}
+ * <br> Uses {@link javax.swing.JOptionPane}
+ * @author Nina Jeliazkova
+ *
+ */
+public class SelectListDialog {
+
+	/**
+	 * Singleton class
+	 *
+	 */
+	protected SelectListDialog() {
+		super();
+	}
+	public static Object selectFromList(Component parent, String dlgCaption, String panelCaption,
+			ListTableModel list,
+			ActionMap actions) {
+		return selectFromList(parent,dlgCaption,panelCaption,list,actions,new Dimension(300,150));
+	}
+	public static Object selectFromList(Component parent, String dlgCaption, String panelCaption,
+			ListTableModel list,
+			ActionMap actions, 
+			Dimension size) {
+		ListPanel panel = new ListPanel(panelCaption, list, actions);
+		panel.addListSelectionListener(panel);
+        DetailsTextPane text = new DetailsTextPane(list.getList());
+        text.setEditable(false);
+        panel.addListSelectionListener(text);
+        text.setPreferredSize(size);
+        JSplitPane split = new JSplitPane(JSplitPane.VERTICAL_SPLIT, panel,new JScrollPane(text)); 
+            
+		JOptionPane pane = new JOptionPane(split, JOptionPane.PLAIN_MESSAGE,
+				JOptionPane.OK_CANCEL_OPTION);
+
+
+		/*
+		 * for( int i = 0; i < options.length; i++ )
+		 * options[i].addActionListener( new OptionPaneActionListener( pane ) );
+		 */
+		JDialog dialog = pane.createDialog(parent, dlgCaption);
+		dialog.setVisible(true);
+		if (pane.getValue() == null) return null;
+		int value = ((Integer) pane.getValue()).intValue();
+		if (value == 0)
+			return panel.getSelectedObject();
+		else
+			return null;
+	}
+
+	/**
+	 * Launches a dialog with a several lists arranged in a {@link JTabbedPane}.
+	 *  
+	 * @param caption dialog caption
+	 * @param panels  an array of {@link ListPanel} to be arranged as tab pages 
+	 * @return Object the selected object
+	 */
+	public static Object selectFromList(String caption, ListPanel[] panels) {
+		JTabbedPane tabbedPane = new JTabbedPane();
+
+		for (int i = 0; i < panels.length; i++) {
+			panels[i].addListSelectionListener(panels[i]);
+			tabbedPane.addTab(panels[i].caption, null, panels[i],
+					panels[i].caption);
+		}
+		JOptionPane pane = new JOptionPane(tabbedPane,
+				JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION);
+
+		JDialog dialog = pane.createDialog(null, caption);
+		dialog.setVisible(true);
+		
+		Object o = pane.getValue();
+		if (o == null) return null;
+		int value = ((Integer) pane.getValue()).intValue();
+
+		if (value == 0) {
+			ListPanel panel = panels[tabbedPane.getSelectedIndex()];
+			return panel.getSelectedObject();
+		} else
+			return null;
+	}
+	
+	/**
+	 * Provides a list of names of the classes implementing {@link IDecisionRule}
+	 * If the user selects an object, the rule is created and returned <br>
+	 * Uses {@link Introspection#getAvailableRuleTypes(ClassLoader)}
+	 * @param classLoader
+	 * @return the rule selected
+	 */
+
+	public static IDecisionRule selectNewRule(Component parent,ClassLoader classLoader) {
+		ToxTreePackageEntries ruleTypes = Introspection.getAvailableRuleTypes(classLoader);
+		
+		Object name = selectFromList(parent,"Select a rule","Available rules:", 
+				new ToxTreePackageEntryModel(ruleTypes), null);
+		if ((name != null) && (name instanceof ToxTreePackageEntry)) 
+			try {
+				Object o = Introspection.loadCreateObject(((ToxTreePackageEntry) name).getClassName());
+				if (o instanceof IDecisionRule)
+					return (IDecisionRule) o;
+				else {
+					o = null;
+					return null;
+				}
+			} catch (Exception x) { x.printStackTrace(); return null;}
+		else
+			return null;
+	}
+	/**
+	 * Provides a list of names of the classes implementing {@link IDecisionRule}
+	 * If the user selects an object, a {@link DecisionNode} containing the rule is created and returned <br>
+	 * Uses {@link Introspection#getAvailableRuleTypes(ClassLoader)}
+	 * @param classLoader
+	 * @return the decision node
+	 */
+	public static DecisionNode selectNewNode(Component parent,ClassLoader classLoader) {
+		ToxTreePackageEntries ruleTypes = Introspection.getAvailableRuleTypes(classLoader);
+		Object name = selectFromList(parent,"Select a rule","Available rules:", new ToxTreePackageEntryModel(ruleTypes), null);
+		if ((name != null) && (name instanceof ToxTreePackageEntry)) 
+		try {
+			Object o = Introspection.loadCreateObject(((ToxTreePackageEntry) name).getClassName());
+			if (o instanceof IDecisionRule)
+				return new DecisionNode((IDecisionRule) o);
+			else {
+				o = null;
+				return null;
+			}
+		} catch (Exception x) {x.printStackTrace(); return null;}
+		else
+			return null;
+	}
+
+	/**
+	 * Provides a list of names of the classes implementing {@link IDecisionMethod}
+	 * If the user selects a name, the tree is created and returned <br>
+	 * Uses {@link Introspection#getAvailableTreeTypes(ClassLoader)}
+	 * @param classLoader
+	 * @return tree instance {@link IDecisionMethod}
+	 */
+	public static IDecisionMethod selectNewTree(Component parent,ClassLoader classLoader) {
+		ArrayList ruleTypes = Introspection.getAvailableTreeTypes(classLoader);
+		Object name = selectFromList(parent,"Select a tree","Available decision trees:", new ListTableModel(ruleTypes),
+				null);
+		if ((name != null) && (name instanceof ToxTreePackageEntry)) try {
+			Object o = Introspection.loadCreateObject(((ToxTreePackageEntry) name).getClassName());
+			if (o instanceof IDecisionMethod)
+				return (IDecisionMethod) o;
+			else {
+				o = null;
+				return null;
+			}
+		} catch (Exception x) {x.printStackTrace(); return null;} 
+		else
+			return null;
+	}
+
+	/**
+ 	 * Provides a list of names of the classes implementing {@link IDecisionCategory}
+	 * If the user selects an object, the tree is created and returned <br>
+	 * Uses {@link Introspection#getAvailableCategoryTypes(ClassLoader)}
+	 * @param classLoader
+	 * @return a decision category {@link IDecisionCategory}
+	 */
+	public static IDecisionCategory selectNewCategory(Component parent,ClassLoader classLoader) {
+		ArrayList ruleTypes = Introspection.getAvailableCategoryTypes(classLoader);
+		Object name = selectFromList(parent,"Select category","Available category:", new ListTableModel(ruleTypes), null);
+		if ((name != null) && (name instanceof ToxTreePackageEntry)) try {
+			Object o = Introspection.loadCreateObject(((ToxTreePackageEntry) name).getClassName());
+			if (o instanceof IDecisionCategory)
+				return (IDecisionCategory) o;
+			else {
+				o = null;
+				return null;
+			}
+		} catch (Exception x) { return null;}
+		else
+			return null;
+	}
+	
+}
+
+class SelectAction extends AbstractAction {
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 8468861279706657194L;
+
+	public void actionPerformed(ActionEvent arg0) {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public void putValue(String arg0, Object arg1) {
+		// TODO Auto-generated method stub
+		super.putValue(arg0, arg1);
+	}
+}
+
+class CancelAction extends AbstractAction {
+	private static final long serialVersionUID = 7787228466222735812L;
+
+	public void actionPerformed(ActionEvent arg0) {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public void putValue(String arg0, Object arg1) {
+		// TODO Auto-generated method stub
+		super.putValue(arg0, arg1);
+	}
+
+	
+}
+
+class OptionPaneActionListener extends Object implements ActionListener {
+
+	/**
+	 * The JOptionPane which the action source we are listening on lives.
+	 */
+	JOptionPane optionPane;
+
+	public OptionPaneActionListener(JOptionPane optionPane) {
+		this.optionPane = optionPane;
+	} // OptionPaneActionListener
+
+	public void actionPerformed(ActionEvent event) {
+		optionPane.setValue(event.getSource());
+	} // actionPerformed
+
+} // OptionPaneButton
+
+class DetailsTextPane extends JTextPane implements ListSelectionListener {
+    /**
+     * 
+     */
+    private static final long serialVersionUID = 8340434694455983277L;
+    protected List list;
+    public DetailsTextPane(List list) {
+        super();
+        setEditorKit(new HTMLEditorKit());
+        this.list = list;
+		addHyperlinkListener(new HyperlinkListener() {
+		    public void hyperlinkUpdate(HyperlinkEvent e) {
+		        if(e.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
+		        	try { 
+		        		if(Desktop.isDesktopSupported()) {
+		        		    Desktop.getDesktop().browse(e.getURL().toURI());
+		        		} else 
+		        			Tools.openURL(e.getURL().toString());
+		        	} catch (Exception x) {
+		        		x.printStackTrace();
+		        	}
+		        }
+		    }
+		});
+    }
+
+    
+    public void valueChanged(ListSelectionEvent e) {
+        if (e.getValueIsAdjusting())
+            return;
+        ListSelectionModel lsm = (ListSelectionModel) e.getSource();
+
+        if (!lsm.isSelectionEmpty())
+            try {
+                //System.out.println(lsm.getMinSelectionIndex());
+                if (list == null) setText("");
+                else {
+                    Object o = list.get(lsm.getMinSelectionIndex());
+                    if (o == null) setText("");
+                    else if (o instanceof IDecisionMethod) {
+                        setText(((IDecisionMethod)o).getExplanation());
+                    } else if (o instanceof IDecisionCategory) {
+                        setText(((IDecisionCategory)o).getExplanation());    
+                    } else if (o instanceof IDecisionRule) {
+                        setText(((IDecisionRule)o).getExplanation());
+                    }                                
+                    else setText(o.toString()); 
+                }
+            } catch (Exception x) {
+                setText("");
+                //x.printStackTrace();
+            }
+
+        
+    }
+}

data/Toxtree-v2.6.13/src/toxtree/ui/tree/ToxTreeEditorPanel.java

@@ -0,0 +1,154 @@
+/*
+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.ui.tree;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.event.FocusEvent;
+import java.awt.event.FocusListener;
+import java.util.Observable;
+import java.util.Observer;
+
+import javax.swing.BorderFactory;
+import javax.swing.JEditorPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextField;
+
+import toxTree.core.IToxTreeEditor;
+
+/**
+ * Absatract class, implementing {@link IToxTreeEditor}.
+ * @author Nina Jeliazkova nina@acad.bg
+ * <b>Modified</b> Dec 17, 2006
+ */
+public abstract class ToxTreeEditorPanel extends JPanel implements IToxTreeEditor, FocusListener,
+		Observer {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -763213118243686164L;
+    protected JTextField idField ;
+    protected JTextField nameField ;
+    protected JEditorPane explanation;
+    protected JScrollPane explanationPane; 
+    protected Color bgColor = new Color(250,250,250);
+    protected boolean editable = true;
+
+
+	public ToxTreeEditorPanel(Object object) {
+		super(new BorderLayout());
+		addWidgets(object);
+	}
+
+	public ToxTreeEditorPanel() {
+		this(null);
+	}
+
+	protected void addWidgets(Object object) {
+    	JPanel pp = new JPanel();
+    	pp.setLayout(new BorderLayout());
+    	pp.setBackground(bgColor);
+    	
+        idField = new JTextField();
+        idField.addFocusListener(this);
+        idField.setPreferredSize(new Dimension(64,24));
+        idField.setEditable(editable);
+        idField.setBorder(BorderFactory.createTitledBorder("ID"));
+        idField.setBackground(bgColor);
+        pp.add(idField,BorderLayout.WEST);
+        
+        nameField = new JTextField();
+        nameField.addFocusListener(this);
+        nameField.setEditable(editable);
+        nameField.setBorder(BorderFactory.createTitledBorder("Title"));
+        nameField.setBackground(bgColor);
+        pp.add(nameField,BorderLayout.CENTER);
+        
+        explanation = new JEditorPane("text/html","");
+        explanation.addFocusListener(this);
+        explanation.setBackground(bgColor);
+        explanation.setEditable(editable);
+        explanation.setAutoscrolls(true);
+        //explanation.setLineWrap(true);
+        //explanation.setWrapStyleWord(true);
+        explanationPane = new JScrollPane(explanation,
+					JScrollPane.VERTICAL_SCROLLBAR_ALWAYS,
+                    JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
+        explanation.setPreferredSize(new Dimension(200,200));
+        explanationPane.setBorder(BorderFactory.createTitledBorder("Explanation"));        
+        explanationPane.setBackground(bgColor);
+
+        add(pp,BorderLayout.NORTH);
+	}
+	public abstract void setID(String id);
+	public abstract void setTitle(String title);
+	public abstract void setExplanation(String explanation);
+
+	public abstract String getID();
+	public abstract String getTitle();
+	public abstract String getExplanation();
+	
+	public void focusGained(FocusEvent arg0) {
+	}
+
+	public void focusLost(FocusEvent e) {
+        if (e.getSource() ==nameField) {
+            setTitle(nameField.getText());
+        } else if (e.getSource() ==idField) {
+            setID(idField.getText());
+        } else if (e.getSource() ==explanation) 
+            setExplanation(explanation.getText());      
+	}
+	
+	public void update(Observable arg0, Object arg1) {
+        idField.setText(getID());        
+        nameField.setText(getTitle());
+        explanation.setText(getExplanation());
+	}
+
+	public Component getVisualCompoment() {
+		return this;
+	}
+
+	public boolean isEditable() {
+		return editable;
+	}
+
+	public void setEditable(boolean editable) {
+		this.editable = editable;
+		idField.setEditable(editable);
+		nameField.setEditable(editable);
+		explanation.setEditable(editable);
+
+	}
+
+}
+
+