/*
  File: GraphObjectSelection.java

  Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)

  The Cytoscape Consortium is:
  - Institute for Systems Biology
  - University of California San Diego
  - Memorial Sloan-Kettering Cancer Center
  - Institut Pasteur
  - Agilent Technologies

  This library 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
  any later version.

  This library 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.  The software and
  documentation provided hereunder is on an "as is" basis, and the
  Institute for Systems Biology and the Whitehead Institute
  have no obligations to provide maintenance, support,
  updates, enhancements or modifications.  In no event shall the
  Institute for Systems Biology and the Whitehead Institute
  be liable to any party for direct, indirect, special,
  incidental or consequential damages, including lost profits, arising
  out of the use of this software and its documentation, even if the
  Institute for Systems Biology and the Whitehead Institute
  have been advised of the possibility of such damage.  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 library; if not, write to the Free Software Foundation,
  Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package cytoscape.dialogs;

import ViolinStrings.Strings;

import cytoscape.CyNetwork;
import cytoscape.Cytoscape;
import cytoscape.logger.CyLogger;

import cytoscape.data.CyAttributes;

import cytoscape.ding.DingNetworkView;

import cytoscape.view.CyNetworkView;

import giny.model.Node;

import java.awt.GridLayout;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;

import java.lang.reflect.Constructor;

import java.util.ArrayList;
import java.util.Iterator;
import java.util.Set;
import java.util.TreeSet;

import javax.swing.AbstractAction;
import javax.swing.ButtonGroup;
import javax.swing.DefaultListModel;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JLabel;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JRadioButton;
import javax.swing.JScrollPane;
import javax.swing.JSplitPane;
import javax.swing.JTextField;
import javax.swing.SwingUtilities;
import javax.swing.border.TitledBorder;


/**
 *
 */
public class GraphObjectSelection extends JPanel implements ActionListener {
	JTextField searchField;
	JCheckBox regexpSearch;
	JCheckBox clearSelection;
	JRadioButton hideFailed;
	JRadioButton grayFailed;
	JRadioButton selectPassed;
	JList selectedAttributes;
	JList allAttributes;
	CyNetwork cyNetwork;
	CyAttributes nodeAttributes;
	CyAttributes edgeAttributes;
	DingNetworkView graphView;
	CyNetworkView networkView;

	/**
	 * Creates a new GraphObjectSelection object.
	 */
	public GraphObjectSelection() {
		initialize();
	}

	protected void initialize() {
		networkView = Cytoscape.getCurrentNetworkView();
		cyNetwork = networkView.getNetwork();
		nodeAttributes = Cytoscape.getNodeAttributes();
		edgeAttributes = Cytoscape.getEdgeAttributes();

		// Create the Node Selection Panel
		JPanel searchPanel = new JPanel();
		searchPanel.setBorder(new TitledBorder("Describe Filter"));
		searchPanel.add(new JLabel("Filter: "));
		searchField = new JTextField(30);
		searchField.addActionListener(this);
		searchPanel.add(searchField);
		regexpSearch = new JCheckBox("Regexp?");
		searchPanel.add(regexpSearch);
		searchPanel.add(new JButton(new AbstractAction("Go!") {
				public void actionPerformed(ActionEvent e) {
					// Do this in the GUI Event Dispatch thread...
					SwingUtilities.invokeLater(new Runnable() {
							public void run() {
								// do the search
								performSearch();
							}
						});
				}
			}));

		// Create the All Attributes List Panel
		JPanel allAttributesPanel = new JPanel();
		allAttributesPanel.setBorder(new TitledBorder("All Available String Attributes"));

		String[] node_attribute_names = nodeAttributes.getAttributeNames();
		ArrayList string_attributes = new ArrayList(node_attribute_names.length);
		ArrayList number_attributes = new ArrayList(node_attribute_names.length);
		ArrayList other_attributes = new ArrayList(node_attribute_names.length);

		for (int i = 0; i < node_attribute_names.length; ++i) {
			Class type = deduceClass(node_attribute_names[i]);
			CyLogger.getLogger().info("Attr: " + node_attribute_names[i] + " Class: " + type.getName());

			if (type.getName().equals(String.class.getName())) {
				string_attributes.add(node_attribute_names[i]);
			} else if (type.getName().equals(Double.class.getName())) {
				number_attributes.add(node_attribute_names[i]);
			} else {
				other_attributes.add(node_attribute_names[i]);
			}
		}

		DefaultListModel model_nodes = new DefaultListModel();
		Iterator string_atts = string_attributes.iterator();

		for (int i = 0; string_atts.hasNext(); ++i) {
			model_nodes.add(i, (String) string_atts.next());
		}

		allAttributes = new JList(model_nodes);

		JScrollPane scrollPaneAll = new JScrollPane();
		scrollPaneAll.getViewport().setView(allAttributes);
		allAttributesPanel.add(scrollPaneAll);

		// Create the Selection Panel
		JPanel selectedAttributesPanel = new JPanel();
		selectedAttributesPanel.setBorder(new TitledBorder("Selected Attributes"));
		selectedAttributes = new JList(new DefaultListModel());

		JScrollPane scrollPaneSel = new JScrollPane();
		scrollPaneSel.getViewport().setView(selectedAttributes);
		allAttributesPanel.add(scrollPaneSel);
		selectedAttributesPanel.add(scrollPaneSel);

		// Create the Center Panel
		JPanel centerPanel = new JPanel();
		centerPanel.setLayout(new GridLayout(0, 1));

		JPanel controlPanel = new JPanel();
		controlPanel.setBorder(new TitledBorder("Control"));
		controlPanel.add(new JButton(new AbstractAction("+") {
				public void actionPerformed(ActionEvent e) {
					// Do this in the GUI Event Dispatch thread...
					SwingUtilities.invokeLater(new Runnable() {
							public void run() {
								// Add the Attributes selected in the all attributes
								// list to the selectionlist

								// get the selected attributes
								Object[] attributes = allAttributes.getSelectedValues();

								// add them to the selection list
								Set current_selection = new TreeSet(java.util.Arrays.asList(((DefaultListModel) selectedAttributes
								                                                             .getModel())
								                                                            .toArray()));
								current_selection.addAll(java.util.Arrays.asList(attributes));

								DefaultListModel new_model = new DefaultListModel();
								Iterator sel = current_selection.iterator();

								while (sel.hasNext()) {
									new_model.addElement(sel.next());
								}

								selectedAttributes.setModel(new_model);
							}
						});
				}
			}));
		controlPanel.add(new JButton(new AbstractAction("-") {
				public void actionPerformed(ActionEvent e) {
					// Do this in the GUI Event Dispatch thread...
					SwingUtilities.invokeLater(new Runnable() {
							public void run() {
								// Remove all Selected Attributes in the Selection List
								Object[] attributes = selectedAttributes.getSelectedValues();
								DefaultListModel dlm = (DefaultListModel) selectedAttributes
								                                                                                                                                                                                           .getModel();

								for (int i = 0; i < attributes.length; ++i) {
									dlm.removeElement(attributes[i]);
								}
							}
						});
				}
			}));
		controlPanel.add(new JButton(new AbstractAction("Update") {
				public void actionPerformed(ActionEvent e) {
					// Do this in the GUI Event Dispatch thread...
					SwingUtilities.invokeLater(new Runnable() {
							public void run() {
								// update the integration view
								// integration.updateView();
							}
						});
				}
			}));

		clearSelection = new JCheckBox("Clear", false);
		controlPanel.add(clearSelection);
		centerPanel.add(controlPanel);

		JPanel actionPanel = new JPanel();
		ButtonGroup actionGroup = new ButtonGroup();
		actionPanel.setBorder(new TitledBorder("Action to Take"));

		hideFailed = new JRadioButton("Hide Failed", true);
		actionGroup.add(hideFailed);
		actionPanel.add(hideFailed);

		grayFailed = new JRadioButton("Gray Failed", false);
		actionGroup.add(grayFailed);
		actionPanel.add(grayFailed);

		selectPassed = new JRadioButton("Select Passed", false);
		actionGroup.add(selectPassed);
		actionPanel.add(selectPassed);

		centerPanel.add(actionPanel);

		JSplitPane all_center_1 = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true, centerPanel,
		                                         allAttributesPanel);
		JSplitPane sel = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT, true, selectedAttributesPanel,
		                                all_center_1);
		JSplitPane all = new JSplitPane(JSplitPane.VERTICAL_SPLIT, true, searchPanel, sel);
		add(all);
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @return  DOCUMENT ME!
	 */
	public Object[] getSelectionList() {
		return ((DefaultListModel) selectedAttributes.getModel()).toArray();
	}

	/**
	 *  DOCUMENT ME!
	 *
	 * @param event DOCUMENT ME!
	 */
	public void actionPerformed(ActionEvent event) {
		// when ENTER is pressed do a search
		this.graphView = (DingNetworkView) networkView.getView();
		performSearch();

		// update the view
	} // actionPerformed

	/**
	 *  DOCUMENT ME!
	 */
	public void performSearch() {
		ArrayList passes = new ArrayList();
		Object[] selected_attributes_o = getSelectionList();
		String[] selected_attributes = new String[selected_attributes_o.length];

		for (int i = 0; i < selected_attributes_o.length; ++i) {
			selected_attributes[i] = (String) selected_attributes_o[i];
		}

		if (regexpSearch.isSelected()) {
			CyLogger.getLogger().info("not Implemented");
		} else {
			String[] pattern = searchField.getText().split("\\s");
			String[] nodes_with_attribute;

			for (int i = 0; i < selected_attributes.length; ++i) {
				// nodes_with_attribute = nodeAttributes.getObjectNames(
				// selected_attributes[i] );
				nodes_with_attribute = nodeAttributes.getAttributeNames();

				for (int j = 0; j < nodes_with_attribute.length; ++j) {
					// get the String Value for the node for the given attribute
					String value = nodeAttributes.getStringAttribute(selected_attributes[i],
					                                                 nodes_with_attribute[j]);

					for (int p = 0; p < pattern.length; ++p)
						if (Strings.isLike(value, pattern[p], 0, true)) {
							// this means that:
							// the value, which is associated with a given
							// selected attribute
							// and a node name is like one of the strings in the
							// search
							// box, which includes wildcards.
							// passes.add( graphView.getNodeView(
							// nodes_with_attribute[j] ) );
							// CyLogger.getLogger().info( nodes_with_attribute[j]+"
							// Matches Pattern: "+pattern[p]+" on Attribute:
							// "+selected_attributes[i]+" and the object is a:
							// "+ ( nodeAttributes.getGraphObject(
							// nodes_with_attribute[j]) ).getClass().getName()
							// );
							// passes.add( graphView.getNodeView( ( Node
							// )nodeAttributes.getGraphObject(
							// nodes_with_attribute[j]) ) );
							// CyLogger.getLogger().info( "This got added to Passed:
							// "+graphView.getNodeView( ( Node
							// )nodeAttributes.getGraphObject(
							// nodes_with_attribute[j]) ) );
							passes.add(nodes_with_attribute[j]);
						}
				}
			}
		}

		// Iterator views = networkView.getView().getNodeViewsList().iterator();
		// while ( views.hasNext() ) {
		// CyLogger.getLogger().info( "On Crack: "+views.next() );
		// }

		// Hide the Failed Nodes
		if (hideFailed.isSelected()) {
			// restore all EdgeViews prior to hiding
			graphView.showGraphObjects(graphView.getEdgeViewsList());

			Iterator all_nodes = networkView.getView().getGraphPerspective().nodesList().iterator();

			while (all_nodes.hasNext()) {
				Node node = (Node) all_nodes.next();

				if (passes.contains(node.getIdentifier())) {
					graphView.showGraphObject(graphView.getNodeView(node));
				} else {
					graphView.hideGraphObject(graphView.getNodeView(node));
				}
			}
		}
		// gray the Failed
		else if (grayFailed.isSelected()) {
			graphView.showGraphObjects(graphView.getEdgeViewsList());
			graphView.showGraphObjects(graphView.getNodeViewsList());

			Iterator all_nodes = graphView.getGraphPerspective().nodesList().iterator();

			while (all_nodes.hasNext()) {
				Node node = (Node) all_nodes.next();

				if (passes.contains(node.getIdentifier())) {
					graphView.getNodeView(node).setTransparency(1f);
				} else {
					graphView.getNodeView(node).setTransparency(0.5f);
				}
			}
		}
		// select those who passed
		else if (selectPassed.isSelected()) {
			graphView.showGraphObjects(graphView.getEdgeViewsList());
			graphView.showGraphObjects(graphView.getNodeViewsList());

			Iterator all_nodes = graphView.getGraphPerspective().nodesList().iterator();

			while (all_nodes.hasNext()) {
				Node node = (Node) all_nodes.next();

				if (passes.contains(node.getIdentifier())) {
					graphView.getNodeView(node).setSelected(true);
				} else {
					graphView.getNodeView(node).setSelected(false);
				}
			}
		}
	}

	/**
	 * determine (heuristically) the most-specialized class instance which can
	 * be constructed from the supplied string.
	 */
	static private Class deduceClass(String string) {
		String[] classNames = {
		                          "java.net.URL", "java.lang.Integer", // using
		                                                               // this
		                                                               // breaks
		                                                               // the
		                                                               // vizmapper,
		                                                               // see
		                                                               // below
		"java.lang.Double", "java.lang.String"
		                      };

		/**
		 * vizmapper error: Exception in thread "main"
		 * java.lang.ClassCastException: java.lang.Double at
		 * java.lang.Integer.compareTo(Integer.java:913) at
		 * cytoscape.vizmap.ContinuousMapper.getRangeValue(ContinuousMapper.java:78)
		 */
		for (int i = 0; i < classNames.length; i++) {
			try {
				Object obj = createInstanceFromString(Class.forName(classNames[i]), string);

				return obj.getClass();
			} catch (Exception e) {
				; // try the next class
			}
		} // for i

		return null;
	} // deduceClass

	/**
	 * given a string and a class, dynamically create an instance of that class
	 * from the string
	 */
	static private Object createInstanceFromString(Class requestedClass, String ctorArg)
	    throws Exception {
		Class[] ctorArgsClasses = new Class[1];
		ctorArgsClasses[0] = Class.forName("java.lang.String");

		Object[] ctorArgs = new Object[1];
		ctorArgs[0] = new String(ctorArg);

		Constructor ctor = requestedClass.getConstructor(ctorArgsClasses);

		return ctor.newInstance(ctorArgs);
	}
}