GraphMenu.java

/* GraphMenu.java
 *
 * created: Tue Sep 18 2001
 *
 * This file is part of Artemis
 *
 * Copyright (C) 2001  Genome Research Limited
 *
 * 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., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/GraphMenu.java,v 1.11 2009-08-03 10:29:32 tjc Exp $
 */

package uk.ac.sanger.artemis.components;

import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.chado.Graph;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.plot.Algorithm;
import uk.ac.sanger.artemis.plot.BaseAlgorithm;
import uk.ac.sanger.artemis.plot.CodonUsageAlgorithm;
import uk.ac.sanger.artemis.plot.CodonUsageWeight;
import uk.ac.sanger.artemis.plot.UserDataAlgorithm;
import uk.ac.sanger.artemis.sequence.Strand;
import uk.ac.sanger.artemis.util.DatabaseDocument;
import uk.ac.sanger.artemis.util.Document;

import java.awt.Cursor;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.io.IOException;
import java.io.File;
import java.net.URL;
import java.util.List;
import java.util.Vector;

import javax.swing.*;

/**
 *  This menu controls one particular BasePlotGroup.
 *
 *  @author Kim Rutherford <kmr@sanger.ac.uk>
 *  @version $Id: GraphMenu.java,v 1.11 2009-08-03 10:29:32 tjc Exp $
 **/

public class GraphMenu extends JMenu 
{
  private static final long serialVersionUID = 1L;

  /**
   *  The JFrame reference that was passed to the constructor.
   **/
  private JFrame frame;

  /**
   *  The BasePlotGroup that was passed to the constructor.
   **/
  private BasePlotGroup base_plot_group;

  /**
   *  The EntryGroup object that was passed to the constructor.
   **/
  private EntryGroup entry_group = null;

  /**
   *  The FeatureDisplay that was passed to the constructor.
   **/
  private FeatureDisplay feature_display;
  
  private JMenu menuSubMenu = new JMenu("Other Graphs");

  /**
   *  This list of the CheckboxMenuItems for the graphs is stored so that we
   *  can turn them all off with "Hide All Graphs".
   **/
  private Vector algorithm_menu_items = new Vector ();

  private JSplitPane splitPane;
  
  /**
   *  Create a new GraphMenu object and all it's menu items.
   *  @param frame The JFrame that owns this JMenu.
   *  @param entry_group The EntryGroup containing the sequence to plot.
   *  @param base_plot_group The BasePlotGroup that this menu controls.
   *  @param view_menu This ViewMenu is updated when a usage plot is added.
   *  @param add_menu This AddMenu is updated when a usage plot is added.
   *  @param menu_name The name of the new menu.
   **/
  public GraphMenu (final JFrame frame,
                    final EntryGroup entry_group,
                    final BasePlotGroup base_plot_group,
                    final FeatureDisplay feature_display,
                    final String menu_name, 
                    final JSplitPane splitPane) 
  {
    super (menu_name);
    this.frame = frame;
    this.entry_group = entry_group;
    this.base_plot_group = base_plot_group;
    this.feature_display = feature_display;
    this.splitPane = splitPane;

    final BaseAlgorithm [] orig_algorithms =
      base_plot_group.getPlotAlgorithms ();

    final JMenuItem hide_all_graphs_item = new JMenuItem ("Hide All Graphs");
    hide_all_graphs_item.addActionListener (new ActionListener () 
    {
      public void actionPerformed (ActionEvent event)
      {
        final BaseAlgorithm [] current_algorithms =
          base_plot_group.getPlotAlgorithms ();

        for (int i = 0 ; i < current_algorithms.length ; ++i)
        {
          final BaseAlgorithm this_algorithm = current_algorithms[i];

          base_plot_group.setVisibleByAlgorithm (this_algorithm, false);

          final JCheckBoxMenuItem this_menu_item =
            (JCheckBoxMenuItem) algorithm_menu_items.elementAt (i);

          this_menu_item.setState (false);
        }
        if (getParent () != null) 
        {
          // XXX change to revalidate().
          frame.validate ();
        }
      }
    });
    add (hide_all_graphs_item);

    addSeparator ();

    if (Options.readWritePossible ()) 
    {
      final JMenuItem usage_plot_item = new JMenuItem ("Add Usage Plots ...");
      usage_plot_item.addActionListener (new ActionListener () 
      {
        public void actionPerformed (ActionEvent event) 
        {
          addUsagePlot ();
          adjustSplitPane(true);
        }
      });
      add (usage_plot_item);

      final JMenuItem user_plot_item = new JMenuItem ("Add User Plot ...");
      user_plot_item.addActionListener (new ActionListener () 
      {
        public void actionPerformed (ActionEvent event)
        {
          try
          {
            addUserPlot (null);
            adjustSplitPane(true);
          }
          catch(java.lang.OutOfMemoryError emem)
          {
            JOptionPane.showMessageDialog(frame, 
                "Out of memory. Increase the maximum memory"+
                "\navailable for this application and try again.", 
                "Out Of Memory", 
                JOptionPane.WARNING_MESSAGE);
            frame.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
          }
        }
      });

      add (user_plot_item);
      
      if(getEntryGroup().getSequenceEntry().getEMBLEntry() instanceof 
         DatabaseDocumentEntry)
      {
        final JMenu database_user_plot = new JMenu("Add Database Plot ...");
        final DatabaseDocument dbDoc = 
          (DatabaseDocument) ((DocumentEntry) entry_group
            .getSequenceEntry().getEMBLEntry()).getDocument();

        try
        {
          boolean hasGraphs = addDatabaseUserPlot(dbDoc, database_user_plot);
          database_user_plot.setEnabled(hasGraphs);
          add(database_user_plot);
        }
        catch(Exception e)
        {
          e.printStackTrace();
        }
      }
      
      addSeparator ();
    }

    boolean useSubMenu = false;
    for (int i = 0 ; i < orig_algorithms.length ; ++i)
    {
      final BaseAlgorithm this_algorithm = orig_algorithms[i];

      if(this_algorithm.getAlgorithmName().startsWith("Cumulative AT"))
        useSubMenu = true;
      addAlgorithm (this_algorithm, false, useSubMenu);
    }
    if(useSubMenu)
      add(menuSubMenu);

    if (Options.getOptions ().getProperty ("codon_usage_file") != null)
    {
      final String codon_usage_file_name =
        Options.getOptions ().getProperty ("codon_usage_file");

      try 
      {
        addUsagePlot (new File (codon_usage_file_name), true, false);
        addUsagePlot (new File (codon_usage_file_name), false, false);
        
        if (getParent () != null)
        {
          // XXX change to revalidate().
          frame.validate ();
        }
      } 
      catch (IOException e) 
      {
        new MessageDialog (frame, "error while reading usage data: " + e);
      }
    }
    
    // add user plots from the command line JVM option
    if(System.getProperty("userplot") != null)
    {
      String plots[] = System.getProperty("userplot").split("[\\s,]");
      try
      {
        for(int i=0;i<plots.length; i++)
        {
          if(plots[i].startsWith("http:") ||
             plots[i].startsWith("file:") ||
             plots[i].startsWith("ftp:"))
          {
            uk.ac.sanger.artemis.util.Document document =
              new uk.ac.sanger.artemis.util.URLDocument (new URL(plots[i]));
            addUserPlot (document);
          }
          else
          {
            File f = new File(plots[i]);
            if(f.exists())
            {
              uk.ac.sanger.artemis.util.Document document =
                new uk.ac.sanger.artemis.util.FileDocument (f);
              addUserPlot (document);
            }
            else
              System.err.println(plots[i]+" not found.");
          }
        }
        splitPane.setDividerSize(3);
        splitPane.setDividerLocation(150);
      }
      catch(Exception e){}
    }
  }

  /**
   *  Create a new GraphMenu object and all it's menu items.
   *  @param frame The JFrame that owns this JMenu.
   *  @param entry_group The EntryGroup containing the sequence to plot.
   *  @param base_plot_group The BasePlotGroup that this menu controls.
   *  @param view_menu This ViewMenu is updated when a usage plot is added.
   *  @param add_menu This AddMenu is updated when a usage plot is added.
   *  @param menu_name The name of the new menu.
   **/
  public GraphMenu (final JFrame frame,
                    final EntryGroup entry_group,
                    final BasePlotGroup base_plot_group,
                    final FeatureDisplay feature_display,
                    final JSplitPane splitPane) 
  {
    this (frame, entry_group, base_plot_group, feature_display, "Graph",splitPane);
  }

  /**
   *  Add a menu item for the given algorithm to the Display menu.
   *  @param is_visible The JCheckBoxMenuItem starts in the true state if and
   *    only if this is true.
   *  @return The new JCheckBoxMenuItem
   **/
  private JCheckBoxMenuItem addAlgorithm (final BaseAlgorithm algorithm,
                                        final boolean is_visible,
                                        final boolean useSubMenu) 
  {
    final JCheckBoxMenuItem new_item =
      new JCheckBoxMenuItem (algorithm.getAlgorithmName (), is_visible);

    new_item.addItemListener (new ItemListener () 
    {
      public void itemStateChanged(ItemEvent event) 
      {
        base_plot_group.setVisibleByAlgorithm (algorithm,
                                               new_item.isSelected());
        adjustSplitPane(new_item.isSelected());
      }
    });

    if(useSubMenu)
      menuSubMenu.add(new_item);
    else
      add (new_item);

    algorithm_menu_items.addElement (new_item);

    return new_item;
  }
  
  /**
   * Adjust the JSplitPane divider position if all plots are
   * hidden or if a single graph has been made visible.
   * @param thisGraphOn
   */
  private void adjustSplitPane(final boolean thisGraphOn)
  {
    if(splitPane == null)
      return;
      
    final BaseAlgorithm [] current_algorithms =
      base_plot_group.getPlotAlgorithms ();

    boolean usageDisplayed = false;
    int nvisible = 0;
    for (int i = 0 ; i < current_algorithms.length ; ++i)
    {
      final JCheckBoxMenuItem this_menu_item =
        (JCheckBoxMenuItem) algorithm_menu_items.elementAt (i);

       if(this_menu_item.isSelected())
       {
         nvisible++;
         if(this_menu_item.getText().indexOf("Codon Usage") > -1)
           usageDisplayed = true;
         else
           usageDisplayed = false;
       }
    }

    if(nvisible == 0)
    {
      splitPane.setDividerSize(0);
      splitPane.setDividerLocation(0);
    }
    else if( ( thisGraphOn && nvisible == 1 ) ||
             (usageDisplayed && nvisible == 2) )
    {
      splitPane.setDividerSize(3);
      splitPane.setDividerLocation(0.2d);
    }
  }

  /**
   *  Ask the user for a file name, then read the codon usage data from that
   *  file, then make and add forward and a reverse BasePlot component using
   *  the data.
   **/
  private void addUsagePlot () 
  {
    final JFrame frame = Utilities.getComponentFrame (base_plot_group);

    final StickyFileChooser dialog = new StickyFileChooser ();

    dialog.setDialogTitle ("Select a codon usage data file name ...");
    dialog.setDialogType (JFileChooser.OPEN_DIALOG);

    final int status = dialog.showOpenDialog (frame);

    if (status != JFileChooser.APPROVE_OPTION ||
        dialog.getSelectedFile () == null)
    {
      return;
    }

    final File file =
      new File (dialog.getCurrentDirectory (),
                dialog.getSelectedFile ().getName ());

    if (file.length () != 0)
    {
      try 
      {
        final BasePlot new_forward_plot =
          addUsagePlot (file, true, true);
        final BasePlot new_reverse_plot =
          addUsagePlot (file, false, true);

        final Algorithm forward_algorithm = new_forward_plot.getAlgorithm ();
        final Algorithm reverse_algorithm = new_reverse_plot.getAlgorithm ();

        base_plot_group.setVisibleByAlgorithm (forward_algorithm, true);
        base_plot_group.setVisibleByAlgorithm (reverse_algorithm, true);
      } 
      catch (IOException e) 
      {
        new MessageDialog (Utilities.getComponentFrame (base_plot_group),
                           "error while reading usage data: " + e);
      }
    }
  }

  /**
   *  Read the codon usage data from the given File, then make and add a
   *  BasePlot component using the data.
   *  @param use_forward_strand The plot will be a forward plot if and only if
   *    this is true.
   *  @param is_visible The plot will start off visible if and only if this is
   *    true.
   *  @return The BasePlot that was added.
   **/
  private BasePlot addUsagePlot (final File codon_usage_file,
                                 final boolean use_forward_strand,
                                 final boolean is_visible)
      throws IOException 
  {
    final CodonUsageAlgorithm codon_usage_algorithm;

    if (use_forward_strand) 
    {
      final Strand forward_strand =
        entry_group.getBases ().getForwardStrand ();

      final CodonUsageWeight usage_weights =
        new CodonUsageWeight (codon_usage_file, forward_strand);

      codon_usage_algorithm =
        new CodonUsageAlgorithm (forward_strand, usage_weights);
    } 
    else 
    {
      final Strand backward_strand =
        entry_group.getBases ().getReverseStrand ();

      final CodonUsageWeight usage_weights =
        new CodonUsageWeight (codon_usage_file, backward_strand);

      codon_usage_algorithm =
        new CodonUsageAlgorithm (backward_strand, usage_weights);
    }

    addAlgorithm (codon_usage_algorithm, is_visible, false);

    final BasePlot new_plot =
      base_plot_group.addAlgorithm (codon_usage_algorithm);

    base_plot_group.setVisibleByAlgorithm (codon_usage_algorithm, is_visible);

    // XXX hack to force the BasePlot to initialise
    final DisplayAdjustmentEvent event =
      new DisplayAdjustmentEvent (this,
                                  feature_display.getFirstVisibleForwardBase (),
                                  feature_display.getLastVisibleForwardBase (),
                                  feature_display.getMaxVisibleBases (),
                                  feature_display.getScaleValue (),
                                  feature_display.getScaleFactor (),
                                  feature_display.isRevCompDisplay (),
                                  DisplayAdjustmentEvent.ALL_CHANGE_ADJUST_EVENT);

    base_plot_group.displayAdjustmentValueChanged (event);

    return new_plot;
  }

  /**
   * Add a UserDataAlgorithm from the database to the display. 
   * This returns true only if graph data is found.
   * @param dbDoc
   * @param database_user_plot
   * @return
   */
  private boolean addDatabaseUserPlot(final DatabaseDocument dbDoc,
                                      final JMenu database_user_plot)
  {
    List graphs = dbDoc.getGraphs();
    if(graphs == null || graphs.size() == 0)
      return false;
    
    for (int i = 0; i < graphs.size(); i++)
    {
      final Graph graph = (Graph) graphs.get(i);
      JMenuItem menuGraph = new JMenuItem(graph.getName());
      database_user_plot.add(menuGraph);
      
      menuGraph.addActionListener(new ActionListener()
      {
        public void actionPerformed(ActionEvent event)
        {
          try
          {
            Document doc = dbDoc.getGraphData(graph.getGraphId(), graph.getName());
            final JCheckBox logTransform = new JCheckBox("Use log(data+1)", false);
            JOptionPane.showMessageDialog(frame, logTransform, 
                "Transform", JOptionPane.QUESTION_MESSAGE);
            frame.setCursor(new Cursor(Cursor.WAIT_CURSOR));
            try
            {
              UserDataAlgorithm new_algorithm = new UserDataAlgorithm(
                  getEntryGroup().getBases().getForwardStrand(), doc, 
                  logTransform.isSelected());
              final BasePlot new_base_plot = base_plot_group.addAlgorithm(new_algorithm);

              base_plot_group.setVisibleByAlgorithm(new_algorithm, true);
              addAlgorithm(new_algorithm, true, false);

              // XXX hack to force the BasePlot to initialise
              final DisplayAdjustmentEvent e = new DisplayAdjustmentEvent(
                  this, feature_display.getFirstVisibleForwardBase(),
                  feature_display.getLastVisibleForwardBase(),
                  feature_display.getMaxVisibleBases(), 
                  feature_display.getScaleValue(),
                  feature_display.getScaleFactor(),
                  feature_display.isRevCompDisplay(),
                  DisplayAdjustmentEvent.ALL_CHANGE_ADJUST_EVENT);

              base_plot_group.displayAdjustmentValueChanged(e);
            }
            catch (IOException e)
            {
              e.printStackTrace();
            }
            frame.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
            adjustSplitPane(true);
          }
          catch (java.lang.OutOfMemoryError emem)
          {
            JOptionPane.showMessageDialog(frame,
                "Out of memory. Increase the maximum memory"
                    + "\navailable for this application and try again.",
                "Out Of Memory", JOptionPane.WARNING_MESSAGE);
            frame.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
          }
        }
      });
    }
    return true;
  }
  
  /**
   *  Add a UserDataAlgorithm to the display.
   **/
  private void addUserPlot (uk.ac.sanger.artemis.util.Document document) 
  {
    final JCheckBox logTransform = new JCheckBox("Use log(data+1)", false);
    if (document == null)
    {
      final JFrame frame = Utilities.getComponentFrame(base_plot_group);
      final StickyFileChooser dialog = new StickyFileChooser();

      dialog.setDialogTitle("Select a data file name ...");
      dialog.setDialogType(JFileChooser.OPEN_DIALOG);

      dialog.setAccessory(logTransform);

      final int status = dialog.showOpenDialog(frame);
      if(status != JFileChooser.APPROVE_OPTION || 
         dialog.getSelectedFile() == null)
      {
        return;
      }

      File file = new File(dialog.getCurrentDirectory(), 
                      dialog.getSelectedFile().getName());
      
      document =
        new uk.ac.sanger.artemis.util.FileDocument (file);
    }
    
    frame.setCursor(new Cursor(Cursor.WAIT_CURSOR));
    
    final Strand forward_strand =
        getEntryGroup ().getBases ().getForwardStrand ();

      try 
      {
        final UserDataAlgorithm new_algorithm =
          new UserDataAlgorithm (forward_strand, document, logTransform.isSelected());

        final BasePlot new_base_plot =
          base_plot_group.addAlgorithm (new_algorithm);

        base_plot_group.setVisibleByAlgorithm (new_algorithm, true);

        addAlgorithm (new_algorithm, true, false);

        // XXX hack to force the BasePlot to initialise
        final DisplayAdjustmentEvent event =
          new DisplayAdjustmentEvent (this,
                                      feature_display.getFirstVisibleForwardBase (),
                                      feature_display.getLastVisibleForwardBase (),
                                      feature_display.getMaxVisibleBases (),
                                      feature_display.getScaleValue (),
                                      feature_display.getScaleFactor (),
                                      feature_display.isRevCompDisplay (),
                                      DisplayAdjustmentEvent.ALL_CHANGE_ADJUST_EVENT);

        base_plot_group.displayAdjustmentValueChanged (event);

        if (getParent () != null) 
        {
          // XXX change to revalidate().
          frame.validate ();
        }
      }
      catch (IOException e) 
      {
        new MessageDialog (Utilities.getComponentFrame (base_plot_group),
                           "error while reading user data: " + e);
      }
    
    frame.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
  }

  /**
   *  Return the JFrame that was passed to the constructor.
   **/
  private JFrame getParentFrame () 
  {
    return frame;
  }

  /**
   *  Return the EntryGroup that was passed to the constructor.
   **/
  private EntryGroup getEntryGroup () 
  {
    return entry_group;
  }

}