/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * 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 jalview.gui;

import jalview.jbgui.*;
import javax.swing.table.AbstractTableModel;
import javax.swing.event.*;
import jalview.util.TableSorter;
import java.awt.event.*;
import javax.swing.*;
import java.util.*;


import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
import org.biojava.dasobert.dasregistry.DasSource;
import org.biojava.dasobert.dasregistry.Das1Source;
import java.awt.BorderLayout;

public class DasSourceBrowser extends GDasSourceBrowser
    implements Runnable, ListSelectionListener
{
  static DasSource[] dasSources = null;

  Hashtable localSources = null;

  Vector selectedSources;

  String DEFAULT_REGISTRY = "http://das.sanger.ac.uk/registry/das1/sources/";

  boolean loadingDasSources = false;


  public DasSourceBrowser()
  {
    registryURL.setText(jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",
        DEFAULT_REGISTRY) );

    setSelectedFromProperties();

    displayFullDetails(null);
    table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);

    filter1.addListSelectionListener(this);
    filter2.addListSelectionListener(this);
    filter3.addListSelectionListener(this);

    //Ask to be notified of selection changes.
    ListSelectionModel rowSM = table.getSelectionModel();
    rowSM.addListSelectionListener(new ListSelectionListener()
    {
      public void valueChanged(ListSelectionEvent e)
      {
        ListSelectionModel lsm = (ListSelectionModel) e.getSource();
        if (!lsm.isSelectionEmpty())
        {
          int selectedRow = lsm.getMinSelectionIndex();
          displayFullDetails(table.getValueAt(selectedRow, 0).toString());
        }
      }
    });

    table.addMouseListener(new MouseAdapter()
        {
          public void mouseClicked(MouseEvent evt)
          {
            if(evt.getClickCount()==2
               || SwingUtilities.isRightMouseButton(evt))
              editRemoveLocalSource(evt);
          }
        });

    if(dasSources!=null)
    {
       init();
    }
  }

  public void paintComponent(java.awt.Graphics g)
  {
    if (dasSources == null && !loadingDasSources)
    {
      Thread worker = new Thread(this);
      worker.start();
    }
  }

  void init()
  {
    int dSize = dasSources.length;
    Object[][] data = new Object[dSize][2];
    for (int i = 0; i < dSize; i++)
    {
      data[i][0] = dasSources[i].getNickname();
      data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
          getNickname()));
    }

    refreshTableData(data);
    setCapabilities(dasSources);

    javax.swing.SwingUtilities.invokeLater(new Runnable()
        {
          public void run()
          {
            TableSorter sorter = (TableSorter)table.getModel();
            sorter.setSortingStatus(1, TableSorter.DESCENDING);
            sorter.setSortingStatus(1, TableSorter.NOT_SORTED);
          }
        });

    progressBar.setIndeterminate(false);
    progressBar.setVisible(false);
    addLocal.setVisible(true);
    refresh.setVisible(true);
  }


  public void refreshTableData(Object[][] data)
  {
    TableSorter sorter = new TableSorter(new DASTableModel(data));
    sorter.setTableHeader(table.getTableHeader());
    table.setModel(sorter);
  }

  void displayFullDetails(String nickName)
  {

    StringBuffer text = new StringBuffer(
        "<HTML><font size=\"2\" face=\"Verdana, Arial, Helvetica, sans-serif\">");

    if (nickName == null)
    {
      fullDetails.setText(text +
                          "Select a DAS service from the table"
                          + " to read a full description here.</font></html>");
      return;
    }

    int dSize = dasSources.length;
    for (int i = 0; i < dSize; i++)
    {
      if (!dasSources[i].getNickname().equals(nickName))
        continue;

      DasSource ds = dasSources[i];

      text.append("<font color=\"#0000FF\">Id:</font> " + dasSources[i].getId() +
                  "<br>");
      text.append("<font color=\"#0000FF\">Nickname:</font> " +
                  dasSources[i].getNickname() + "<br>");
      text.append("<font color=\"#0000FF\">URL:</font> " + dasSources[i].getUrl() +
                  "<br>");

      text.append("<font color=\"#0000FF\">Admin Email:</font> <a href=\"mailto:"
                  +dasSources[i].getAdminemail()
                  +"\">"+dasSources[i].getAdminemail()+"</a>" +
                  "<br>");


      text.append("<font color=\"#0000FF\">Registered at:</font> " + dasSources[i].getRegisterDate() +
                        "<br>");

      text.append("<font color=\"#0000FF\">Last successful test:</font> " + dasSources[i].getLeaseDate() +
                        "<br>");

      text.append("<font color=\"#0000FF\">Labels:</font> ");
      for(int s=0; s<dasSources[i].getLabels().length; s++)
      {
        text.append( dasSources[i].getLabels()[s]);
        if(s<dasSources[i].getLabels().length-1)
          text.append(",");
        text.append(" ");
      }
      text.append("<br>");



      text.append("<font color=\"#0000FF\">Capabilities:</font> ");
      String[] scap = dasSources[i].getCapabilities();
      for (int j = 0; j < scap.length; j++)
      {
        text.append(scap[j]);
        if (j < scap.length - 1)
          text.append(", ");
      }
      text.append("<br>");

      text.append("<font color=\"#0000FF\">Coordinates:</font> ");
      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();
      for (int j = 0; j < dcs.length; j++)
      {
        text.append("(" + dcs[j].getUniqueId() + ") "
                    + dcs[j].getCategory() + ", " + dcs[j].getName());
        if (dcs[j].getNCBITaxId() != 0)
          text.append(", " + dcs[j].getNCBITaxId());
        if (dcs[j].getOrganismName().length() > 0)
          text.append(", " + dcs[j].getOrganismName());

        text.append("<br>");
      }

      text.append("<font color=\"#0000FF\">Description:</font> " +
                  dasSources[i].getDescription() + "<br>");


      if (dasSources[i].getHelperurl()!=null
          && dasSources[i].getHelperurl().length() > 0)
      {
        text.append("<font color=\"#0000FF\"><a href=\"" +
                    dasSources[i].getHelperurl()
                    + "\">Go to site</a></font<br>");
      }

      text.append("</font></html>");

      break;
    }

    fullDetails.setText(text.toString());
    javax.swing.SwingUtilities.invokeLater(new Runnable()
    {
      public void run()
      {
        fullDetailsScrollpane.getVerticalScrollBar().setValue(0);
      }
    });
  }


  public void run()
  {
    loadingDasSources = true;

    addLocal.setVisible(false);
    refresh.setVisible(false);
    progressBar.setVisible(true);
    progressBar.setIndeterminate(true);

    dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();

    appendLocalSources();

    init();

    loadingDasSources = false;

  }

  public Vector getSelectedSources()
  {
    Vector selected = new Vector();
    for (int r = 0; r < selectedSources.size(); r++)
    {
        for (int i = 0; i < dasSources.length; i++)
        {
          if (dasSources[i].getNickname().equals(
              selectedSources.elementAt(r)))
          {
            selected.addElement(dasSources[i]);
            break;
          }
        }
    }

    return selected;
  }

  public DasSource[] getDASSource()
  {
    if(dasSources==null)
    {
     dasSources = jalview.io.DasSequenceFeatureFetcher.getDASSources();
     appendLocalSources();
    }

    return dasSources;
  }

  public void refresh_actionPerformed(ActionEvent e)
  {
    saveProperties(jalview.bin.Cache.applicationProperties);

    Thread worker = new Thread(this);
    worker.start();
  }

  private void setCapabilities(DasSource[] sources)
  {
    Vector authority = new Vector();
    Vector type = new Vector();
    Vector label = new Vector();

    authority.addElement("Any");
    type.addElement("Any");
    label.addElement("Any");

    for (int i = 0; i < sources.length; i++)
    {
      DasSource ds = sources[i];

      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();

      for (int j = 0; j < dcs.length; j++)
      {
        if (!type.contains(dcs[j].getCategory()))
          type.addElement(dcs[j].getCategory());

        if (!authority.contains(dcs[j].getName()))
          authority.addElement(dcs[j].getName());
      }

      String[] slabels = ds.getLabels();
      for (int s = 0; s < slabels.length; s++)
      {
        if (!label.contains(slabels[s]))
        {
          label.addElement(slabels[s]);
        }
      }

    }

    filter1.setListData(authority);
    filter2.setListData(type);
    filter3.setListData(label);

    javax.swing.SwingUtilities.invokeLater(new Runnable()
    {
      public void run()
      {
        filter1.setSelectedIndex(0);
        filter2.setSelectedIndex(0);
        filter3.setSelectedIndex(0);
      }
    });
  }

  public void amendLocal(boolean newSource)
  {
    String url = "http://localhost:8080/", nickname = "";

    if(!newSource)
    {
      int selectedRow = table.getSelectionModel().getMinSelectionIndex();
      nickname = table.getValueAt(selectedRow, 0).toString();
      url = ((DasSource)localSources.get(nickname)).getUrl();
    }

    JTextField nametf = new JTextField(nickname, 40);
    JTextField urltf = new JTextField(url, 40);

    JPanel panel = new JPanel(new BorderLayout());
    JPanel pane12 = new JPanel(new BorderLayout());
    pane12.add(new JLabel("Nickname: "), BorderLayout.CENTER);
    pane12.add(nametf, BorderLayout.EAST);
    panel.add(pane12, BorderLayout.NORTH);
    pane12 = new JPanel(new BorderLayout());
    pane12.add(new JLabel("URL: "), BorderLayout.CENTER);
    pane12.add(urltf, BorderLayout.EAST);
    panel.add(pane12, BorderLayout.SOUTH);


    int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
        panel, "Enter Nickname & URL of Local DAS Source",
        JOptionPane.OK_CANCEL_OPTION);

       if (reply != JOptionPane.OK_OPTION )
       {
           return;
       }

       if(!urltf.getText().endsWith("/"))
         urltf.setText(urltf.getText()+"/");

       Das1Source local = new Das1Source();

       local.setUrl(urltf.getText());
       local.setNickname(nametf.getText());


       if(localSources==null)
         localSources = new Hashtable();

       localSources.put(local.getNickname(), local);

       if(!newSource && !nickname.equals(nametf.getText()))
       {
         localSources.remove(nickname);
       }

       int size = dasSources.length;
       int adjust = newSource ? 1 : 0;

       Object[][] data = new Object[size+adjust][2];
       for (int i = 0; i < size; i++)
       {
         if(!newSource && dasSources[i].getNickname().equals(nickname))
         {
           ((DasSource)dasSources[i]).setNickname(local.getNickname());
           ((DasSource)dasSources[i]).setUrl(local.getUrl());
           data[i][0] = local.getNickname();
           data[i][1] = new Boolean(true);
         }
         else
         {
           data[i][0] = dasSources[i].getNickname();
           data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
               getNickname()));
         }
       }

       if(newSource)
       {
         data[size][0] = local.getNickname();
         data[size][1] = new Boolean(true);
         selectedSources.add(local.getNickname());
       }

       DasSource [] tmp = new DasSource[size+adjust];

       System.arraycopy(dasSources, 0, tmp, 0, size);

       if(newSource)
         tmp[size] = local;

       dasSources = tmp;

       refreshTableData(data);

       SwingUtilities.invokeLater(new Runnable()
       {
         public void run()
         {
           scrollPane.getVerticalScrollBar().setValue(
               scrollPane.getVerticalScrollBar().getMaximum()
               );
         }
       });

       displayFullDetails(local.getNickname());
     }

    public void editRemoveLocalSource(MouseEvent evt)
    {
      int selectedRow = table.getSelectionModel().getMinSelectionIndex();
      if(selectedRow==-1)
        return;

      String nickname = table.getValueAt(selectedRow, 0).toString();

      if (!localSources.containsKey(nickname))
      {
        JOptionPane.showInternalMessageDialog(Desktop.desktop,
        "You can only edit or remove local DAS Sources!",
         "Public DAS source - not editable",
         JOptionPane.WARNING_MESSAGE);
        return;
      }


      Object[] options = {"Edit", "Remove", "Cancel"};
      int choice = JOptionPane.showInternalOptionDialog(Desktop.desktop,
    "Do you want to edit or remove "+nickname+"?",
    "Edit / Remove Local DAS Source",
    JOptionPane.YES_NO_CANCEL_OPTION,
    JOptionPane.QUESTION_MESSAGE,
    null,
    options,
    options[2]);

      switch(choice)
      {
        case 0: amendLocal(false);   break;
        case 1:
          localSources.remove(nickname);
          selectedSources.remove(nickname);
          Object[][] data = new Object[dasSources.length-1][2];
          DasSource [] tmp = new DasSource[dasSources.length-1];
          int index = 0;
          for (int i = 0; i < dasSources.length; i++)
          {
            if (dasSources[i].getNickname().equals(nickname))
            {
              continue;
            }
            else
            {
              tmp[index] = dasSources[i];
              data[index][0] = dasSources[i].getNickname();
              data[index][1] = new Boolean(selectedSources.contains(dasSources[i].
                  getNickname()));
              index++;
            }
          }
           dasSources = tmp;
           refreshTableData(data);
           SwingUtilities.invokeLater(new Runnable()
           {
             public void run()
             {
               scrollPane.getVerticalScrollBar().setValue(
                   scrollPane.getVerticalScrollBar().getMaximum()
                   );
             }
           });

          break;
      }
    }

    void appendLocalSources()
    {
      if(localSources==null)
        return;

      int size = dasSources!=null ? dasSources.length : 0;
      int lsize = localSources.size();

      Object[][] data = new Object[size+lsize][2];
      for (int i = 0; i < size; i++)
      {
        data[i][0] = dasSources[i].getNickname();
        data[i][1] = new Boolean(selectedSources.contains(dasSources[i].
            getNickname()));
      }

      DasSource [] tmp = new DasSource[size+lsize];
      if(dasSources!=null)
        System.arraycopy(dasSources, 0, tmp, 0, size);

      Enumeration en = localSources.keys();
      int index = size;
      while(en.hasMoreElements())
      {
        String key = en.nextElement().toString();
        data[index][0] = key;
        data[index][1] = new Boolean(false);
        tmp[index] = new Das1Source();
        tmp[index].setNickname(key);
        tmp[index].setUrl( ((DasSource)localSources.get(key)).getUrl() );

        index++;
      }

      dasSources = tmp;

      refreshTableData(data);
  }

  public void valueChanged(ListSelectionEvent evt)
  {
    //Called when the MainTable selection changes
    if (evt.getValueIsAdjusting() )
    {
      return;
    }


    displayFullDetails(null);

    // Filter the displayed data sources
    int dSize = dasSources.length;


    ArrayList names = new ArrayList();
    ArrayList selected = new ArrayList();
    DasSource ds;

    //The features filter is not visible, but we must still
    //filter the das source list here.
    //July 2006 - only 6 sources fo not serve features
    Object [] dummyFeatureList = new Object[]{"features"};

    for (int i = 0; i < dSize; i++)
    {
      ds = dasSources[i];
      DasCoordinateSystem[] dcs = ds.getCoordinateSystem();

      if (dcs.length == 0 && ds.getCapabilities().length == 0
          && filter1.getSelectedIndex() == 0
          && filter2.getSelectedIndex() == 0
          && filter3.getSelectedIndex() == 0)
      {
        //THIS IS A FIX FOR LOCAL SOURCES WHICH DO NOT
        //HAVE COORDINATE SYSTEMS, INFO WHICH AT PRESENT
        //IS ADDED FROM THE REGISTRY
        names.add(ds.getNickname());
        selected.add(new Boolean(
              selectedSources.contains(ds.getNickname())));
        continue;
      }


      if (!selectedInList(dummyFeatureList, ds.getCapabilities())
      ||  !selectedInList(filter3.getSelectedValues(),
                          ds.getLabels()))
      {
        continue;
      }

      for (int j = 0; j < dcs.length; j++)
      {
        if (   selectedInList(filter1.getSelectedValues(),
                           new String[]
                           {dcs[j].getName()})
            && selectedInList(filter2.getSelectedValues(),
                              new String[]
                              {dcs[j].getCategory()}))
        {
          names.add(ds.getNickname());
          selected.add(new Boolean(
              selectedSources.contains(ds.getNickname())));
          break;
        }
      }
    }

    dSize = names.size();
    Object[][] data = new Object[dSize][2];
    for (int d = 0; d < dSize; d++)
    {
      data[d][0] = names.get(d);
      data[d][1] = selected.get(d);
    }

    refreshTableData(data);
  }

  boolean selectedInList(Object [] selection, String[] items)
  {
    for (int i = 0; i < selection.length; i++)
    {
      if (selection[i].equals("Any") )
        return true;

      for (int j = 0; j < items.length; j++)
      {
        if (selection[i].equals(items[j]))
          return true;
      }
    }

    return false;
  }

  void setSelectedFromProperties()
  {
     String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
     StringTokenizer st = new StringTokenizer(active, "\t");
     selectedSources = new Vector();
     while(st.hasMoreTokens())
     {
       selectedSources.addElement(st.nextToken());
     }

     String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
     if(local!=null)
     {
       if(localSources == null)
         localSources = new Hashtable();

       st = new StringTokenizer(local, "\t");
       while(st.hasMoreTokens())
       {
         String token = st.nextToken();
         int bar = token.indexOf("|");
         Das1Source source = new Das1Source();

         source.setUrl(token.substring(bar + 1));
         source.setNickname(token.substring(0, bar));

         localSources.put(source.getNickname(), source);
       }
     }
  }

  public void reset_actionPerformed(ActionEvent e)
  {
    registryURL.setText(DEFAULT_REGISTRY);
  }

  public void saveProperties(Properties properties)
  {
    if (registryURL.getText() == null || registryURL.getText().length() < 1)
      properties.remove("DAS_REGISTRY_URL");
    else
      properties.setProperty("DAS_REGISTRY_URL", registryURL.getText());

    StringBuffer sb = new StringBuffer();
    for(int r=0; r<table.getModel().getRowCount(); r++)
    {
      if( ((Boolean)table.getValueAt(r,1)).booleanValue())
      {
        sb.append(table.getValueAt(r,0)+"\t");
      }
    }

    properties.setProperty("DAS_ACTIVE_SOURCE", sb.toString() );

    if(localSources!=null)
    {
      sb = new StringBuffer();
      Enumeration en = localSources.keys();
      while(en.hasMoreElements())
      {
        String token = en.nextElement().toString();
        sb.append(token+"|"
                  + ((DasSource)localSources.get(token)).getUrl()
                  +"\t");
      }

      properties.setProperty("DAS_LOCAL_SOURCE", sb.toString());
    }

  }

  class DASTableModel
      extends AbstractTableModel
  {

    public DASTableModel(Object[][] data)
    {
      this.data = data;
    }

    private String[] columnNames = new String[]  {"Nickname", "Use Source"};

    private Object[][] data;

    public int getColumnCount()
    {
      return columnNames.length;
    }

    public int getRowCount()
    {
      return data.length;
    }

    public String getColumnName(int col)
    {
      return columnNames[col];
    }

    public Object getValueAt(int row, int col)
    {
      return data[row][col];
    }

    /*
     * JTable uses this method to determine the default renderer/
     * editor for each cell.  If we didn't implement this method,
     * then the last column would contain text ("true"/"false"),
     * rather than a check box.
     */
    public Class getColumnClass(int c)
    {
      return getValueAt(0, c).getClass();
    }

    /*
     * Don't need to implement this method unless your table's
     * editable.
     */
    public boolean isCellEditable(int row, int col)
    {
      //Note that the data/cell address is constant,
      //no matter where the cell appears onscreen.
      return col == 1;

    }

    /*
     * Don't need to implement this method unless your table's
     * data can change.
     */
    public void setValueAt(Object value, int row, int col)
    {
      data[row][col] = value;
      fireTableCellUpdated(row, col);

      String name = getValueAt(row,0).toString();
      boolean selected = ((Boolean)value).booleanValue();

      if(selectedSources.contains(name) && !selected)
        selectedSources.remove(name);

      if(!selectedSources.contains(name) && selected)
        selectedSources.add(name);
    }
  }
}