src/jalview/jbgui/GStructureViewer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.api.structures.JalviewStructureDisplayI;
  24 import jalview.gui.ColourMenuHelper.ColourChangeListener;
  25 import jalview.util.MessageManager;
  26
  27 import java.awt.BorderLayout;
  28 import java.awt.GridLayout;
  29 import java.awt.event.ActionEvent;
  30 import java.awt.event.ActionListener;
  31 import java.util.ArrayList;
  32 import java.util.List;
  33
  34 import javax.swing.JCheckBoxMenuItem;
  35 import javax.swing.JInternalFrame;
  36 import javax.swing.JLabel;
  37 import javax.swing.JMenu;
  38 import javax.swing.JMenuBar;
  39 import javax.swing.JMenuItem;
  40 import javax.swing.JPanel;
  41 import javax.swing.JRadioButtonMenuItem;
  42
  43 public abstract class GStructureViewer extends JInternalFrame
  44         implements JalviewStructureDisplayI, ColourChangeListener
  45 {
  46   // private AAStructureBindingModel bindingModel;
  47
  48   protected JMenu savemenu;
  49
  50   protected JMenu viewMenu;
  51
  52   protected JMenu colourMenu;
  53
  54   protected JMenu chainMenu;
  55
  56   protected JMenu viewerActionMenu;
  57
  58   protected JMenuItem alignStructs;
  59
  60   protected JCheckBoxMenuItem showAlignmentOnly;
  61
  62   protected JCheckBoxMenuItem hideHiddenRegions;
  63
  64   protected JMenuItem fitToWindow;
  65
  66   protected JRadioButtonMenuItem seqColour;
  67
  68   protected JRadioButtonMenuItem chainColour;
  69
  70   protected JRadioButtonMenuItem chargeColour;
  71
  72   protected JRadioButtonMenuItem viewerColour;
  73
  74   protected JMenuItem helpItem;
  75
  76   protected JLabel statusBar;
  77
  78   protected JPanel statusPanel;
  79
  80   /**
  81    * Constructor
  82    */
  83   public GStructureViewer()
  84   {
  85     try
  86     {
  87       jbInit();
  88     } catch (Exception ex)
  89     {
  90       ex.printStackTrace();
  91     }
  92   }
  93
  94   private void jbInit() throws Exception
  95   {
  96     JMenuBar menuBar = new JMenuBar();
  97     this.setJMenuBar(menuBar);
  98
  99     JMenu fileMenu = new JMenu();
 100     fileMenu.setText(MessageManager.getString("action.file"));
 101
 102     savemenu = new JMenu();
 103     savemenu.setActionCommand(
 104             MessageManager.getString("action.save_image"));
 105     savemenu.setText(MessageManager.getString("action.save_as"));
 106
 107     JMenuItem pdbFile = new JMenuItem();
 108     pdbFile.setText(MessageManager.getString("label.pdb_file"));
 109     pdbFile.addActionListener(new ActionListener()
 110     {
 111       @Override
 112       public void actionPerformed(ActionEvent actionEvent)
 113       {
 114         pdbFile_actionPerformed(actionEvent);
 115       }
 116     });
 117
 118     JMenuItem png = new JMenuItem();
 119     png.setText("PNG");
 120     png.addActionListener(new ActionListener()
 121     {
 122       @Override
 123       public void actionPerformed(ActionEvent actionEvent)
 124       {
 125         png_actionPerformed(actionEvent);
 126       }
 127     });
 128
 129     JMenuItem eps = new JMenuItem();
 130     eps.setText("EPS");
 131     eps.addActionListener(new ActionListener()
 132     {
 133       @Override
 134       public void actionPerformed(ActionEvent actionEvent)
 135       {
 136         eps_actionPerformed(actionEvent);
 137       }
 138     });
 139
 140     JMenuItem viewMapping = new JMenuItem();
 141     viewMapping.setText(MessageManager.getString("label.view_mapping"));
 142     viewMapping.addActionListener(new ActionListener()
 143     {
 144       @Override
 145       public void actionPerformed(ActionEvent actionEvent)
 146       {
 147         viewMapping_actionPerformed(actionEvent);
 148       }
 149     });
 150
 151     viewMenu = new JMenu();
 152     viewMenu.setText(MessageManager.getString("action.view"));
 153
 154     chainMenu = new JMenu();
 155     chainMenu.setText(MessageManager.getString("action.show_chain"));
 156
 157     fitToWindow = new JMenuItem();
 158     fitToWindow.setText(MessageManager.getString("label.fit_to_window"));
 159     fitToWindow.addActionListener(new ActionListener()
 160     {
 161       @Override
 162       public void actionPerformed(ActionEvent actionEvent)
 163       {
 164         fitToWindow_actionPerformed();
 165       }
 166     });
 167
 168     JMenu helpMenu = new JMenu();
 169     helpMenu.setText(MessageManager.getString("action.help"));
 170     helpItem = new JMenuItem();
 171     helpItem.setText(MessageManager.getString("label.jmol_help"));
 172     helpItem.addActionListener(new ActionListener()
 173     {
 174       @Override
 175       public void actionPerformed(ActionEvent actionEvent)
 176       {
 177         showHelp_actionPerformed(actionEvent);
 178       }
 179     });
 180     alignStructs = new JMenuItem();
 181     alignStructs.setText(
 182             MessageManager.getString("label.superpose_structures"));
 183     alignStructs.addActionListener(new ActionListener()
 184     {
 185       @Override
 186       public void actionPerformed(ActionEvent actionEvent)
 187       {
 188         alignStructs_actionPerformed(actionEvent);
 189       }
 190     });
 191
 192     viewerActionMenu = new JMenu(); // text set in sub-classes
 193     viewerActionMenu.setVisible(false);
 194     viewerActionMenu.add(alignStructs);
 195     colourMenu = new JMenu();
 196     colourMenu.setText(MessageManager.getString("label.colours"));
 197     fileMenu.add(savemenu);
 198     fileMenu.add(viewMapping);
 199     savemenu.add(pdbFile);
 200     savemenu.add(png);
 201     savemenu.add(eps);
 202     viewMenu.add(chainMenu);
 203     helpMenu.add(helpItem);
 204
 205     menuBar.add(fileMenu);
 206     menuBar.add(viewMenu);
 207     menuBar.add(colourMenu);
 208     menuBar.add(viewerActionMenu);
 209     menuBar.add(helpMenu);
 210
 211     statusPanel = new JPanel();
 212     statusPanel.setLayout(new GridLayout());
 213     this.getContentPane().add(statusPanel, BorderLayout.SOUTH);
 214     statusBar = new JLabel();
 215     statusPanel.add(statusBar, null);
 216   }
 217
 218   protected void fitToWindow_actionPerformed()
 219   {
 220   }
 221
 222   protected void highlightSelection_actionPerformed()
 223   {
 224   }
 225
 226   protected void viewerColour_actionPerformed(ActionEvent actionEvent)
 227   {
 228   }
 229
 230   protected abstract String alignStructs_actionPerformed(
 231           ActionEvent actionEvent);
 232
 233   public void pdbFile_actionPerformed(ActionEvent actionEvent)
 234   {
 235
 236   }
 237
 238   public void png_actionPerformed(ActionEvent actionEvent)
 239   {
 240
 241   }
 242
 243   public void eps_actionPerformed(ActionEvent actionEvent)
 244   {
 245
 246   }
 247
 248   public void viewMapping_actionPerformed(ActionEvent actionEvent)
 249   {
 250
 251   }
 252
 253   public void seqColour_actionPerformed(ActionEvent actionEvent)
 254   {
 255
 256   }
 257
 258   public void chainColour_actionPerformed(ActionEvent actionEvent)
 259   {
 260
 261   }
 262
 263   public void chargeColour_actionPerformed(ActionEvent actionEvent)
 264   {
 265
 266   }
 267
 268   public void background_actionPerformed(ActionEvent actionEvent)
 269   {
 270
 271   }
 272
 273   public void showHelp_actionPerformed(ActionEvent actionEvent)
 274   {
 275
 276   }
 277
 278   /**
 279    * Saves the selected entries in the 'View Chain' menu into a list. Entries are
 280    * formatted as "pdbid:chainid". Only the selected chains should be drawn in the
 281    * structure display.
 282    */
 283   protected void setSelectedChains()
 284   {
 285     List<String> chains = new ArrayList<>();
 286     for (int i = 0; i < chainMenu.getItemCount(); i++)
 287     {
 288       JMenuItem menuItem = chainMenu.getItem(i);
 289       if (menuItem instanceof JCheckBoxMenuItem)
 290       {
 291         JCheckBoxMenuItem item = (JCheckBoxMenuItem) menuItem;
 292         if (item.isSelected())
 293         {
 294           chains.add(item.getText().split(" ")[0]);
 295         }
 296       }
 297     }
 298     getBinding().setChainsToShow(chains);
 299   }
 300 }