2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.jbgui;
20 import jalview.util.MessageManager;
23 import java.awt.event.ActionListener;
24 import java.awt.event.ActionEvent;
26 public class GStructureViewer extends JInternalFrame
28 public GStructureViewer()
33 } catch (Exception ex)
39 private void jbInit() throws Exception
41 this.setJMenuBar(menuBar);
42 fileMenu.setText(MessageManager.getString("action.file"));
43 savemenu.setActionCommand(MessageManager.getString("action.save_image"));
44 savemenu.setText(MessageManager.getString("action.save_as"));
45 pdbFile.setText(MessageManager.getString("label.pdb_file"));
46 pdbFile.addActionListener(new ActionListener()
48 public void actionPerformed(ActionEvent actionEvent)
50 pdbFile_actionPerformed(actionEvent);
54 png.addActionListener(new ActionListener()
56 public void actionPerformed(ActionEvent actionEvent)
58 png_actionPerformed(actionEvent);
62 eps.addActionListener(new ActionListener()
64 public void actionPerformed(ActionEvent actionEvent)
66 eps_actionPerformed(actionEvent);
69 viewMapping.setText(MessageManager.getString("label.view_mapping"));
70 viewMapping.addActionListener(new ActionListener()
72 public void actionPerformed(ActionEvent actionEvent)
74 viewMapping_actionPerformed(actionEvent);
77 viewMenu.setText(MessageManager.getString("action.view"));
78 chainMenu.setText(MessageManager.getString("action.show_chain"));
79 colourMenu.setText(MessageManager.getString("label.colours"));
80 backGround.setText(MessageManager.getString("label.background_colour") + "...");
81 backGround.addActionListener(new ActionListener()
83 public void actionPerformed(ActionEvent actionEvent)
85 backGround_actionPerformed(actionEvent);
88 seqColour.setSelected(false);
89 seqColour.setText(MessageManager.getString("action.by_sequence"));
90 seqColour.addActionListener(new ActionListener()
92 public void actionPerformed(ActionEvent actionEvent)
94 seqColour_actionPerformed(actionEvent);
97 chainColour.setText(MessageManager.getString("action.by_chain"));
98 chainColour.addActionListener(new ActionListener()
100 public void actionPerformed(ActionEvent actionEvent)
102 chainColour_actionPerformed(actionEvent);
105 chargeColour.setText(MessageManager.getString("label.charge_cysteine"));
106 chargeColour.addActionListener(new ActionListener()
108 public void actionPerformed(ActionEvent actionEvent)
110 chargeColour_actionPerformed(actionEvent);
113 zappoColour.setText(MessageManager.getString("label.zappo"));
114 zappoColour.addActionListener(new ActionListener()
116 public void actionPerformed(ActionEvent actionEvent)
118 zappoColour_actionPerformed(actionEvent);
121 taylorColour.setText(MessageManager.getString("label.taylor"));
122 taylorColour.addActionListener(new ActionListener()
124 public void actionPerformed(ActionEvent actionEvent)
126 taylorColour_actionPerformed(actionEvent);
129 hydroColour.setText(MessageManager.getString("label.hydrophobicity"));
130 hydroColour.addActionListener(new ActionListener()
132 public void actionPerformed(ActionEvent actionEvent)
134 hydroColour_actionPerformed(actionEvent);
137 strandColour.setText(MessageManager.getString("label.strand_propensity"));
138 strandColour.addActionListener(new ActionListener()
140 public void actionPerformed(ActionEvent actionEvent)
142 strandColour_actionPerformed(actionEvent);
145 helixColour.setText(MessageManager.getString("label.helix_propensity"));
146 helixColour.addActionListener(new ActionListener()
148 public void actionPerformed(ActionEvent actionEvent)
150 helixColour_actionPerformed(actionEvent);
153 turnColour.setText(MessageManager.getString("label.turn_propensity"));
154 turnColour.addActionListener(new ActionListener()
156 public void actionPerformed(ActionEvent actionEvent)
158 turnColour_actionPerformed(actionEvent);
161 buriedColour.setText(MessageManager.getString("label.buried_index"));
162 buriedColour.addActionListener(new ActionListener()
164 public void actionPerformed(ActionEvent actionEvent)
166 buriedColour_actionPerformed(actionEvent);
169 purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
170 purinePyrimidineColour.addActionListener(new ActionListener()
172 public void actionPerformed(ActionEvent actionEvent)
174 purinePyrimidineColour_actionPerformed(actionEvent);
178 userColour.setText(MessageManager.getString("action.user_defined"));
179 userColour.addActionListener(new ActionListener()
181 public void actionPerformed(ActionEvent actionEvent)
183 userColour_actionPerformed(actionEvent);
186 jmolColour.setSelected(false);
187 jmolColour.setText(MessageManager.getString("label.colour_with_jmol"));
188 jmolColour.setToolTipText(MessageManager.getString("label.let_jmol_manage_structure_colours"));
189 jmolColour.addActionListener(new ActionListener()
191 public void actionPerformed(ActionEvent actionEvent)
193 jmolColour_actionPerformed(actionEvent);
196 helpMenu.setText(MessageManager.getString("action.help"));
197 jmolHelp.setText(MessageManager.getString("label.jmol_help"));
198 jmolHelp.addActionListener(new ActionListener()
200 public void actionPerformed(ActionEvent actionEvent)
202 jmolHelp_actionPerformed(actionEvent);
205 alignStructs.setText(MessageManager.getString("label.align_structures"));
206 alignStructs.addActionListener(new ActionListener()
208 public void actionPerformed(ActionEvent actionEvent)
210 alignStructs_actionPerformed(actionEvent);
213 jmolActionMenu.setText(MessageManager.getString("label.jmol"));
214 menuBar.add(fileMenu);
215 menuBar.add(viewMenu);
216 menuBar.add(colourMenu);
217 menuBar.add(jmolActionMenu);
218 jmolActionMenu.setVisible(false);
219 menuBar.add(helpMenu);
220 fileMenu.add(savemenu);
221 fileMenu.add(viewMapping);
222 savemenu.add(pdbFile);
225 viewMenu.add(chainMenu);
227 colourMenu.add(seqColour);
228 colourMenu.add(chainColour);
229 colourMenu.add(chargeColour);
230 colourMenu.add(zappoColour);
231 colourMenu.add(taylorColour);
232 colourMenu.add(hydroColour);
233 colourMenu.add(helixColour);
234 colourMenu.add(strandColour);
235 colourMenu.add(turnColour);
236 colourMenu.add(buriedColour);
237 colourMenu.add(purinePyrimidineColour);
238 colourMenu.add(userColour);
239 colourMenu.add(jmolColour);
240 colourMenu.add(backGround);
242 colourButtons.add(seqColour);
243 colourButtons.add(chainColour);
244 colourButtons.add(chargeColour);
245 colourButtons.add(zappoColour);
246 colourButtons.add(taylorColour);
247 colourButtons.add(hydroColour);
248 colourButtons.add(helixColour);
249 colourButtons.add(strandColour);
250 colourButtons.add(turnColour);
251 colourButtons.add(buriedColour);
252 colourButtons.add(userColour);
253 colourButtons.add(jmolColour);
255 helpMenu.add(jmolHelp);
256 jmolActionMenu.add(alignStructs);
259 protected void jmolColour_actionPerformed(ActionEvent actionEvent)
263 protected void alignStructs_actionPerformed(ActionEvent actionEvent)
267 JMenuBar menuBar = new JMenuBar();
269 JMenu fileMenu = new JMenu();
271 JMenu savemenu = new JMenu();
273 JMenuItem pdbFile = new JMenuItem();
275 JMenuItem png = new JMenuItem();
277 JMenuItem eps = new JMenuItem();
279 JMenuItem viewMapping = new JMenuItem();
281 protected JMenu viewMenu = new JMenu();
283 protected JMenu chainMenu = new JMenu();
285 JMenu jMenu1 = new JMenu();
287 protected JMenu colourMenu = new JMenu();
289 protected JMenu jmolActionMenu = new JMenu();
291 protected JMenuItem alignStructs = new JMenuItem();
293 JMenuItem backGround = new JMenuItem();
295 protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
297 protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
299 protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
301 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
303 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
305 protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
307 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
309 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
311 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
313 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
315 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
317 protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
319 protected JRadioButtonMenuItem jmolColour = new JRadioButtonMenuItem();
321 protected ButtonGroup colourButtons = new ButtonGroup();
323 JMenu helpMenu = new JMenu();
325 JMenuItem jmolHelp = new JMenuItem();
327 public void pdbFile_actionPerformed(ActionEvent actionEvent)
332 public void png_actionPerformed(ActionEvent actionEvent)
337 public void eps_actionPerformed(ActionEvent actionEvent)
342 public void viewMapping_actionPerformed(ActionEvent actionEvent)
347 public void seqColour_actionPerformed(ActionEvent actionEvent)
352 public void chainColour_actionPerformed(ActionEvent actionEvent)
357 public void chargeColour_actionPerformed(ActionEvent actionEvent)
362 public void zappoColour_actionPerformed(ActionEvent actionEvent)
367 public void taylorColour_actionPerformed(ActionEvent actionEvent)
372 public void hydroColour_actionPerformed(ActionEvent actionEvent)
377 public void helixColour_actionPerformed(ActionEvent actionEvent)
382 public void strandColour_actionPerformed(ActionEvent actionEvent)
387 public void turnColour_actionPerformed(ActionEvent actionEvent)
392 public void buriedColour_actionPerformed(ActionEvent actionEvent)
397 public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
402 public void userColour_actionPerformed(ActionEvent actionEvent)
407 public void backGround_actionPerformed(ActionEvent actionEvent)
412 public void jmolHelp_actionPerformed(ActionEvent actionEvent)