2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, 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;
21 import java.awt.event.ActionListener;
22 import java.awt.event.ActionEvent;
24 public class GStructureViewer extends JInternalFrame
26 public GStructureViewer()
31 } catch (Exception ex)
37 private void jbInit() throws Exception
39 this.setJMenuBar(menuBar);
40 fileMenu.setText("File");
41 savemenu.setActionCommand("Save Image");
42 savemenu.setText("Save As");
43 pdbFile.setText("PDB File");
44 pdbFile.addActionListener(new ActionListener()
46 public void actionPerformed(ActionEvent actionEvent)
48 pdbFile_actionPerformed(actionEvent);
52 png.addActionListener(new ActionListener()
54 public void actionPerformed(ActionEvent actionEvent)
56 png_actionPerformed(actionEvent);
60 eps.addActionListener(new ActionListener()
62 public void actionPerformed(ActionEvent actionEvent)
64 eps_actionPerformed(actionEvent);
67 viewMapping.setText("View Mapping");
68 viewMapping.addActionListener(new ActionListener()
70 public void actionPerformed(ActionEvent actionEvent)
72 viewMapping_actionPerformed(actionEvent);
75 viewMenu.setText("View");
76 chainMenu.setText("Show Chain");
77 colourMenu.setText("Colours");
78 backGround.setText("Background Colour...");
79 backGround.addActionListener(new ActionListener()
81 public void actionPerformed(ActionEvent actionEvent)
83 backGround_actionPerformed(actionEvent);
86 seqColour.setSelected(false);
87 seqColour.setText("By Sequence");
88 seqColour.addActionListener(new ActionListener()
90 public void actionPerformed(ActionEvent actionEvent)
92 seqColour_actionPerformed(actionEvent);
95 chainColour.setText("By Chain");
96 chainColour.addActionListener(new ActionListener()
98 public void actionPerformed(ActionEvent actionEvent)
100 chainColour_actionPerformed(actionEvent);
103 chargeColour.setText("Charge & Cysteine");
104 chargeColour.addActionListener(new ActionListener()
106 public void actionPerformed(ActionEvent actionEvent)
108 chargeColour_actionPerformed(actionEvent);
111 zappoColour.setText("Zappo");
112 zappoColour.addActionListener(new ActionListener()
114 public void actionPerformed(ActionEvent actionEvent)
116 zappoColour_actionPerformed(actionEvent);
119 taylorColour.setText("Taylor");
120 taylorColour.addActionListener(new ActionListener()
122 public void actionPerformed(ActionEvent actionEvent)
124 taylorColour_actionPerformed(actionEvent);
127 hydroColour.setText("Hydro");
128 hydroColour.addActionListener(new ActionListener()
130 public void actionPerformed(ActionEvent actionEvent)
132 hydroColour_actionPerformed(actionEvent);
135 strandColour.setText("Strand");
136 strandColour.addActionListener(new ActionListener()
138 public void actionPerformed(ActionEvent actionEvent)
140 strandColour_actionPerformed(actionEvent);
143 helixColour.setText("Helix Propensity");
144 helixColour.addActionListener(new ActionListener()
146 public void actionPerformed(ActionEvent actionEvent)
148 helixColour_actionPerformed(actionEvent);
151 turnColour.setText("Turn Propensity");
152 turnColour.addActionListener(new ActionListener()
154 public void actionPerformed(ActionEvent actionEvent)
156 turnColour_actionPerformed(actionEvent);
159 buriedColour.setText("Buried Index");
160 buriedColour.addActionListener(new ActionListener()
162 public void actionPerformed(ActionEvent actionEvent)
164 buriedColour_actionPerformed(actionEvent);
167 userColour.setText("User Defined ...");
168 userColour.addActionListener(new ActionListener()
170 public void actionPerformed(ActionEvent actionEvent)
172 userColour_actionPerformed(actionEvent);
175 jmolColour.setSelected(false);
176 jmolColour.setText("Colour with Jmol");
177 jmolColour.setToolTipText("Let Jmol manage structure colours.");
178 jmolColour.addActionListener(new ActionListener()
180 public void actionPerformed(ActionEvent actionEvent)
182 jmolColour_actionPerformed(actionEvent);
186 helpMenu.setText("Help");
187 jmolHelp.setText("Jmol Help");
188 jmolHelp.addActionListener(new ActionListener()
190 public void actionPerformed(ActionEvent actionEvent)
192 jmolHelp_actionPerformed(actionEvent);
195 alignStructs.setText("Align structures");
196 alignStructs.addActionListener(new ActionListener()
198 public void actionPerformed(ActionEvent actionEvent)
200 alignStructs_actionPerformed(actionEvent);
203 jmolActionMenu.setText("Jmol");
204 menuBar.add(fileMenu);
205 menuBar.add(viewMenu);
206 menuBar.add(colourMenu);
207 menuBar.add(jmolActionMenu);
208 jmolActionMenu.setVisible(false);
209 menuBar.add(helpMenu);
210 fileMenu.add(savemenu);
211 fileMenu.add(viewMapping);
212 savemenu.add(pdbFile);
215 viewMenu.add(chainMenu);
217 colourMenu.add(seqColour);
218 colourMenu.add(chainColour);
219 colourMenu.add(chargeColour);
220 colourMenu.add(zappoColour);
221 colourMenu.add(taylorColour);
222 colourMenu.add(hydroColour);
223 colourMenu.add(helixColour);
224 colourMenu.add(strandColour);
225 colourMenu.add(turnColour);
226 colourMenu.add(buriedColour);
227 colourMenu.add(userColour);
228 colourMenu.add(jmolColour);
229 colourMenu.add(backGround);
231 colourButtons.add(seqColour);
232 colourButtons.add(chainColour);
233 colourButtons.add(chargeColour);
234 colourButtons.add(zappoColour);
235 colourButtons.add(taylorColour);
236 colourButtons.add(hydroColour);
237 colourButtons.add(helixColour);
238 colourButtons.add(strandColour);
239 colourButtons.add(turnColour);
240 colourButtons.add(buriedColour);
241 colourButtons.add(userColour);
242 colourButtons.add(jmolColour);
244 helpMenu.add(jmolHelp);
245 jmolActionMenu.add(alignStructs);
248 protected void jmolColour_actionPerformed(ActionEvent actionEvent)
252 protected void alignStructs_actionPerformed(ActionEvent actionEvent)
256 JMenuBar menuBar = new JMenuBar();
258 JMenu fileMenu = new JMenu();
260 JMenu savemenu = new JMenu();
262 JMenuItem pdbFile = new JMenuItem();
264 JMenuItem png = new JMenuItem();
266 JMenuItem eps = new JMenuItem();
268 JMenuItem viewMapping = new JMenuItem();
270 protected JMenu viewMenu = new JMenu();
272 protected JMenu chainMenu = new JMenu();
274 JMenu jMenu1 = new JMenu();
276 protected JMenu colourMenu = new JMenu();
278 protected JMenu jmolActionMenu = new JMenu();
280 protected JMenuItem alignStructs = new JMenuItem();
282 JMenuItem backGround = new JMenuItem();
284 protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
286 protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
288 protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
290 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
292 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
294 protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
296 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
298 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
300 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
302 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
304 protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
306 protected JRadioButtonMenuItem jmolColour = new JRadioButtonMenuItem();
308 protected ButtonGroup colourButtons = new ButtonGroup();
310 JMenu helpMenu = new JMenu();
312 JMenuItem jmolHelp = new JMenuItem();
314 public void pdbFile_actionPerformed(ActionEvent actionEvent)
319 public void png_actionPerformed(ActionEvent actionEvent)
324 public void eps_actionPerformed(ActionEvent actionEvent)
329 public void viewMapping_actionPerformed(ActionEvent actionEvent)
334 public void seqColour_actionPerformed(ActionEvent actionEvent)
339 public void chainColour_actionPerformed(ActionEvent actionEvent)
344 public void chargeColour_actionPerformed(ActionEvent actionEvent)
349 public void zappoColour_actionPerformed(ActionEvent actionEvent)
354 public void taylorColour_actionPerformed(ActionEvent actionEvent)
359 public void hydroColour_actionPerformed(ActionEvent actionEvent)
364 public void helixColour_actionPerformed(ActionEvent actionEvent)
369 public void strandColour_actionPerformed(ActionEvent actionEvent)
374 public void turnColour_actionPerformed(ActionEvent actionEvent)
379 public void buriedColour_actionPerformed(ActionEvent actionEvent)
384 public void userColour_actionPerformed(ActionEvent actionEvent)
389 public void backGround_actionPerformed(ActionEvent actionEvent)
394 public void jmolHelp_actionPerformed(ActionEvent actionEvent)