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;
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 purinePyrimidineColour.setText("Purine/Pyrimidine");
168 purinePyrimidineColour.addActionListener(new ActionListener()
170 public void actionPerformed(ActionEvent actionEvent)
172 purinePyrimidineColour_actionPerformed(actionEvent);
176 userColour.setText("User Defined ...");
177 userColour.addActionListener(new ActionListener()
179 public void actionPerformed(ActionEvent actionEvent)
181 userColour_actionPerformed(actionEvent);
184 jmolColour.setSelected(false);
185 jmolColour.setText("Colour with Jmol");
186 jmolColour.setToolTipText("Let Jmol manage structure colours.");
187 jmolColour.addActionListener(new ActionListener()
189 public void actionPerformed(ActionEvent actionEvent)
191 jmolColour_actionPerformed(actionEvent);
194 helpMenu.setText("Help");
195 jmolHelp.setText("Jmol Help");
196 jmolHelp.addActionListener(new ActionListener()
198 public void actionPerformed(ActionEvent actionEvent)
200 jmolHelp_actionPerformed(actionEvent);
203 alignStructs.setText("Align structures");
204 alignStructs.addActionListener(new ActionListener()
206 public void actionPerformed(ActionEvent actionEvent)
208 alignStructs_actionPerformed(actionEvent);
211 jmolActionMenu.setText("Jmol");
212 menuBar.add(fileMenu);
213 menuBar.add(viewMenu);
214 menuBar.add(colourMenu);
215 menuBar.add(jmolActionMenu);
216 jmolActionMenu.setVisible(false);
217 menuBar.add(helpMenu);
218 fileMenu.add(savemenu);
219 fileMenu.add(viewMapping);
220 savemenu.add(pdbFile);
223 viewMenu.add(chainMenu);
225 colourMenu.add(seqColour);
226 colourMenu.add(chainColour);
227 colourMenu.add(chargeColour);
228 colourMenu.add(zappoColour);
229 colourMenu.add(taylorColour);
230 colourMenu.add(hydroColour);
231 colourMenu.add(helixColour);
232 colourMenu.add(strandColour);
233 colourMenu.add(turnColour);
234 colourMenu.add(buriedColour);
235 colourMenu.add(purinePyrimidineColour);
236 colourMenu.add(userColour);
237 colourMenu.add(jmolColour);
238 colourMenu.add(backGround);
240 colourButtons.add(seqColour);
241 colourButtons.add(chainColour);
242 colourButtons.add(chargeColour);
243 colourButtons.add(zappoColour);
244 colourButtons.add(taylorColour);
245 colourButtons.add(hydroColour);
246 colourButtons.add(helixColour);
247 colourButtons.add(strandColour);
248 colourButtons.add(turnColour);
249 colourButtons.add(buriedColour);
250 colourButtons.add(userColour);
251 colourButtons.add(jmolColour);
253 helpMenu.add(jmolHelp);
254 jmolActionMenu.add(alignStructs);
257 protected void jmolColour_actionPerformed(ActionEvent actionEvent)
261 protected void alignStructs_actionPerformed(ActionEvent actionEvent)
265 JMenuBar menuBar = new JMenuBar();
267 JMenu fileMenu = new JMenu();
269 JMenu savemenu = new JMenu();
271 JMenuItem pdbFile = new JMenuItem();
273 JMenuItem png = new JMenuItem();
275 JMenuItem eps = new JMenuItem();
277 JMenuItem viewMapping = new JMenuItem();
279 protected JMenu viewMenu = new JMenu();
281 protected JMenu chainMenu = new JMenu();
283 JMenu jMenu1 = new JMenu();
285 protected JMenu colourMenu = new JMenu();
287 protected JMenu jmolActionMenu = new JMenu();
289 protected JMenuItem alignStructs = new JMenuItem();
291 JMenuItem backGround = new JMenuItem();
293 protected JRadioButtonMenuItem seqColour = new JRadioButtonMenuItem();
295 protected JRadioButtonMenuItem chainColour = new JRadioButtonMenuItem();
297 protected JRadioButtonMenuItem chargeColour = new JRadioButtonMenuItem();
299 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
301 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
303 protected JRadioButtonMenuItem hydroColour = new JRadioButtonMenuItem();
305 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
307 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
309 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
311 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
313 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
315 protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
317 protected JRadioButtonMenuItem jmolColour = new JRadioButtonMenuItem();
319 protected ButtonGroup colourButtons = new ButtonGroup();
321 JMenu helpMenu = new JMenu();
323 JMenuItem jmolHelp = new JMenuItem();
325 public void pdbFile_actionPerformed(ActionEvent actionEvent)
330 public void png_actionPerformed(ActionEvent actionEvent)
335 public void eps_actionPerformed(ActionEvent actionEvent)
340 public void viewMapping_actionPerformed(ActionEvent actionEvent)
345 public void seqColour_actionPerformed(ActionEvent actionEvent)
350 public void chainColour_actionPerformed(ActionEvent actionEvent)
355 public void chargeColour_actionPerformed(ActionEvent actionEvent)
360 public void zappoColour_actionPerformed(ActionEvent actionEvent)
365 public void taylorColour_actionPerformed(ActionEvent actionEvent)
370 public void hydroColour_actionPerformed(ActionEvent actionEvent)
375 public void helixColour_actionPerformed(ActionEvent actionEvent)
380 public void strandColour_actionPerformed(ActionEvent actionEvent)
385 public void turnColour_actionPerformed(ActionEvent actionEvent)
390 public void buriedColour_actionPerformed(ActionEvent actionEvent)
395 public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
400 public void userColour_actionPerformed(ActionEvent actionEvent)
405 public void backGround_actionPerformed(ActionEvent actionEvent)
410 public void jmolHelp_actionPerformed(ActionEvent actionEvent)