2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
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
10 * of the License, or (at your option) any later version.
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.
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.
23 import jalview.appletgui.AlignmentPanel;
24 import jalview.appletgui.EmbmenuFrame;
25 import jalview.datamodel.PDBEntry;
26 import jalview.datamodel.SequenceI;
27 import jalview.io.DataSourceType;
28 import jalview.schemes.BuriedColourScheme;
29 import jalview.schemes.HelixColourScheme;
30 import jalview.schemes.HydrophobicColourScheme;
31 import jalview.schemes.StrandColourScheme;
32 import jalview.schemes.TaylorColourScheme;
33 import jalview.schemes.TurnColourScheme;
34 import jalview.schemes.ZappoColourScheme;
35 import jalview.util.MessageManager;
37 import java.awt.BorderLayout;
38 import java.awt.CheckboxGroup;
39 import java.awt.CheckboxMenuItem;
40 import java.awt.Frame;
42 import java.awt.MenuBar;
43 import java.awt.MenuItem;
44 import java.awt.event.ActionEvent;
45 import java.awt.event.ActionListener;
46 import java.awt.event.ItemEvent;
47 import java.awt.event.ItemListener;
49 public class AppletPDBViewer extends EmbmenuFrame implements
50 ActionListener, ItemListener
52 AppletPDBCanvas pdbcanvas;
54 public AppletPDBViewer(PDBEntry pdbentry, SequenceI[] seq,
55 String[] chains, AlignmentPanel ap, DataSourceType protocol)
60 } catch (Exception ex)
65 pdbcanvas = new AppletPDBCanvas(pdbentry, seq, chains, ap, protocol);
67 embedMenuIfNeeded(pdbcanvas);
68 add(pdbcanvas, BorderLayout.CENTER);
70 StringBuffer title = new StringBuffer(seq[0].getName() + ":"
71 + pdbcanvas.pdbentry.getFile());
73 jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
78 public void actionPerformed(ActionEvent evt)
80 if (evt.getSource() == mapping)
82 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
84 Frame frame = new Frame();
86 jalview.bin.JalviewLite.addFrame(frame,
87 MessageManager.getString("label.pdb_sequence_mapping"), 500,
89 cap.setText(pdbcanvas.mappingDetails.toString());
92 else if (evt.getSource() == charge)
94 pdbcanvas.bysequence = false;
95 pdbcanvas.pdb.setChargeColours();
98 else if (evt.getSource() == chain)
100 pdbcanvas.bysequence = false;
101 pdbcanvas.pdb.setChainColours();
103 else if (evt.getSource() == seqButton)
105 pdbcanvas.bysequence = true;
106 pdbcanvas.colourBySequence();
109 else if (evt.getSource() == zappo)
111 pdbcanvas.setColours(new ZappoColourScheme());
113 else if (evt.getSource() == taylor)
115 pdbcanvas.setColours(new TaylorColourScheme());
117 else if (evt.getSource() == hydro)
119 pdbcanvas.setColours(new HydrophobicColourScheme());
121 else if (evt.getSource() == helix)
123 pdbcanvas.setColours(new HelixColourScheme());
125 else if (evt.getSource() == strand)
127 pdbcanvas.setColours(new StrandColourScheme());
129 else if (evt.getSource() == turn)
131 pdbcanvas.setColours(new TurnColourScheme());
133 else if (evt.getSource() == buried)
135 pdbcanvas.setColours(new BuriedColourScheme());
137 else if (evt.getSource() == user)
139 pdbcanvas.bysequence = false;
140 new jalview.appletgui.UserDefinedColours(pdbcanvas);
143 pdbcanvas.redrawneeded = true;
149 public void itemStateChanged(ItemEvent evt)
151 if (evt.getSource() == allchains)
153 pdbcanvas.setAllchainsVisible(allchains.getState());
155 else if (evt.getSource() == wire)
157 pdbcanvas.wire = !pdbcanvas.wire;
159 else if (evt.getSource() == depth)
161 pdbcanvas.depthcue = !pdbcanvas.depthcue;
163 else if (evt.getSource() == zbuffer)
165 pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
167 pdbcanvas.redrawneeded = true;
171 private void jbInit() throws Exception
173 setMenuBar(jMenuBar1);
174 fileMenu.setLabel(MessageManager.getString("action.file"));
175 coloursMenu.setLabel(MessageManager.getString("label.colours"));
176 mapping.setLabel(MessageManager.getString("label.view_mapping"));
177 mapping.addActionListener(this);
178 wire.setLabel(MessageManager.getString("label.wireframe"));
179 wire.addItemListener(this);
180 depth.setState(true);
181 depth.setLabel(MessageManager.getString("label.depthcue"));
182 depth.addItemListener(this);
183 zbuffer.setState(true);
184 zbuffer.setLabel(MessageManager.getString("label.z_buffering"));
185 zbuffer.addItemListener(this);
186 charge.setLabel(MessageManager.getString("label.charge_cysteine"));
187 charge.addActionListener(this);
188 hydro.setLabel(MessageManager.getString("label.hydrophobicity"));
189 hydro.addActionListener(this);
190 chain.setLabel(MessageManager.getString("action.by_chain"));
191 chain.addActionListener(this);
192 seqButton.setLabel(MessageManager.getString("action.by_sequence"));
193 seqButton.addActionListener(this);
195 .setLabel(MessageManager.getString("label.all_chains_visible"));
196 allchains.addItemListener(this);
197 viewMenu.setLabel(MessageManager.getString("action.view"));
198 zappo.setLabel(MessageManager.getString("label.zappo"));
199 zappo.addActionListener(this);
200 taylor.setLabel(MessageManager.getString("label.taylor"));
201 taylor.addActionListener(this);
202 helix.setLabel(MessageManager.getString("label.helix_propensity"));
203 helix.addActionListener(this);
204 strand.setLabel(MessageManager.getString("label.strand_propensity"));
205 strand.addActionListener(this);
206 turn.setLabel(MessageManager.getString("label.turn_propensity"));
207 turn.addActionListener(this);
208 buried.setLabel(MessageManager.getString("label.buried_index"));
209 buried.addActionListener(this);
210 user.setLabel(MessageManager.getString("action.user_defined"));
211 user.addActionListener(this);
212 jMenuBar1.add(fileMenu);
213 jMenuBar1.add(coloursMenu);
214 jMenuBar1.add(viewMenu);
215 fileMenu.add(mapping);
218 coloursMenu.add(seqButton);
219 coloursMenu.add(chain);
220 coloursMenu.add(charge);
221 coloursMenu.add(zappo);
222 coloursMenu.add(taylor);
223 coloursMenu.add(hydro);
224 coloursMenu.add(helix);
225 coloursMenu.add(strand);
226 coloursMenu.add(turn);
227 coloursMenu.add(buried);
228 coloursMenu.add(user);
231 viewMenu.add(zbuffer);
232 viewMenu.add(allchains);
233 allchains.setState(true);
236 MenuBar jMenuBar1 = new MenuBar();
238 Menu fileMenu = new Menu();
240 Menu coloursMenu = new Menu();
242 MenuItem mapping = new MenuItem();
244 CheckboxGroup bg = new CheckboxGroup();
246 CheckboxMenuItem wire = new CheckboxMenuItem();
248 CheckboxMenuItem depth = new CheckboxMenuItem();
250 CheckboxMenuItem zbuffer = new CheckboxMenuItem();
252 MenuItem charge = new MenuItem();
254 MenuItem hydro = new MenuItem();
256 MenuItem chain = new MenuItem();
258 MenuItem seqButton = new MenuItem();
260 CheckboxMenuItem allchains = new CheckboxMenuItem();
262 Menu viewMenu = new Menu();
264 MenuItem turn = new MenuItem();
266 MenuItem strand = new MenuItem();
268 MenuItem helix = new MenuItem();
270 MenuItem taylor = new MenuItem();
272 MenuItem zappo = new MenuItem();
274 MenuItem buried = new MenuItem();
276 MenuItem user = new MenuItem();
278 // End StructureListener
279 // //////////////////////////