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.schemes.BuriedColourScheme;
28 import jalview.schemes.HelixColourScheme;
29 import jalview.schemes.HydrophobicColourScheme;
30 import jalview.schemes.StrandColourScheme;
31 import jalview.schemes.TaylorColourScheme;
32 import jalview.schemes.TurnColourScheme;
33 import jalview.schemes.ZappoColourScheme;
34 import jalview.util.MessageManager;
36 import java.awt.BorderLayout;
37 import java.awt.CheckboxGroup;
38 import java.awt.CheckboxMenuItem;
39 import java.awt.Frame;
41 import java.awt.MenuBar;
42 import java.awt.MenuItem;
43 import java.awt.event.ActionEvent;
44 import java.awt.event.ActionListener;
45 import java.awt.event.ItemEvent;
46 import java.awt.event.ItemListener;
48 public class AppletPDBViewer extends EmbmenuFrame implements
49 ActionListener, ItemListener
51 AppletPDBCanvas pdbcanvas;
53 public AppletPDBViewer(PDBEntry pdbentry, SequenceI[] seq,
54 String[] chains, AlignmentPanel ap, String protocol)
59 } catch (Exception ex)
64 pdbcanvas = new AppletPDBCanvas(pdbentry, seq, chains, ap, protocol);
66 embedMenuIfNeeded(pdbcanvas);
67 add(pdbcanvas, BorderLayout.CENTER);
69 StringBuffer title = new StringBuffer(seq[0].getName() + ":"
70 + pdbcanvas.pdbentry.getFile());
72 jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
76 public void actionPerformed(ActionEvent evt)
78 if (evt.getSource() == mapping)
80 jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
82 Frame frame = new Frame();
84 jalview.bin.JalviewLite.addFrame(frame,
85 MessageManager.getString("label.pdb_sequence_mapping"), 500,
87 cap.setText(pdbcanvas.mappingDetails.toString());
90 else if (evt.getSource() == charge)
92 pdbcanvas.bysequence = false;
93 pdbcanvas.pdb.setChargeColours();
96 else if (evt.getSource() == chain)
98 pdbcanvas.bysequence = false;
99 pdbcanvas.pdb.setChainColours();
101 else if (evt.getSource() == seqButton)
103 pdbcanvas.bysequence = true;
104 pdbcanvas.colourBySequence();
107 else if (evt.getSource() == zappo)
109 pdbcanvas.setColours(new ZappoColourScheme());
111 else if (evt.getSource() == taylor)
113 pdbcanvas.setColours(new TaylorColourScheme());
115 else if (evt.getSource() == hydro)
117 pdbcanvas.setColours(new HydrophobicColourScheme());
119 else if (evt.getSource() == helix)
121 pdbcanvas.setColours(new HelixColourScheme());
123 else if (evt.getSource() == strand)
125 pdbcanvas.setColours(new StrandColourScheme());
127 else if (evt.getSource() == turn)
129 pdbcanvas.setColours(new TurnColourScheme());
131 else if (evt.getSource() == buried)
133 pdbcanvas.setColours(new BuriedColourScheme());
135 else if (evt.getSource() == user)
137 pdbcanvas.bysequence = false;
138 new jalview.appletgui.UserDefinedColours(pdbcanvas);
141 pdbcanvas.redrawneeded = true;
146 public void itemStateChanged(ItemEvent evt)
148 if (evt.getSource() == allchains)
150 pdbcanvas.setAllchainsVisible(allchains.getState());
152 else if (evt.getSource() == wire)
154 pdbcanvas.wire = !pdbcanvas.wire;
156 else if (evt.getSource() == depth)
158 pdbcanvas.depthcue = !pdbcanvas.depthcue;
160 else if (evt.getSource() == zbuffer)
162 pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
164 pdbcanvas.redrawneeded = true;
168 private void jbInit() throws Exception
170 setMenuBar(jMenuBar1);
171 fileMenu.setLabel(MessageManager.getString("action.file"));
172 coloursMenu.setLabel(MessageManager.getString("label.colours"));
173 mapping.setLabel(MessageManager.getString("label.view_mapping"));
174 mapping.addActionListener(this);
175 wire.setLabel(MessageManager.getString("label.wireframe"));
176 wire.addItemListener(this);
177 depth.setState(true);
178 depth.setLabel(MessageManager.getString("label.depthcue"));
179 depth.addItemListener(this);
180 zbuffer.setState(true);
181 zbuffer.setLabel(MessageManager.getString("label.z_buffering"));
182 zbuffer.addItemListener(this);
183 charge.setLabel(MessageManager.getString("label.charge_cysteine"));
184 charge.addActionListener(this);
185 hydro.setLabel(MessageManager.getString("label.hydrophobicity"));
186 hydro.addActionListener(this);
187 chain.setLabel(MessageManager.getString("action.by_chain"));
188 chain.addActionListener(this);
189 seqButton.setLabel(MessageManager.getString("action.by_sequence"));
190 seqButton.addActionListener(this);
192 .setLabel(MessageManager.getString("label.all_chains_visible"));
193 allchains.addItemListener(this);
194 viewMenu.setLabel(MessageManager.getString("action.view"));
195 zappo.setLabel(MessageManager.getString("label.zappo"));
196 zappo.addActionListener(this);
197 taylor.setLabel(MessageManager.getString("label.taylor"));
198 taylor.addActionListener(this);
199 helix.setLabel(MessageManager.getString("label.helix_propensity"));
200 helix.addActionListener(this);
201 strand.setLabel(MessageManager.getString("label.strand_propensity"));
202 strand.addActionListener(this);
203 turn.setLabel(MessageManager.getString("label.turn_propensity"));
204 turn.addActionListener(this);
205 buried.setLabel(MessageManager.getString("label.buried_index"));
206 buried.addActionListener(this);
207 user.setLabel(MessageManager.getString("action.user_defined"));
208 user.addActionListener(this);
209 jMenuBar1.add(fileMenu);
210 jMenuBar1.add(coloursMenu);
211 jMenuBar1.add(viewMenu);
212 fileMenu.add(mapping);
215 coloursMenu.add(seqButton);
216 coloursMenu.add(chain);
217 coloursMenu.add(charge);
218 coloursMenu.add(zappo);
219 coloursMenu.add(taylor);
220 coloursMenu.add(hydro);
221 coloursMenu.add(helix);
222 coloursMenu.add(strand);
223 coloursMenu.add(turn);
224 coloursMenu.add(buried);
225 coloursMenu.add(user);
228 viewMenu.add(zbuffer);
229 viewMenu.add(allchains);
230 allchains.setState(true);
233 MenuBar jMenuBar1 = new MenuBar();
235 Menu fileMenu = new Menu();
237 Menu coloursMenu = new Menu();
239 MenuItem mapping = new MenuItem();
241 CheckboxGroup bg = new CheckboxGroup();
243 CheckboxMenuItem wire = new CheckboxMenuItem();
245 CheckboxMenuItem depth = new CheckboxMenuItem();
247 CheckboxMenuItem zbuffer = new CheckboxMenuItem();
249 MenuItem charge = new MenuItem();
251 MenuItem hydro = new MenuItem();
253 MenuItem chain = new MenuItem();
255 MenuItem seqButton = new MenuItem();
257 CheckboxMenuItem allchains = new CheckboxMenuItem();
259 Menu viewMenu = new Menu();
261 MenuItem turn = new MenuItem();
263 MenuItem strand = new MenuItem();
265 MenuItem helix = new MenuItem();
267 MenuItem taylor = new MenuItem();
269 MenuItem zappo = new MenuItem();
271 MenuItem buried = new MenuItem();
273 MenuItem user = new MenuItem();
275 // End StructureListener
276 // //////////////////////////