2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
22 import java.awt.event.*;
24 import jalview.appletgui.*;
25 import jalview.datamodel.*;
26 import jalview.schemes.*;
29 public class AppletPDBViewer
30 extends EmbmenuFrame implements ActionListener, ItemListener
32 AppletPDBCanvas pdbcanvas;
34 public AppletPDBViewer(PDBEntry pdbentry,
49 pdbcanvas = new AppletPDBCanvas(pdbentry, seq, chains, ap, protocol);
51 embedMenuIfNeeded(pdbcanvas);
52 add(pdbcanvas, BorderLayout.CENTER);
54 StringBuffer title = new StringBuffer(seq[0].getName()
56 + pdbcanvas.pdbentry.getFile());
58 jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
64 public void actionPerformed(ActionEvent evt)
66 if (evt.getSource() == mapping)
68 jalview.appletgui.CutAndPasteTransfer cap
69 = new jalview.appletgui.CutAndPasteTransfer(false, null);
70 Frame frame = new Frame();
72 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500,
74 cap.setText(pdbcanvas.mappingDetails.toString());
77 else if (evt.getSource() == charge)
79 pdbcanvas.bysequence = false;
80 pdbcanvas.pdb.setChargeColours();
83 else if (evt.getSource() == chain)
85 pdbcanvas.bysequence = false;
86 pdbcanvas.pdb.setChainColours();
88 else if (evt.getSource() == seqButton)
90 pdbcanvas.bysequence = true;
91 pdbcanvas.colourBySequence();
94 else if (evt.getSource() == zappo)
96 pdbcanvas.setColours(new ZappoColourScheme());
98 else if (evt.getSource() == taylor)
100 pdbcanvas.setColours(new TaylorColourScheme());
102 else if (evt.getSource() == hydro)
104 pdbcanvas.setColours(new HydrophobicColourScheme());
106 else if (evt.getSource() == helix)
108 pdbcanvas.setColours(new HelixColourScheme());
110 else if (evt.getSource() == strand)
112 pdbcanvas.setColours(new StrandColourScheme());
114 else if (evt.getSource() == turn)
116 pdbcanvas.setColours(new TurnColourScheme());
118 else if (evt.getSource() == buried)
120 pdbcanvas.setColours(new BuriedColourScheme());
122 else if (evt.getSource() == user)
124 pdbcanvas.bysequence = false;
125 new jalview.appletgui.UserDefinedColours(pdbcanvas);
128 pdbcanvas.redrawneeded = true;
133 public void itemStateChanged(ItemEvent evt)
135 if (evt.getSource() == allchains)
137 pdbcanvas.setAllchainsVisible(allchains.getState());
139 else if (evt.getSource() == wire)
141 pdbcanvas.wire = !pdbcanvas.wire;
143 else if (evt.getSource() == depth)
145 pdbcanvas.depthcue = !pdbcanvas.depthcue;
147 else if (evt.getSource() == zbuffer)
149 pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
151 pdbcanvas.redrawneeded = true;
155 private void jbInit()
158 setMenuBar(jMenuBar1);
159 fileMenu.setLabel("File");
160 coloursMenu.setLabel("Colours");
161 mapping.setLabel("View Mapping");
162 mapping.addActionListener(this);
163 wire.setLabel("Wireframe");
164 wire.addItemListener(this);
165 depth.setState(true);
166 depth.setLabel("Depthcue");
167 depth.addItemListener(this);
168 zbuffer.setState(true);
169 zbuffer.setLabel("Z Buffering");
170 zbuffer.addItemListener(this);
171 charge.setLabel("Charge & Cysteine");
172 charge.addActionListener(this);
173 hydro.setLabel("Hydrophobicity");
174 hydro.addActionListener(this);
175 chain.setLabel("By Chain");
176 chain.addActionListener(this);
177 seqButton.setLabel("By Sequence");
178 seqButton.addActionListener(this);
179 allchains.setLabel("All Chains Visible");
180 allchains.addItemListener(this);
181 viewMenu.setLabel("View");
182 zappo.setLabel("Zappo");
183 zappo.addActionListener(this);
184 taylor.setLabel("Taylor");
185 taylor.addActionListener(this);
186 helix.setLabel("Helix Propensity");
187 helix.addActionListener(this);
188 strand.setLabel("Strand Propensity");
189 strand.addActionListener(this);
190 turn.setLabel("Turn Propensity");
191 turn.addActionListener(this);
192 buried.setLabel("Buried Index");
193 buried.addActionListener(this);
194 user.setLabel("User Defined...");
195 user.addActionListener(this);
196 jMenuBar1.add(fileMenu);
197 jMenuBar1.add(coloursMenu);
198 jMenuBar1.add(viewMenu);
199 fileMenu.add(mapping); ;
201 coloursMenu.add(seqButton);
202 coloursMenu.add(chain);
203 coloursMenu.add(charge);
204 coloursMenu.add(zappo);
205 coloursMenu.add(taylor);
206 coloursMenu.add(hydro);
207 coloursMenu.add(helix);
208 coloursMenu.add(strand);
209 coloursMenu.add(turn);
210 coloursMenu.add(buried);
211 coloursMenu.add(user);
214 viewMenu.add(zbuffer);
215 viewMenu.add(allchains);
216 allchains.setState(true);
219 MenuBar jMenuBar1 = new MenuBar();
220 Menu fileMenu = new Menu();
221 Menu coloursMenu = new Menu();
222 MenuItem mapping = new MenuItem();
223 CheckboxGroup bg = new CheckboxGroup();
224 CheckboxMenuItem wire = new CheckboxMenuItem();
225 CheckboxMenuItem depth = new CheckboxMenuItem();
226 CheckboxMenuItem zbuffer = new CheckboxMenuItem();
228 MenuItem charge = new MenuItem();
229 MenuItem hydro = new MenuItem();
230 MenuItem chain = new MenuItem();
231 MenuItem seqButton = new MenuItem();
233 CheckboxMenuItem allchains = new CheckboxMenuItem();
234 Menu viewMenu = new Menu();
235 MenuItem turn = new MenuItem();
236 MenuItem strand = new MenuItem();
237 MenuItem helix = new MenuItem();
238 MenuItem taylor = new MenuItem();
239 MenuItem zappo = new MenuItem();
240 MenuItem buried = new MenuItem();
241 MenuItem user = new MenuItem();
244 //End StructureListener
245 ////////////////////////////