2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
22 import java.awt.event.*;
\r
24 import jalview.appletgui.*;
\r
25 import jalview.datamodel.*;
\r
26 import jalview.schemes.*;
\r
27 import jalview.structure.StructureListener;
\r
28 import jalview.structure.*;
\r
30 public class AppletPDBViewer
\r
31 extends Frame implements ActionListener, ItemListener
\r
33 AppletPDBCanvas pdbcanvas;
\r
35 public AppletPDBViewer(PDBEntry pdbentry,
\r
44 catch (Exception ex)
\r
46 ex.printStackTrace();
\r
49 pdbcanvas = new AppletPDBCanvas(pdbentry, seq, ap, protocol);
\r
52 add(pdbcanvas, BorderLayout.CENTER);
\r
54 StringBuffer title = new StringBuffer(seq[0].getName()
\r
56 + pdbcanvas.pdbentry.getFile());
\r
58 jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
\r
64 public void actionPerformed(ActionEvent evt)
\r
66 if (evt.getSource() == mapping)
\r
68 jalview.appletgui.CutAndPasteTransfer cap
\r
69 = new jalview.appletgui.CutAndPasteTransfer(false, null);
\r
70 Frame frame = new Frame();
\r
72 jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 500,
\r
74 cap.setText(pdbcanvas.mappingDetails.toString());
\r
77 else if (evt.getSource() == charge)
\r
79 pdbcanvas.bysequence = false;
\r
80 pdbcanvas.pdb.setChargeColours();
\r
83 else if (evt.getSource() == chain)
\r
85 pdbcanvas.bysequence = false;
\r
86 pdbcanvas.pdb.setChainColours();
\r
88 else if (evt.getSource() == seqButton)
\r
90 pdbcanvas.bysequence = true;
\r
91 pdbcanvas.colourBySequence(pdbcanvas.ap.getSequenceRenderer(),
\r
92 pdbcanvas.ap.av.getShowSequenceFeatures() ?
\r
93 pdbcanvas.ap.getFeatureRenderer() : null);
\r
96 else if (evt.getSource() == zappo)
\r
98 pdbcanvas.setColours(new ZappoColourScheme());
\r
100 else if (evt.getSource() == taylor)
\r
102 pdbcanvas.setColours(new TaylorColourScheme());
\r
104 else if (evt.getSource() == hydro)
\r
106 pdbcanvas.setColours(new HydrophobicColourScheme());
\r
108 else if (evt.getSource() == helix)
\r
110 pdbcanvas.setColours(new HelixColourScheme());
\r
112 else if (evt.getSource() == strand)
\r
114 pdbcanvas.setColours(new StrandColourScheme());
\r
116 else if (evt.getSource() == turn)
\r
118 pdbcanvas.setColours(new TurnColourScheme());
\r
120 else if (evt.getSource() == buried)
\r
122 pdbcanvas.setColours(new BuriedColourScheme());
\r
124 else if (evt.getSource() == user)
\r
126 pdbcanvas.bysequence = false;
\r
127 new jalview.appletgui.UserDefinedColours(pdbcanvas);
\r
130 pdbcanvas.redrawneeded = true;
\r
131 pdbcanvas.repaint();
\r
135 public void itemStateChanged(ItemEvent evt)
\r
137 if (evt.getSource() == allchains)
\r
139 pdbcanvas.setAllchainsVisible(allchains.getState());
\r
141 else if (evt.getSource() == wire)
\r
143 pdbcanvas.wire = !pdbcanvas.wire;
\r
145 else if (evt.getSource() == depth)
\r
147 pdbcanvas.depthcue = !pdbcanvas.depthcue;
\r
149 else if (evt.getSource() == zbuffer)
\r
151 pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
\r
153 pdbcanvas.redrawneeded = true;
\r
154 pdbcanvas.repaint();
\r
157 private void jbInit()
\r
160 setMenuBar(jMenuBar1);
\r
161 fileMenu.setLabel("File");
\r
162 coloursMenu.setLabel("Colours");
\r
163 mapping.setLabel("View Mapping");
\r
164 mapping.addActionListener(this);
\r
165 wire.setLabel("Wireframe");
\r
166 wire.addItemListener(this);
\r
167 depth.setState(true);
\r
168 depth.setLabel("Depthcue");
\r
169 depth.addItemListener(this);
\r
170 zbuffer.setState(true);
\r
171 zbuffer.setLabel("Z Buffering");
\r
172 zbuffer.addItemListener(this);
\r
173 charge.setLabel("Charge & Cysteine");
\r
174 charge.addActionListener(this);
\r
175 hydro.setLabel("Hydrophobicity");
\r
176 hydro.addActionListener(this);
\r
177 chain.setLabel("By Chain");
\r
178 chain.addActionListener(this);
\r
179 seqButton.setLabel("By Sequence");
\r
180 seqButton.addActionListener(this);
\r
181 allchains.setLabel("All Chains Visible");
\r
182 allchains.addItemListener(this);
\r
183 viewMenu.setLabel("View");
\r
184 zappo.setLabel("Zappo");
\r
185 zappo.addActionListener(this);
\r
186 taylor.setLabel("Taylor");
\r
187 taylor.addActionListener(this);
\r
188 helix.setLabel("Helix Propensity");
\r
189 helix.addActionListener(this);
\r
190 strand.setLabel("Strand Propensity");
\r
191 strand.addActionListener(this);
\r
192 turn.setLabel("Turn Propensity");
\r
193 turn.addActionListener(this);
\r
194 buried.setLabel("Buried Index");
\r
195 buried.addActionListener(this);
\r
196 user.setLabel("User Defined...");
\r
197 user.addActionListener(this);
\r
198 jMenuBar1.add(fileMenu);
\r
199 jMenuBar1.add(coloursMenu);
\r
200 jMenuBar1.add(viewMenu);
\r
201 fileMenu.add(mapping); ;
\r
203 coloursMenu.add(seqButton);
\r
204 coloursMenu.add(chain);
\r
205 coloursMenu.add(charge);
\r
206 coloursMenu.add(zappo);
\r
207 coloursMenu.add(taylor);
\r
208 coloursMenu.add(hydro);
\r
209 coloursMenu.add(helix);
\r
210 coloursMenu.add(strand);
\r
211 coloursMenu.add(turn);
\r
212 coloursMenu.add(buried);
\r
213 coloursMenu.add(user);
\r
214 viewMenu.add(wire);
\r
215 viewMenu.add(depth);
\r
216 viewMenu.add(zbuffer);
\r
217 viewMenu.add(allchains);
\r
218 allchains.setState(true);
\r
221 MenuBar jMenuBar1 = new MenuBar();
\r
222 Menu fileMenu = new Menu();
\r
223 Menu coloursMenu = new Menu();
\r
224 MenuItem mapping = new MenuItem();
\r
225 CheckboxGroup bg = new CheckboxGroup();
\r
226 CheckboxMenuItem wire = new CheckboxMenuItem();
\r
227 CheckboxMenuItem depth = new CheckboxMenuItem();
\r
228 CheckboxMenuItem zbuffer = new CheckboxMenuItem();
\r
230 MenuItem charge = new MenuItem();
\r
231 MenuItem hydro = new MenuItem();
\r
232 MenuItem chain = new MenuItem();
\r
233 MenuItem seqButton = new MenuItem();
\r
235 CheckboxMenuItem allchains = new CheckboxMenuItem();
\r
236 Menu viewMenu = new Menu();
\r
237 MenuItem turn = new MenuItem();
\r
238 MenuItem strand = new MenuItem();
\r
239 MenuItem helix = new MenuItem();
\r
240 MenuItem taylor = new MenuItem();
\r
241 MenuItem zappo = new MenuItem();
\r
242 MenuItem buried = new MenuItem();
\r
243 MenuItem user = new MenuItem();
\r
246 //End StructureListener
\r
247 ////////////////////////////
\r