Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AppletPDBViewer	49	111	21	147	0.00%	Show methods

Class AppletPDBViewer

Class AppletPDBViewer	Line # 49	Total Statements 111	Complexity 21	Uncovered Elements 147	TOTAL Coverage 0.00%
AppletPDBViewer(PDBEntry,SequenceI[],String[],AlignmentPanel,DataSourceType)   AppletPDBViewer(PDBEntry,SequenceI[],String[],AlignmentPanel,DataSourceType)	5454	8.08	2.02	8.08	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	7777	34.034	13.013	58.058	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	148148	10.010	5.05	18.018	0.0 0.00%
jbInit() : void   jbInit() : void	171171	59.059	1.01	59.059	0.0 0.00%

 

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1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
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.
11		*
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.
16		*
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.
20		*/
21		package mc_view;
22
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;
36
37		import java.awt.BorderLayout;
38		import java.awt.CheckboxGroup;
39		import java.awt.CheckboxMenuItem;
40		import java.awt.Frame;
41		import java.awt.Menu;
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;
48
		0% Uncovered Elements: 147 (147) Complexity: 21 Complexity Density: 0.19
49		public class AppletPDBViewer extends EmbmenuFrame
50		implements ActionListener, ItemListener
51		{
52		AppletPDBCanvas pdbcanvas;
53
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.25
54	0	public AppletPDBViewer(PDBEntry pdbentry, SequenceI[] seq,...
55		String[] chains, AlignmentPanel ap, DataSourceType protocol)
56		{
57	0	try
58		{
59	0	jbInit();
60		} catch (Exception ex)
61		{
62	0	ex.printStackTrace();
63		}
64
65	0	pdbcanvas = new AppletPDBCanvas(pdbentry, seq, chains, ap, protocol);
66
67	0	embedMenuIfNeeded(pdbcanvas);
68	0	add(pdbcanvas, BorderLayout.CENTER);
69
70	0	StringBuffer title = new StringBuffer(
71		seq[0].getName() + ":" + pdbcanvas.pdbentry.getFile());
72
73	0	jalview.bin.JalviewLite.addFrame(this, title.toString(), 400, 400);
74
75		}
76
		0% Uncovered Elements: 58 (58) Complexity: 13 Complexity Density: 0.38
77	0	@Override...
78		public void actionPerformed(ActionEvent evt)
79		{
80	0	if (evt.getSource() == mapping)
81		{
82	0	jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer(
83		false, null);
84	0	Frame frame = new Frame();
85	0	frame.add(cap);
86	0	jalview.bin.JalviewLite.addFrame(frame,
87		MessageManager.getString("label.pdb_sequence_mapping"), 500,
88		600);
89	0	cap.setText(pdbcanvas.mappingDetails.toString());
90
91		}
92	0	else if (evt.getSource() == charge)
93		{
94	0	pdbcanvas.bysequence = false;
95	0	pdbcanvas.pdb.setChargeColours();
96		}
97
98	0	else if (evt.getSource() == chain)
99		{
100	0	pdbcanvas.bysequence = false;
101	0	pdbcanvas.pdb.setChainColours();
102		}
103	0	else if (evt.getSource() == seqButton)
104		{
105	0	pdbcanvas.bysequence = true;
106	0	pdbcanvas.colourBySequence();
107
108		}
109	0	else if (evt.getSource() == zappo)
110		{
111	0	pdbcanvas.setColours(new ZappoColourScheme());
112		}
113	0	else if (evt.getSource() == taylor)
114		{
115	0	pdbcanvas.setColours(new TaylorColourScheme());
116		}
117	0	else if (evt.getSource() == hydro)
118		{
119	0	pdbcanvas.setColours(new HydrophobicColourScheme());
120		}
121	0	else if (evt.getSource() == helix)
122		{
123	0	pdbcanvas.setColours(new HelixColourScheme());
124		}
125	0	else if (evt.getSource() == strand)
126		{
127	0	pdbcanvas.setColours(new StrandColourScheme());
128		}
129	0	else if (evt.getSource() == turn)
130		{
131	0	pdbcanvas.setColours(new TurnColourScheme());
132		}
133	0	else if (evt.getSource() == buried)
134		{
135	0	pdbcanvas.setColours(new BuriedColourScheme());
136		}
137	0	else if (evt.getSource() == user)
138		{
139	0	pdbcanvas.bysequence = false;
140	0	new jalview.appletgui.UserDefinedColours(pdbcanvas);
141		}
142
143	0	pdbcanvas.redrawneeded = true;
144	0	pdbcanvas.repaint();
145
146		}
147
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.5
148	0	@Override...
149		public void itemStateChanged(ItemEvent evt)
150		{
151	0	if (evt.getSource() == allchains)
152		{
153	0	pdbcanvas.setAllchainsVisible(allchains.getState());
154		}
155	0	else if (evt.getSource() == wire)
156		{
157	0	pdbcanvas.wire = !pdbcanvas.wire;
158		}
159	0	else if (evt.getSource() == depth)
160		{
161	0	pdbcanvas.depthcue = !pdbcanvas.depthcue;
162		}
163	0	else if (evt.getSource() == zbuffer)
164		{
165	0	pdbcanvas.zbuffer = !pdbcanvas.zbuffer;
166		}
167	0	pdbcanvas.redrawneeded = true;
168	0	pdbcanvas.repaint();
169		}
170
		0% Uncovered Elements: 59 (59) Complexity: 1 Complexity Density: 0.02
171	0	private void jbInit() throws Exception...
172		{
173	0	setMenuBar(jMenuBar1);
174	0	fileMenu.setLabel(MessageManager.getString("action.file"));
175	0	coloursMenu.setLabel(MessageManager.getString("label.colours"));
176	0	mapping.setLabel(MessageManager.getString("label.view_mapping"));
177	0	mapping.addActionListener(this);
178	0	wire.setLabel(MessageManager.getString("label.wireframe"));
179	0	wire.addItemListener(this);
180	0	depth.setState(true);
181	0	depth.setLabel(MessageManager.getString("label.depthcue"));
182	0	depth.addItemListener(this);
183	0	zbuffer.setState(true);
184	0	zbuffer.setLabel(MessageManager.getString("label.z_buffering"));
185	0	zbuffer.addItemListener(this);
186	0	charge.setLabel(MessageManager.getString("label.charge_cysteine"));
187	0	charge.addActionListener(this);
188	0	hydro.setLabel(
189		MessageManager.getString("label.colourScheme_hydrophobic"));
190	0	hydro.addActionListener(this);
191	0	chain.setLabel(MessageManager.getString("action.by_chain"));
192	0	chain.addActionListener(this);
193	0	seqButton.setLabel(MessageManager.getString("action.by_sequence"));
194	0	seqButton.addActionListener(this);
195	0	allchains
196		.setLabel(MessageManager.getString("label.all_chains_visible"));
197	0	allchains.addItemListener(this);
198	0	viewMenu.setLabel(MessageManager.getString("action.view"));
199	0	zappo.setLabel(MessageManager.getString("label.colourScheme_zappo"));
200	0	zappo.addActionListener(this);
201	0	taylor.setLabel(MessageManager.getString("label.colourScheme_taylor"));
202	0	taylor.addActionListener(this);
203	0	helix.setLabel(MessageManager
204		.getString("label.colourScheme_helix_propensity"));
205	0	helix.addActionListener(this);
206	0	strand.setLabel(MessageManager
207		.getString("label.colourScheme_strand_propensity"));
208	0	strand.addActionListener(this);
209	0	turn.setLabel(
210		MessageManager.getString("label.colourScheme_turn_propensity"));
211	0	turn.addActionListener(this);
212	0	buried.setLabel(
213		MessageManager.getString("label.colourScheme_buried_index"));
214	0	buried.addActionListener(this);
215	0	user.setLabel(MessageManager.getString("action.user_defined"));
216	0	user.addActionListener(this);
217	0	jMenuBar1.add(fileMenu);
218	0	jMenuBar1.add(coloursMenu);
219	0	jMenuBar1.add(viewMenu);
220	0	fileMenu.add(mapping);
221	0	;
222
223	0	coloursMenu.add(seqButton);
224	0	coloursMenu.add(chain);
225	0	coloursMenu.add(charge);
226	0	coloursMenu.add(zappo);
227	0	coloursMenu.add(taylor);
228	0	coloursMenu.add(hydro);
229	0	coloursMenu.add(helix);
230	0	coloursMenu.add(strand);
231	0	coloursMenu.add(turn);
232	0	coloursMenu.add(buried);
233	0	coloursMenu.add(user);
234	0	viewMenu.add(wire);
235	0	viewMenu.add(depth);
236	0	viewMenu.add(zbuffer);
237	0	viewMenu.add(allchains);
238	0	allchains.setState(true);
239		}
240
241		MenuBar jMenuBar1 = new MenuBar();
242
243		Menu fileMenu = new Menu();
244
245		Menu coloursMenu = new Menu();
246
247		MenuItem mapping = new MenuItem();
248
249		CheckboxGroup bg = new CheckboxGroup();
250
251		CheckboxMenuItem wire = new CheckboxMenuItem();
252
253		CheckboxMenuItem depth = new CheckboxMenuItem();
254
255		CheckboxMenuItem zbuffer = new CheckboxMenuItem();
256
257		MenuItem charge = new MenuItem();
258
259		MenuItem hydro = new MenuItem();
260
261		MenuItem chain = new MenuItem();
262
263		MenuItem seqButton = new MenuItem();
264
265		CheckboxMenuItem allchains = new CheckboxMenuItem();
266
267		Menu viewMenu = new Menu();
268
269		MenuItem turn = new MenuItem();
270
271		MenuItem strand = new MenuItem();
272
273		MenuItem helix = new MenuItem();
274
275		MenuItem taylor = new MenuItem();
276
277		MenuItem zappo = new MenuItem();
278
279		MenuItem buried = new MenuItem();
280
281		MenuItem user = new MenuItem();
282
283		// End StructureListener
284		// //////////////////////////
285
286		}