Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AppletJmolBinding	37	22	23	0.00%	Show methods

Class AppletJmolBinding

Class AppletJmolBinding	Line # 37	Total Statements 22	Complexity 23	TOTAL Coverage 0.00%
AppletJmolBinding(AppletJmol,StructureSelectionManager,PDBEntry[],SequenceI[][],DataSourceType)   AppletJmolBinding(AppletJmol,StructureSelectionManager,PDBEntry[],SequenceI[][],DataSourceType)	4545	2.02	1.01	0.0 0.00%
getSequenceRenderer(AlignmentViewPanel) : jalview.api.SequenceRenderer   getSequenceRenderer(AlignmentViewPanel) : jalview.api.SequenceRenderer	5353	1.01	1.01	0.0 0.00%
sendConsoleEcho(String) : void   sendConsoleEcho(String) : void	6060	3.03	2.02	0.0 0.00%
sendConsoleMessage(String) : void   sendConsoleMessage(String) : void	7171	2.02	4.04	0.0 0.00%
showUrl(String,String) : void   showUrl(String,String) : void	8181	1.01	1.01	0.0 0.00%
refreshGUI() : void   refreshGUI() : void	8888	1.01	1.01	0.0 0.00%
updateColours(Object) : void   updateColours(Object) : void	9494	2.02	1.01	0.0 0.00%
showUrl(String) : void   showUrl(String) : void	101101	2.02	2.02	0.0 0.00%
newJmolPopup(boolean,String,boolean) : void   newJmolPopup(boolean,String,boolean) : void	113113	0.00	1.01	-1.0 -1.0 -
notifyScriptTermination(String,int) : void   notifyScriptTermination(String,int) : void	120120	0.00	1.01	-1.0 -1.0 -
selectionChanged(BS) : void   selectionChanged(BS) : void	126126	0.00	1.01	-1.0 -1.0 -
refreshPdbEntries() : void   refreshPdbEntries() : void	133133	0.00	1.01	-1.0 -1.0 -
showConsole(boolean) : void   showConsole(boolean) : void	139139	1.01	1.01	0.0 0.00%
createJmolConsole(Container,String) : JmolAppConsoleInterface   createJmolConsole(Container,String) : JmolAppConsoleInterface	145145	3.03	1.01	0.0 0.00%
releaseUIResources() : void   releaseUIResources() : void	154154	2.02	1.01	0.0 0.00%
releaseReferences(Object) : void   releaseReferences(Object) : void	161161	0.00	1.01	-1.0 -1.0 -
resizeInnerPanel(String) : int[]   resizeInnerPanel(String) : int[]	166166	1.01	1.01	0.0 0.00%
getJSpecViewProperty(String) : Map<String, Object>   getJSpecViewProperty(String) : Map<String, Object>	172172	1.01	1.01	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 jalview.appletgui;
22
23		import jalview.api.AlignmentViewPanel;
24		import jalview.datamodel.PDBEntry;
25		import jalview.datamodel.SequenceI;
26		import jalview.ext.jmol.JalviewJmolBinding;
27		import jalview.io.DataSourceType;
28		import jalview.structure.StructureSelectionManager;
29
30		import java.awt.Container;
31		import java.util.Map;
32
33		import org.jmol.api.JmolAppConsoleInterface;
34		import org.jmol.console.AppletConsole;
35		import javajs.util.BS;
36
		0% Uncovered Elements: 44 (44) Complexity: 23 Complexity Density: 1.05
37		class AppletJmolBinding extends JalviewJmolBinding
38		{
39
40		/**
41		* Window that contains the bound Jmol instance
42		*/
43		private AppletJmol appletJmolBinding;
44
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
45	0	public AppletJmolBinding(AppletJmol appletJmol,...
46		StructureSelectionManager sSm, PDBEntry[] pdbentry,
47		SequenceI[][] seq, DataSourceType protocol)
48		{
49	0	super(sSm, pdbentry, seq, protocol);
50	0	appletJmolBinding = appletJmol;
51		}
52
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
53	0	@Override...
54		public jalview.api.SequenceRenderer getSequenceRenderer(
55		AlignmentViewPanel alignment)
56		{
57	0	return new SequenceRenderer(((AlignmentPanel) alignment).av);
58		}
59
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
60	0	@Override...
61		public void sendConsoleEcho(String strEcho)
62		{
63	0	if (appletJmolBinding.scriptWindow == null)
64		{
65	0	appletJmolBinding.showConsole(true);
66		}
67
68	0	appletJmolBinding.addToHistory(strEcho);
69		}
70
		0% Uncovered Elements: 4 (4) Complexity: 4 Complexity Density: 2
71	0	@Override...
72		public void sendConsoleMessage(String strStatus)
73		{
74	0	if (appletJmolBinding.history != null && strStatus != null
75		&& !strStatus.equals("Script completed"))
76		{
77	0	appletJmolBinding.addToHistory(strStatus);
78		}
79		}
80
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
81	0	@Override...
82		public void showUrl(String url, String target)
83		{
84	0	appletJmolBinding.ap.alignFrame.showURL(url, target);
85
86		}
87
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
88	0	@Override...
89		public void refreshGUI()
90		{
91	0	appletJmolBinding.updateTitleAndMenus();
92		}
93
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
94	0	@Override...
95		public void updateColours(Object source)
96		{
97	0	AlignmentPanel ap = (AlignmentPanel) source;
98	0	colourBySequence(ap);
99		}
100
		0% Uncovered Elements: 2 (2) Complexity: 2 Complexity Density: 1
101	0	@Override...
102		public void showUrl(String url)
103		{
104	0	try
105		{
106	0	appletJmolBinding.ap.av.applet.getAppletContext()
107		.showDocument(new java.net.URL(url), "jmol");
108		} catch (java.net.MalformedURLException ex)
109		{
110		}
111		}
112
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
113	0	public void newJmolPopup(boolean translateLocale, String menuName,...
114		boolean asPopup)
115		{
116		// jmolpopup = new JmolAwtPopup(); // is this used?
117		// jmolpopup.jpiInitialize((viewer), menuName);
118		}
119
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
120	0	@Override...
121		public void notifyScriptTermination(String strStatus, int msWalltime)
122		{
123		// do nothing.
124		}
125
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
126	0	@Override...
127		public void selectionChanged(BS arg0)
128		{
129		// TODO Auto-generated method stub
130
131		}
132
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
133	0	@Override...
134		public void refreshPdbEntries()
135		{
136		// noop
137		}
138
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
139	0	@Override...
140		public void showConsole(boolean show)
141		{
142	0	appletJmolBinding.showConsole(show);
143		}
144
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
145	0	@Override...
146		protected JmolAppConsoleInterface createJmolConsole(
147		Container consolePanel, String buttonsToShow)
148		{
149	0	JmolAppConsoleInterface appc = new AppletConsole();
150	0	appc.start(jmolViewer);
151	0	return appc;
152		}
153
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
154	0	@Override...
155		protected void releaseUIResources()
156		{
157	0	appletJmolBinding = null;
158	0	closeConsole();
159		}
160
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
161	0	@Override...
162		public void releaseReferences(Object svl)
163		{
164		}
165
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
166	0	@Override...
167		public int[] resizeInnerPanel(String data)
168		{
169	0	return null;
170		}
171
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
172	0	@Override...
173		public Map<String, Object> getJSpecViewProperty(String arg0)
174		{
175	0	return null;
176		}
177		}