Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ExtJmol	46	28	21	0.00%	Show methods

Class ExtJmol

Class ExtJmol	Line # 46	Total Statements 28	Complexity 21	TOTAL Coverage 0.00%
ExtJmol(AlignFrame,PDBEntry[],SequenceI[][],DataSourceType)   ExtJmol(AlignFrame,PDBEntry[],SequenceI[][],DataSourceType)	5151	1.01	1.01	0.0 0.00%
ExtJmol(Viewer,AlignmentPanel,SequenceI[][])   ExtJmol(Viewer,AlignmentPanel,SequenceI[][])	5858	3.03	1.01	0.0 0.00%
updateColours(Object) : void   updateColours(Object) : void	6666	0.00	1.01	-1.0 -1.0 -
showUrl(String) : void   showUrl(String) : void	7171	1.01	1.01	0.0 0.00%
getSequenceRenderer(AlignmentViewPanel) : SequenceRenderer   getSequenceRenderer(AlignmentViewPanel) : SequenceRenderer	7777	1.01	1.01	0.0 0.00%
notifyScriptTermination(String,int) : void   notifyScriptTermination(String,int) : void	8383	0.00	1.01	-1.0 -1.0 -
sendConsoleEcho(String) : void   sendConsoleEcho(String) : void	8989	0.00	1.01	-1.0 -1.0 -
sendConsoleMessage(String) : void   sendConsoleMessage(String) : void	9595	0.00	1.01	-1.0 -1.0 -
showUrl(String,String) : void   showUrl(String,String) : void	101101	1.01	1.01	0.0 0.00%
refreshGUI() : void   refreshGUI() : void	107107	0.00	1.01	-1.0 -1.0 -
selectionChanged(BS) : void   selectionChanged(BS) : void	113113	1.01	1.01	0.0 0.00%
refreshPdbEntries() : void   refreshPdbEntries() : void	119119	15.015	6.06	0.0 0.00%
showConsole(boolean) : void   showConsole(boolean) : void	152152	1.01	1.01	0.0 0.00%
createJmolConsole(Container,String) : JmolAppConsoleInterface   createJmolConsole(Container,String) : JmolAppConsoleInterface	162162	1.01	1.01	0.0 0.00%
releaseUIResources() : void   releaseUIResources() : void	169169	2.02	1.01	0.0 0.00%
getJSpecViewProperty(String) : Map<String, Object>   getJSpecViewProperty(String) : Map<String, Object>	177177	1.01	1.01	0.0 0.00%

 

Contributing tests

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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.api.SequenceRenderer;
25		import jalview.datamodel.PDBEntry;
26		import jalview.datamodel.SequenceI;
27		import jalview.ext.jmol.JalviewJmolBinding;
28		import jalview.io.DataSourceType;
29
30		import java.awt.Container;
31		import java.util.ArrayList;
32		import java.util.List;
33		import java.util.Map;
34		import java.util.Vector;
35
36		import org.jmol.api.JmolAppConsoleInterface;
37		import javajs.util.BS;
38		import org.jmol.viewer.Viewer;
39
40		/**
41		* bind an alignment view to an external Jmol instance.
42		*
43		* @author JimP
44		*
45		*/
		0% Uncovered Elements: 54 (54) Complexity: 21 Complexity Density: 0.75
46		public class ExtJmol extends JalviewJmolBinding
47		{
48
49		private AlignmentPanel ap;
50
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
51	0	protected ExtJmol(AlignFrame alframe, PDBEntry[] pdbentry,...
52		SequenceI[][] seq, DataSourceType protocol)
53		{
54	0	super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
55		protocol);
56		}
57
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
58	0	public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,...
59		SequenceI[][] seqs)
60		{
61	0	super(alignPanel.getStructureSelectionManager(), seqs, viewer);
62	0	ap = alignPanel;
63	0	notifyFileLoaded(null, null, null, null, 0);
64		}
65
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
66	0	@Override...
67		public void updateColours(Object source)
68		{
69		}
70
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
71	0	@Override...
72		public void showUrl(String arg0)
73		{
74	0	showUrl(arg0, "jmol");
75		}
76
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
77	0	@Override...
78		public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
79		{
80	0	return ((AlignmentPanel) alignment).getSequenceRenderer();
81		}
82
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
83	0	@Override...
84		public void notifyScriptTermination(String strStatus, int msWalltime)
85		{
86		// ignore
87		}
88
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
89	0	@Override...
90		public void sendConsoleEcho(String strEcho)
91		{
92		// ignore
93		}
94
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
95	0	@Override...
96		public void sendConsoleMessage(String strStatus)
97		{
98		// ignore
99		}
100
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
101	0	@Override...
102		public void showUrl(String url, String target)
103		{
104	0	ap.alignFrame.showURL(url, target);
105		}
106
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
107	0	@Override...
108		public void refreshGUI()
109		{
110		// ignore
111		}
112
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
113	0	@Override...
114		public void selectionChanged(BS arg0)
115		{
116	0	System.out.println(arg0);
117		}
118
		0% Uncovered Elements: 25 (25) Complexity: 6 Complexity Density: 0.4
119	0	@Override...
120		public void refreshPdbEntries()
121		{
122	0	List<PDBEntry> pdbe = new ArrayList<>();
123	0	List<String> fileids = new ArrayList<>();
124	0	SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
125	0	for (int s = 0; s < sq.length; s++)
126		{
127	0	Vector<PDBEntry> pdbids = sq[s].getAllPDBEntries();
128	0	if (pdbids != null)
129		{
130	0	for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
131		{
132	0	PDBEntry pentry = pdbids.elementAt(pe);
133	0	if (!fileids.contains(pentry.getId()))
134		{
135	0	pdbe.add(pentry);
136		}
137		else
138		{
139	0	fileids.add(pentry.getId());
140		}
141		}
142		}
143		}
144	0	PDBEntry[] newEntries = new PDBEntry[pdbe.size()];
145	0	for (int pe = 0; pe < pdbe.size(); pe++)
146		{
147	0	newEntries[pe] = pdbe.get(pe);
148		}
149	0	setPdbentry(newEntries);
150		}
151
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
152	0	@Override...
153		public void showConsole(boolean show)
154		{
155		// This never gets called because we haven't overriden the associated Jmol's
156		// console
157	0	System.err.println(
158		"WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
159		+ show);
160		}
161
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
162	0	@Override...
163		protected JmolAppConsoleInterface createJmolConsole(
164		Container consolePanel, String buttonsToShow)
165		{
166	0	return null;
167		}
168
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
169	0	@Override...
170		protected void releaseUIResources()
171		{
172	0	ap = null;
173	0	closeConsole();
174
175		}
176
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
177	0	@Override...
178		public Map<String, Object> getJSpecViewProperty(String arg0)
179		{
180	0	return null;
181		}
182		}