Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
JalviewChimeraBindingModel	33	22	18	46	0.00%	Show methods

Class JalviewChimeraBindingModel

Class JalviewChimeraBindingModel	Line # 33	Total Statements 22	Complexity 18	Uncovered Elements 46	TOTAL Coverage 0.00%
JalviewChimeraBindingModel(ChimeraViewFrame,StructureSelectionManager,PDBEntry[],SequenceI[][],DataSourceType)   JalviewChimeraBindingModel(ChimeraViewFrame,StructureSelectionManager,PDBEntry[],SequenceI[][],DataSourceType)	3737	2.02	1.01	2.02	0.0 0.00%
getFeatureRenderer(AlignmentViewPanel) : FeatureRenderer   getFeatureRenderer(AlignmentViewPanel) : FeatureRenderer	4545	4.04	3.03	8.08	0.0 0.00%
getSequenceRenderer(AlignmentViewPanel) : jalview.api.SequenceRenderer   getSequenceRenderer(AlignmentViewPanel) : jalview.api.SequenceRenderer	5858	1.01	1.01	1.01	0.0 0.00%
run() : void   run() : void	7070	2.02	1.01	2.02	0.0 0.00%
refreshGUI() : void   refreshGUI() : void	6565	1.01	1.01	1.01	0.0 0.00%
updateColours(Object) : void   updateColours(Object) : void	7979	5.05	3.03	9.09	0.0 0.00%
releaseReferences(Object) : void   releaseReferences(Object) : void	9494	0.00	1.01	0.00	-1.0 -1.0 -
releaseUIResources() : void   releaseUIResources() : void	9999	0.00	1.01	0.00	-1.0 -1.0 -
refreshPdbEntries() : void   refreshPdbEntries() : void	104104	0.00	1.01	0.00	-1.0 -1.0 -
run() : void   run() : void	121121	4.04	2.02	6.06	0.0 0.00%
sendAsynchronousCommand(String,String) : void   sendAsynchronousCommand(String,String) : void	113113	2.02	2.02	4.04	0.0 0.00%
getViewer() : JalviewStructureDisplayI   getViewer() : JalviewStructureDisplayI	138138	1.01	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.gui;
22
23		import jalview.api.AlignmentViewPanel;
24		import jalview.api.structures.JalviewStructureDisplayI;
25		import jalview.datamodel.PDBEntry;
26		import jalview.datamodel.SequenceI;
27		import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
28		import jalview.io.DataSourceType;
29		import jalview.structure.StructureSelectionManager;
30
31		import javax.swing.SwingUtilities;
32
		0% Uncovered Elements: 46 (46) Complexity: 18 Complexity Density: 0.82
33		public class JalviewChimeraBindingModel extends JalviewChimeraBinding
34		{
35		private ChimeraViewFrame cvf;
36
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
37	0	public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,...
38		StructureSelectionManager ssm, PDBEntry[] pdbentry,
39		SequenceI[][] sequenceIs, DataSourceType protocol)
40		{
41	0	super(ssm, pdbentry, sequenceIs, protocol);
42	0	cvf = chimeraViewFrame;
43		}
44
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
45	0	@Override...
46		public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
47		{
48	0	AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
49		: (AlignmentPanel) alignment;
50	0	if (ap.av.isShowSequenceFeatures())
51		{
52	0	return ap.getSeqPanel().seqCanvas.fr;
53		}
54
55	0	return null;
56		}
57
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
58	0	@Override...
59		public jalview.api.SequenceRenderer getSequenceRenderer(
60		AlignmentViewPanel alignment)
61		{
62	0	return new SequenceRenderer(((AlignmentPanel) alignment).av);
63		}
64
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
65	0	@Override...
66		public void refreshGUI()
67		{
68	0	javax.swing.SwingUtilities.invokeLater(new Runnable()
69		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
70	0	@Override...
71		public void run()
72		{
73	0	cvf.updateTitleAndMenus();
74	0	cvf.revalidate();
75		}
76		});
77		}
78
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
79	0	@Override...
80		public void updateColours(Object source)
81		{
82	0	AlignmentPanel ap = (AlignmentPanel) source;
83		// ignore events from panels not used to colour this view
84	0	if (!cvf.isUsedforcolourby(ap))
85		{
86	0	return;
87		}
88	0	if (!isLoadingFromArchive())
89		{
90	0	colourBySequence(ap);
91		}
92		}
93
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
94	0	@Override...
95		public void releaseReferences(Object svl)
96		{
97		}
98
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
99	0	@Override...
100		protected void releaseUIResources()
101		{
102		}
103
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
104	0	@Override...
105		public void refreshPdbEntries()
106		{
107		}
108
109		/**
110		* Send an asynchronous command to Chimera, in a new thread, optionally with
111		* an 'in progress' message in a progress bar somewhere
112		*/
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
113	0	@Override...
114		protected void sendAsynchronousCommand(final String command,
115		final String progressMsg)
116		{
117	0	final long handle = progressMsg == null ? 0
118		: cvf.startProgressBar(progressMsg);
119	0	SwingUtilities.invokeLater(new Runnable()
120		{
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
121	0	@Override...
122		public void run()
123		{
124	0	try
125		{
126	0	sendChimeraCommand(command, false);
127		} finally
128		{
129	0	if (progressMsg != null)
130		{
131	0	cvf.stopProgressBar(null, handle);
132		}
133		}
134		}
135		});
136		}
137
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
138	0	@Override...
139		public JalviewStructureDisplayI getViewer()
140		{
141	0	return cvf;
142		}
143		}