Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewChimeraXBindingModel	17	13	9	0.00%	Show methods

Class JalviewChimeraXBindingModel

Class JalviewChimeraXBindingModel	Line # 17	Total Statements 13	Complexity 9	TOTAL Coverage 0.00%
JalviewChimeraXBindingModel(ChimeraViewFrame,StructureSelectionManager,PDBEntry[],SequenceI[][],DataSourceType)   JalviewChimeraXBindingModel(ChimeraViewFrame,StructureSelectionManager,PDBEntry[],SequenceI[][],DataSourceType)	2121	2.02	1.01	0.0 0.00%
getChimeraPaths() : List<String>   getChimeraPaths() : List<String>	2929	1.01	1.01	0.0 0.00%
addChimeraModel(PDBEntry,List<ChimeraModel>) : void   addChimeraModel(PDBEntry,List<ChimeraModel>) : void	3535	4.04	1.01	0.0 0.00%
getCommandFileExtension() : String   getCommandFileExtension() : String	5555	1.01	1.01	0.0 0.00%
getSessionFileExtension() : String   getSessionFileExtension() : String	6767	1.01	1.01	0.0 0.00%
getHelpURL() : String   getHelpURL() : String	7373	1.01	1.01	0.0 0.00%
getViewerType() : ViewerType   getViewerType() : ViewerType	7979	1.01	1.01	0.0 0.00%
getModelId(int,String) : String   getModelId(int,String) : String	8585	1.01	1.01	0.0 0.00%
parseAtomSpec(String) : AtomSpec   parseAtomSpec(String) : AtomSpec	9696	1.01	1.01	0.0 0.00%

 

Contributing tests

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1		package jalview.gui;
2
3		import java.util.List;
4
5		import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
6		import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
7		import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
8		import jalview.datamodel.PDBEntry;
9		import jalview.datamodel.SequenceI;
10		import jalview.ext.rbvi.chimera.ChimeraXCommands;
11		import jalview.gui.StructureViewer.ViewerType;
12		import jalview.io.DataSourceType;
13		import jalview.structure.AtomSpec;
14		import jalview.structure.StructureCommand;
15		import jalview.structure.StructureSelectionManager;
16
		0% Uncovered Elements: 22 (22) Complexity: 9 Complexity Density: 0.69
17		public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
18		{
19		public static final String CHIMERAX_SESSION_EXTENSION = ".cxs";
20
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
21	0	public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,...
22		StructureSelectionManager ssm, PDBEntry[] pdbentry,
23		SequenceI[][] sequenceIs, DataSourceType protocol)
24		{
25	0	super(chimeraViewFrame, ssm, pdbentry, sequenceIs, protocol);
26	0	setStructureCommands(new ChimeraXCommands());
27		}
28
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
29	0	@Override...
30		protected List<String> getChimeraPaths()
31		{
32	0	return StructureManager.getChimeraPaths(true);
33		}
34
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
35	0	@Override...
36		protected void addChimeraModel(PDBEntry pe,
37		List<ChimeraModel> modelsToMap)
38		{
39		/*
40		* ChimeraX hack: force chimera model name to pdbId here
41		*/
42	0	int modelNumber = chimeraMaps.size() + 1;
43	0	String command = "setattr #" + modelNumber + " models name "
44		+ pe.getId();
45	0	executeCommand(new StructureCommand(command), false);
46	0	modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
47		modelNumber, 0));
48		}
49
50		/**
51		* {@inheritDoc}
52		*
53		* @return
54		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
55	0	@Override...
56		protected String getCommandFileExtension()
57		{
58	0	return ".cxc";
59		}
60
61		/**
62		* Returns the file extension to use for a saved viewer session file (.cxs)
63		*
64		* @return
65		* @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#sesformat
66		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	@Override...
68		public String getSessionFileExtension()
69		{
70	0	return CHIMERAX_SESSION_EXTENSION;
71		}
72
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
73	0	@Override...
74		public String getHelpURL()
75		{
76	0	return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
77		}
78
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
79	0	@Override...
80		protected ViewerType getViewerType()
81		{
82	0	return ViewerType.CHIMERAX;
83		}
84
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
85	0	@Override...
86		protected String getModelId(int pdbfnum, String file)
87		{
88	0	return String.valueOf(pdbfnum + 1);
89		}
90
91		/**
92		* Returns a model of the structure positions described by the ChimeraX format atomspec
93		* @param atomSpec
94		* @return
95		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
96	0	protected AtomSpec parseAtomSpec(String atomSpec)...
97		{
98	0	return AtomSpec.fromChimeraXAtomspec(atomSpec);
99		}
100
101		}