Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewChimeraXBindingModel	37	13	9	0.00%	Show methods

Class JalviewChimeraXBindingModel

Class JalviewChimeraXBindingModel	Line # 37	Total Statements 13	Complexity 9	TOTAL Coverage 0.00%
JalviewChimeraXBindingModel(ChimeraViewFrame,StructureSelectionManager,PDBEntry[],SequenceI[][],DataSourceType)   JalviewChimeraXBindingModel(ChimeraViewFrame,StructureSelectionManager,PDBEntry[],SequenceI[][],DataSourceType)	4141	2.02	1.01	0.0 0.00%
getChimeraPaths() : List<String>   getChimeraPaths() : List<String>	4949	1.01	1.01	0.0 0.00%
addChimeraModel(PDBEntry,List<ChimeraModel>) : void   addChimeraModel(PDBEntry,List<ChimeraModel>) : void	5555	4.04	1.01	0.0 0.00%
getCommandFileExtension() : String   getCommandFileExtension() : String	7575	1.01	1.01	0.0 0.00%
getSessionFileExtension() : String   getSessionFileExtension() : String	8787	1.01	1.01	0.0 0.00%
getHelpURL() : String   getHelpURL() : String	9393	1.01	1.01	0.0 0.00%
getViewerType() : ViewerType   getViewerType() : ViewerType	9999	1.01	1.01	0.0 0.00%
getModelId(int,String) : String   getModelId(int,String) : String	105105	1.01	1.01	0.0 0.00%
parseAtomSpec(String) : AtomSpec   parseAtomSpec(String) : AtomSpec	118118	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 java.util.List;
24
25		import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
26		import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
27		import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
28		import jalview.datamodel.PDBEntry;
29		import jalview.datamodel.SequenceI;
30		import jalview.ext.rbvi.chimera.ChimeraXCommands;
31		import jalview.gui.StructureViewer.ViewerType;
32		import jalview.io.DataSourceType;
33		import jalview.structure.AtomSpec;
34		import jalview.structure.StructureCommand;
35		import jalview.structure.StructureSelectionManager;
36
		0% Uncovered Elements: 22 (22) Complexity: 9 Complexity Density: 0.69
37		public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
38		{
39		public static final String CHIMERAX_SESSION_EXTENSION = ".cxs";
40
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
41	0	public JalviewChimeraXBindingModel(ChimeraViewFrame chimeraViewFrame,...
42		StructureSelectionManager ssm, PDBEntry[] pdbentry,
43		SequenceI[][] sequenceIs, DataSourceType protocol)
44		{
45	0	super(chimeraViewFrame, ssm, pdbentry, sequenceIs, protocol);
46	0	setStructureCommands(new ChimeraXCommands());
47		}
48
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
49	0	@Override...
50		protected List<String> getChimeraPaths()
51		{
52	0	return StructureManager.getChimeraPaths(true);
53		}
54
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
55	0	@Override...
56		protected void addChimeraModel(PDBEntry pe,
57		List<ChimeraModel> modelsToMap)
58		{
59		/*
60		* ChimeraX hack: force chimera model name to pdbId here
61		*/
62	0	int modelNumber = chimeraMaps.size() + 1;
63	0	String command = "setattr #" + modelNumber + " models name "
64		+ pe.getId();
65	0	executeCommand(new StructureCommand(command), false);
66	0	modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
67		modelNumber, 0));
68		}
69
70		/**
71		* {@inheritDoc}
72		*
73		* @return
74		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
75	0	@Override...
76		protected String getCommandFileExtension()
77		{
78	0	return ".cxc";
79		}
80
81		/**
82		* Returns the file extension to use for a saved viewer session file (.cxs)
83		*
84		* @return
85		* @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#sesformat
86		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
87	0	@Override...
88		public String getSessionFileExtension()
89		{
90	0	return CHIMERAX_SESSION_EXTENSION;
91		}
92
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
93	0	@Override...
94		public String getHelpURL()
95		{
96	0	return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
97		}
98
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
99	0	@Override...
100		protected ViewerType getViewerType()
101		{
102	0	return ViewerType.CHIMERAX;
103		}
104
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
105	0	@Override...
106		protected String getModelId(int pdbfnum, String file)
107		{
108	0	return String.valueOf(pdbfnum + 1);
109		}
110
111		/**
112		* Returns a model of the structure positions described by the ChimeraX format
113		* atomspec
114		*
115		* @param atomSpec
116		* @return
117		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
118	0	@Override...
119		protected AtomSpec parseAtomSpec(String atomSpec)
120		{
121	0	return AtomSpec.fromChimeraXAtomspec(atomSpec);
122		}
123
124		}