Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ChimeraXCommands	36	57	22	0.00%	Show methods

Class ChimeraXCommands

Class ChimeraXCommands	Line # 36	Total Statements 57	Complexity 22	TOTAL Coverage 0.00%
colourByCharge() : List<StructureCommandI>   colourByCharge() : List<StructureCommandI>	6767	1.01	1.01	0.0 0.00%
getResidueSpec(String) : String   getResidueSpec(String) : String	7373	1.01	1.01	0.0 0.00%
colourResidues(String,Color) : StructureCommandI   colourResidues(String,Color) : StructureCommandI	7979	2.02	1.01	0.0 0.00%
focusView() : StructureCommandI   focusView() : StructureCommandI	8888	1.01	1.01	0.0 0.00%
getModelStartNo() : int   getModelStartNo() : int	9999	1.01	1.01	0.0 0.00%
setAttribute(String,String,AtomSpecModel) : StructureCommandI   setAttribute(String,String,AtomSpecModel) : StructureCommandI	118118	5.05	1.01	0.0 0.00%
openCommandFile(String) : StructureCommandI   openCommandFile(String) : StructureCommandI	131131	1.01	1.01	0.0 0.00%
saveSession(String) : StructureCommandI   saveSession(String) : StructureCommandI	138138	1.01	1.01	0.0 0.00%
getAtomSpec(AtomSpecModel,AtomSpecType) : String   getAtomSpec(AtomSpecModel,AtomSpecType) : String	157157	12.012	4.04	0.0 0.00%
appendModel(StringBuilder,String,AtomSpecModel) : void   appendModel(StringBuilder,String,AtomSpecModel) : void	189189	11.011	2.02	0.0 0.00%
showBackbone() : List<StructureCommandI>   showBackbone() : List<StructureCommandI>	213213	1.01	1.01	0.0 0.00%
superposeStructures(AtomSpecModel,AtomSpecModel,AtomSpecType) : List<StructureCommandI>   superposeStructures(AtomSpecModel,AtomSpecModel,AtomSpecType) : List<StructureCommandI>	219219	8.08	1.01	0.0 0.00%
openSession(String) : StructureCommandI   openSession(String) : StructureCommandI	247247	1.01	1.01	0.0 0.00%
closeViewer() : StructureCommandI   closeViewer() : StructureCommandI	255255	1.01	1.01	0.0 0.00%
startNotifications(String) : List<StructureCommandI>   startNotifications(String) : List<StructureCommandI>	261261	4.04	1.01	0.0 0.00%
stopNotifications() : List<StructureCommandI>   stopNotifications() : List<StructureCommandI>	274274	4.04	1.01	0.0 0.00%
getSelectedResidues() : StructureCommandI   getSelectedResidues() : StructureCommandI	283283	1.01	1.01	0.0 0.00%
listResidueAttributes() : StructureCommandI   listResidueAttributes() : StructureCommandI	289289	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.ext.rbvi.chimera;
22
23		import java.awt.Color;
24		import java.util.ArrayList;
25		import java.util.Arrays;
26		import java.util.List;
27
28		import jalview.structure.AtomSpecModel;
29		import jalview.structure.StructureCommand;
30		import jalview.structure.StructureCommandI;
31		import jalview.structure.StructureCommandsI.AtomSpecType;
32
33		/**
34		* Routines for generating ChimeraX commands for Jalview/ChimeraX binding
35		*/
		0% Uncovered Elements: 83 (83) Complexity: 22 Complexity Density: 0.39
36		public class ChimeraXCommands extends ChimeraCommands
37		{
38		// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#resattr
39		private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
40		"info resattr");
41
42		// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
43		private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand(
44		"exit");
45
46		// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
47		private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
48		"info notify stop selection jalview");
49
50		private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
51		"info notify stop models jalview");
52
53		// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#selection
54		private static final StructureCommand GET_SELECTION = new StructureCommand(
55		"info selection level residue");
56
57		private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
58		"~display all;~ribbon;show @CA|P atoms");
59
60		// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
61		private static final StructureCommand FOCUS_VIEW = new StructureCommand(
62		"view");
63
64		private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
65		"color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
66
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
67	0	@Override...
68		public List<StructureCommandI> colourByCharge()
69		{
70	0	return Arrays.asList(COLOUR_BY_CHARGE);
71		}
72
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
73	0	@Override...
74		public String getResidueSpec(String residue)
75		{
76	0	return ":" + residue;
77		}
78
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
79	0	@Override...
80		public StructureCommandI colourResidues(String atomSpec, Color colour)
81		{
82		// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html
83	0	String colourCode = getColourString(colour);
84
85	0	return new StructureCommand("color " + atomSpec + " " + colourCode);
86		}
87
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
88	0	@Override...
89		public StructureCommandI focusView()
90		{
91	0	return FOCUS_VIEW;
92		}
93
94		/**
95		* {@inheritDoc}
96		*
97		* @return
98		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
99	0	@Override...
100		public int getModelStartNo()
101		{
102	0	return 1;
103		}
104
105		/**
106		* Returns a viewer command to set the given residue attribute value on
107		* residues specified by the AtomSpecModel, for example
108		*
109		* <pre>
110		* setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
111		* </pre>
112		*
113		* @param attributeName
114		* @param attributeValue
115		* @param atomSpecModel
116		* @return
117		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
118	0	@Override...
119		protected StructureCommandI setAttribute(String attributeName,
120		String attributeValue, AtomSpecModel atomSpecModel)
121		{
122	0	StringBuilder sb = new StringBuilder(128);
123	0	sb.append("setattr ")
124		.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
125	0	sb.append(" res ").append(attributeName).append(" '")
126		.append(attributeValue).append("'");
127	0	sb.append(" create true");
128	0	return new StructureCommand(sb.toString());
129		}
130
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
131	0	@Override...
132		public StructureCommandI openCommandFile(String path)
133		{
134		// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html
135	0	return new StructureCommand("open " + path);
136		}
137
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
138	0	@Override...
139		public StructureCommandI saveSession(String filepath)
140		{
141		// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
142		// note ChimeraX will append ".cxs" to the filepath!
143	0	return new StructureCommand("save " + filepath + " format session");
144		}
145
146		/**
147		* Returns the range(s) formatted as a ChimeraX atomspec, for example
148		* <p>
149		* #1/A:2-20,30-40/B:10-20|#2/A:12-30
150		* <p>
151		* Note there is no need to explicitly exclude ALTLOC atoms when
152		* {@code alphaOnly == true}, as this is the default behaviour of ChimeraX (a
153		* change from Chimera)
154		*
155		* @return
156		*/
		0% Uncovered Elements: 18 (18) Complexity: 4 Complexity Density: 0.33
157	0	@Override...
158		public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
159		{
160	0	StringBuilder sb = new StringBuilder(128);
161	0	boolean firstModel = true;
162	0	for (String model : atomSpec.getModels())
163		{
164	0	if (!firstModel)
165		{
166	0	sb.append("|");
167		}
168	0	firstModel = false;
169	0	appendModel(sb, model, atomSpec);
170	0	if (specType == AtomSpecType.ALPHA)
171		{
172	0	sb.append("@CA");
173		}
174	0	if (specType == AtomSpecType.PHOSPHATE)
175		{
176	0	sb.append("@P");
177		}
178		}
179	0	return sb.toString();
180		}
181
182		/**
183		* A helper method to append an atomSpec string for atoms in the given model
184		*
185		* @param sb
186		* @param model
187		* @param atomSpec
188		*/
		0% Uncovered Elements: 13 (13) Complexity: 2 Complexity Density: 0.18
189	0	protected void appendModel(StringBuilder sb, String model,...
190		AtomSpecModel atomSpec)
191		{
192	0	sb.append("#").append(model);
193
194	0	for (String chain : atomSpec.getChains(model))
195		{
196	0	boolean firstPositionForChain = true;
197	0	sb.append("/").append(chain.trim()).append(":");
198	0	List<int[]> rangeList = atomSpec.getRanges(model, chain);
199	0	boolean first = true;
200	0	for (int[] range : rangeList)
201		{
202	0	if (!first)
203		{
204	0	sb.append(",");
205		}
206	0	first = false;
207	0	appendRange(sb, range[0], range[1], chain, firstPositionForChain,
208		true);
209		}
210		}
211		}
212
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
213	0	@Override...
214		public List<StructureCommandI> showBackbone()
215		{
216	0	return Arrays.asList(SHOW_BACKBONE);
217		}
218
		0% Uncovered Elements: 8 (8) Complexity: 1 Complexity Density: 0.12
219	0	@Override...
220		public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
221		AtomSpecModel spec, AtomSpecType backbone)
222		{
223		/*
224		* Form ChimeraX match command to match spec to ref
225		*
226		* match #1/A:2-94 toAtoms #2/A:1-93
227		*
228		* @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html
229		*/
230	0	StringBuilder cmd = new StringBuilder();
231	0	String atomSpec = getAtomSpec(spec, backbone);
232	0	String refSpec = getAtomSpec(ref, backbone);
233	0	cmd.append("align ").append(atomSpec).append(" toAtoms ")
234		.append(refSpec);
235
236		/*
237		* show superposed residues as ribbon, others as chain
238		*/
239	0	cmd.append("; ribbon ");
240	0	cmd.append(getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY)).append("|");
241	0	cmd.append(getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY))
242		.append("; view");
243
244	0	return Arrays.asList(new StructureCommand(cmd.toString()));
245		}
246
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
247	0	@Override...
248		public StructureCommandI openSession(String filepath)
249		{
250		// https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#composite
251		// this version of the command has no dependency on file extension
252	0	return new StructureCommand("open " + filepath + " format session");
253		}
254
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
255	0	@Override...
256		public StructureCommandI closeViewer()
257		{
258	0	return CLOSE_CHIMERAX;
259		}
260
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
261	0	@Override...
262		public List<StructureCommandI> startNotifications(String uri)
263		{
264	0	List<StructureCommandI> cmds = new ArrayList<>();
265	0	cmds.add(new StructureCommand(
266		"info notify start models jalview prefix ModelChanged url "
267		+ uri));
268	0	cmds.add(new StructureCommand(
269		"info notify start selection jalview prefix SelectionChanged url "
270		+ uri));
271	0	return cmds;
272		}
273
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
274	0	@Override...
275		public List<StructureCommandI> stopNotifications()
276		{
277	0	List<StructureCommandI> cmds = new ArrayList<>();
278	0	cmds.add(STOP_NOTIFY_MODELS);
279	0	cmds.add(STOP_NOTIFY_SELECTION);
280	0	return cmds;
281		}
282
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
283	0	@Override...
284		public StructureCommandI getSelectedResidues()
285		{
286	0	return GET_SELECTION;
287		}
288
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
289	0	@Override...
290		public StructureCommandI listResidueAttributes()
291		{
292	0	return LIST_RESIDUE_ATTRIBUTES;
293		}
294		}