Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
StructureCommandsI	35	1	1	0.00%	Show methods
StructureCommandsI.AtomSpecType	134	0	0	-1.0 -	Show methods

Class StructureCommandsI

Class StructureCommandsI	Line # 35	Total Statements 1	Complexity 1	TOTAL Coverage 0.00%
showHetatms(List<String>) : List<StructureCommandI>   showHetatms(List<String>) : List<StructureCommandI>	259259	1.01	1.01	0.0 0.00%

 

Class StructureCommandsI.AtomSpecType

Class StructureCommandsI.AtomSpecType	Line # 134	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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.structure;
22
23		import java.awt.Color;
24		import java.util.Collections;
25		import java.util.List;
26		import java.util.Map;
27
28		/**
29		* Methods that generate commands that can be sent to a molecular structure
30		* viewer program (e.g. Jmol, Chimera, ChimeraX)
31		*
32		* @author gmcarstairs
33		*
34		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 1
35		public interface StructureCommandsI
36		{
37		/**
38		* Returns the command to colour by chain
39		*
40		* @return
41		*/
42		StructureCommandI colourByChain();
43
44		/**
45		* Returns the command to colour residues using a charge-based scheme:
46		* <ul>
47		* <li>Aspartic acid and Glutamic acid (negative charge) red</li>
48		* <li>Lysine and Arginine (positive charge) blue</li>
49		* <li>Cysteine - yellow</li>
50		* <li>all others - white</li>
51		* </ul>
52		*
53		* @return
54		*/
55		List<StructureCommandI> colourByCharge();
56
57		/**
58		* Returns the command to colour residues with the colours provided in the
59		* map, one per three letter residue code
60		*
61		* @param colours
62		* @return
63		*/
64		List<StructureCommandI> colourByResidues(Map<String, Color> colours);
65
66		/**
67		* Returns the command to set the background colour of the structure viewer
68		*
69		* @param col
70		* @return
71		*/
72		StructureCommandI setBackgroundColour(Color col);
73
74		/**
75		* Returns commands to colour mapped residues of structures according to
76		* Jalview's colouring (including feature colouring if applied). Parameter is
77		* a map from Color to a model of all residues assigned that colour.
78		*
79		* @param colourMap
80		* @return
81		*/
82
83		List<StructureCommandI> colourBySequence(
84		Map<Object, AtomSpecModel> colourMap);
85
86		/**
87		* Returns a command to centre the display in the structure viewer
88		*
89		* @return
90		*/
91		StructureCommandI focusView();
92
93		/**
94		* Returns a command to show only the selected chains. The items in the input
95		* list should be formatted as "modelid:chainid".
96		*
97		* @param toShow
98		* @return
99		*/
100		List<StructureCommandI> showChains(List<String> toShow);
101
102		/**
103		* Returns a command to superpose structures by closest positioning of
104		* residues in {@code atomSpec} to the corresponding residues in
105		* {@code refAtoms}. If wanted, this may include commands to visually
106		* highlight the residues that were used for the superposition.
107		*
108		* @param refAtoms
109		* @param atomSpec
110		* @param backbone
111		* - superpose based on which kind of atomType
112		* @return
113		*/
114		List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
115		AtomSpecModel atomSpec, AtomSpecType backbone);
116
117		/**
118		* Returns a command to open a file of commands at the given path
119		*
120		* @param path
121		* @return
122		*/
123		StructureCommandI openCommandFile(String path);
124
125		/**
126		* Returns a command to save the current viewer session state to the given
127		* file
128		*
129		* @param filepath
130		* @return
131		*/
132		StructureCommandI saveSession(String filepath);
133
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
134		enum AtomSpecType
135		{
136		RESIDUE_ONLY, ALPHA, PHOSPHATE
137		};
138
139		/**
140		* Returns a representation of the atom set represented by the model, in
141		* viewer syntax format. If {@code alphaOnly} is true, this is restricted to
142		* Alpha Carbon (peptide) or Phosphorous (rna) only
143		*
144		* @param model
145		* @param specType
146		* @return
147		*/
148		String getAtomSpec(AtomSpecModel model, AtomSpecType specType);
149
150		/**
151		* Returns the lowest model number used by the structure viewer (likely 0 or
152		* 1)
153		*
154		* @return
155		*/
156		// TODO remove by refactoring so command generation is purely driven by
157		// AtomSpecModel objects derived in the binding classes?
158		int getModelStartNo();
159
160		/**
161		* Returns command(s) to show only the backbone of the peptide (cartoons in
162		* Jmol, chain in Chimera)
163		*
164		* @return
165		*/
166		List<StructureCommandI> showBackbone();
167
168		/**
169		* Returns a command to open a file at the given path
170		*
171		* @param file
172		* @return
173		*/
174		// refactor if needed to distinguish loading data or session files
175		StructureCommandI loadFile(String file);
176
177		/**
178		* Returns commands to set atom attributes or properties, given a map of
179		* Jalview features as {featureType, {featureValue, AtomSpecModel}}. The
180		* assumption is that one command can be constructed for each feature type and
181		* value combination, to apply it to one or more residues.
182		*
183		* @param featureValues
184		* @return
185		*/
186		List<StructureCommandI> setAttributes(
187		Map<String, Map<Object, AtomSpecModel>> featureValues);
188
189		/**
190		* Returns command to open a saved structure viewer session file, or null if
191		* not supported
192		*
193		* @param filepath
194		* @return
195		*/
196		StructureCommandI openSession(String filepath);
197
198		/**
199		* Returns command to restore a previously saved version of an existing
200		* structure viewer session file. Default implementation calls 'openSession'
201		*
202		* @param filePath
203		* @return
204		*/
205		StructureCommandI restoreSession(String filePath);
206
207		/**
208		* Returns a command to ask the viewer to close down
209		*
210		* @return
211		*/
212		StructureCommandI closeViewer();
213
214		/**
215		* Returns one or more commands to ask the viewer to notify model or selection
216		* changes to the given uri. Returns null if this is not supported by the
217		* structure viewer.
218		*
219		* @param uri
220		* @return
221		*/
222		List<StructureCommandI> startNotifications(String uri);
223
224		/**
225		* Returns one or more commands to ask the viewer to stop notifying model or
226		* selection changes. Returns null if this is not supported by the structure
227		* viewer.
228		*
229		* @return
230		*/
231		List<StructureCommandI> stopNotifications();
232
233		/**
234		* Returns a command to ask the viewer for its current residue selection, or
235		* null if no such command is supported
236		*
237		* @return
238		*/
239		StructureCommandI getSelectedResidues();
240
241		/**
242		* Returns a command to list the unique names of residue attributes, or null
243		* if no such command is supported
244		*
245		* @return
246		*/
247		StructureCommandI listResidueAttributes();
248
249		/**
250		* Returns a command to list residues with an attribute of the given name,
251		* with attribute value, or null if no such command is supported
252		*
253		* @return
254		*/
255		StructureCommandI getResidueAttributes(String attName);
256
257		List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues);
258
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
259	0	default List<StructureCommandI> showHetatms(List<String> toShow)...
260		{
261	0	return Collections.EMPTY_LIST;
262		}
263		}