Class | Line # | Actions | |||
---|---|---|---|---|---|
StructureCommandsI | 35 | 1 | 1 | ||
StructureCommandsI.AtomSpecType | 134 | 0 | 0 |
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 | */ | |
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 | ||
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 | ||
259 | 0 | default List<StructureCommandI> showHetatms(List<String> toShow) |
260 | { | |
261 | 0 | return Collections.EMPTY_LIST; |
262 | } | |
263 | } |