Class | Line # | Actions | |||
---|---|---|---|---|---|
StructureCommandsI | 14 | 0 | 0 |
1 | package jalview.structure; | |
2 | ||
3 | import java.awt.Color; | |
4 | import java.util.List; | |
5 | import java.util.Map; | |
6 | ||
7 | /** | |
8 | * Methods that generate commands that can be sent to a molecular structure | |
9 | * viewer program (e.g. Jmol, Chimera, ChimeraX) | |
10 | * | |
11 | * @author gmcarstairs | |
12 | * | |
13 | */ | |
14 | public interface StructureCommandsI | |
15 | { | |
16 | /** | |
17 | * Returns the command to colour by chain | |
18 | * | |
19 | * @return | |
20 | */ | |
21 | StructureCommandI colourByChain(); | |
22 | ||
23 | /** | |
24 | * Returns the command to colour residues using a charge-based scheme: | |
25 | * <ul> | |
26 | * <li>Aspartic acid and Glutamic acid (negative charge) red</li> | |
27 | * <li>Lysine and Arginine (positive charge) blue</li> | |
28 | * <li>Cysteine - yellow</li> | |
29 | * <li>all others - white</li> | |
30 | * </ul> | |
31 | * | |
32 | * @return | |
33 | */ | |
34 | List<StructureCommandI> colourByCharge(); | |
35 | ||
36 | /** | |
37 | * Returns the command to colour residues with the colours provided in the | |
38 | * map, one per three letter residue code | |
39 | * | |
40 | * @param colours | |
41 | * @return | |
42 | */ | |
43 | List<StructureCommandI> colourByResidues(Map<String, Color> colours); | |
44 | ||
45 | /** | |
46 | * Returns the command to set the background colour of the structure viewer | |
47 | * | |
48 | * @param col | |
49 | * @return | |
50 | */ | |
51 | StructureCommandI setBackgroundColour(Color col); | |
52 | ||
53 | /** | |
54 | * Returns commands to colour mapped residues of structures according to | |
55 | * Jalview's colouring (including feature colouring if applied). Parameter is | |
56 | * a map from Color to a model of all residues assigned that colour. | |
57 | * | |
58 | * @param colourMap | |
59 | * @return | |
60 | */ | |
61 | ||
62 | List<StructureCommandI> colourBySequence( | |
63 | Map<Object, AtomSpecModel> colourMap); | |
64 | ||
65 | /** | |
66 | * Returns a command to centre the display in the structure viewer | |
67 | * | |
68 | * @return | |
69 | */ | |
70 | StructureCommandI focusView(); | |
71 | ||
72 | /** | |
73 | * Returns a command to show only the selected chains. The items in the input | |
74 | * list should be formatted as "modelid:chainid". | |
75 | * | |
76 | * @param toShow | |
77 | * @return | |
78 | */ | |
79 | List<StructureCommandI> showChains(List<String> toShow); | |
80 | ||
81 | /** | |
82 | * Returns a command to superpose structures by closest positioning of | |
83 | * residues in {@code atomSpec} to the corresponding residues in | |
84 | * {@code refAtoms}. If wanted, this may include commands to visually | |
85 | * highlight the residues that were used for the superposition. | |
86 | * | |
87 | * @param refAtoms | |
88 | * @param atomSpec | |
89 | * @return | |
90 | */ | |
91 | List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms, | |
92 | AtomSpecModel atomSpec); | |
93 | ||
94 | /** | |
95 | * Returns a command to open a file of commands at the given path | |
96 | * | |
97 | * @param path | |
98 | * @return | |
99 | */ | |
100 | StructureCommandI openCommandFile(String path); | |
101 | ||
102 | /** | |
103 | * Returns a command to save the current viewer session state to the given | |
104 | * file | |
105 | * | |
106 | * @param filepath | |
107 | * @return | |
108 | */ | |
109 | StructureCommandI saveSession(String filepath); | |
110 | ||
111 | /** | |
112 | * Returns a representation of the atom set represented by the model, in | |
113 | * viewer syntax format. If {@code alphaOnly} is true, this is restricted to | |
114 | * Alpha Carbon (peptide) or Phosphorous (rna) only | |
115 | * | |
116 | * @param model | |
117 | * @param alphaOnly | |
118 | * @return | |
119 | */ | |
120 | String getAtomSpec(AtomSpecModel model, boolean alphaOnly); | |
121 | ||
122 | /** | |
123 | * Returns the lowest model number used by the structure viewer (likely 0 or | |
124 | * 1) | |
125 | * | |
126 | * @return | |
127 | */ | |
128 | // TODO remove by refactoring so command generation is purely driven by | |
129 | // AtomSpecModel objects derived in the binding classes? | |
130 | int getModelStartNo(); | |
131 | ||
132 | /** | |
133 | * Returns command(s) to show only the backbone of the peptide (cartoons in | |
134 | * Jmol, chain in Chimera) | |
135 | * | |
136 | * @return | |
137 | */ | |
138 | List<StructureCommandI> showBackbone(); | |
139 | ||
140 | /** | |
141 | * Returns a command to open a file at the given path | |
142 | * | |
143 | * @param file | |
144 | * @return | |
145 | */ | |
146 | // refactor if needed to distinguish loading data or session files | |
147 | StructureCommandI loadFile(String file); | |
148 | ||
149 | /** | |
150 | * Returns commands to set atom attributes or properties, given a map of | |
151 | * Jalview features as {featureType, {featureValue, AtomSpecModel}}. The | |
152 | * assumption is that one command can be constructed for each feature type and | |
153 | * value combination, to apply it to one or more residues. | |
154 | * | |
155 | * @param featureValues | |
156 | * @return | |
157 | */ | |
158 | List<StructureCommandI> setAttributes( | |
159 | Map<String, Map<Object, AtomSpecModel>> featureValues); | |
160 | ||
161 | /** | |
162 | * Returns command to open a saved structure viewer session file, or null if | |
163 | * not supported | |
164 | * | |
165 | * @param filepath | |
166 | * @return | |
167 | */ | |
168 | StructureCommandI openSession(String filepath); | |
169 | ||
170 | /** | |
171 | * Returns a command to ask the viewer to close down | |
172 | * | |
173 | * @return | |
174 | */ | |
175 | StructureCommandI closeViewer(); | |
176 | ||
177 | /** | |
178 | * Returns one or more commands to ask the viewer to notify model or selection | |
179 | * changes to the given uri. Returns null if this is not supported by the | |
180 | * structure viewer. | |
181 | * | |
182 | * @param uri | |
183 | * @return | |
184 | */ | |
185 | List<StructureCommandI> startNotifications(String uri); | |
186 | ||
187 | /** | |
188 | * Returns one or more commands to ask the viewer to stop notifying model or | |
189 | * selection changes. Returns null if this is not supported by the structure | |
190 | * viewer. | |
191 | * | |
192 | * @return | |
193 | */ | |
194 | List<StructureCommandI> stopNotifications(); | |
195 | ||
196 | /** | |
197 | * Returns a command to ask the viewer for its current residue selection, or | |
198 | * null if no such command is supported | |
199 | * | |
200 | * @return | |
201 | */ | |
202 | StructureCommandI getSelectedResidues(); | |
203 | ||
204 | /** | |
205 | * Returns a command to list the unique names of residue attributes, or null | |
206 | * if no such command is supported | |
207 | * | |
208 | * @return | |
209 | */ | |
210 | StructureCommandI listResidueAttributes(); | |
211 | ||
212 | /** | |
213 | * Returns a command to list residues with an attribute of the given name, | |
214 | * with attribute value, or null if no such command is supported | |
215 | * | |
216 | * @return | |
217 | */ | |
218 | StructureCommandI getResidueAttributes(String attName); | |
219 | } |