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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.api.structures; | |
22 | ||
23 | import java.io.File; | |
24 | import java.util.Collections; | |
25 | import java.util.List; | |
26 | ||
27 | import jalview.api.AlignmentViewPanel; | |
28 | import jalview.datamodel.PDBEntry; | |
29 | import jalview.datamodel.SequenceI; | |
30 | import jalview.gui.AlignmentPanel; | |
31 | import jalview.gui.StructureViewer; | |
32 | import jalview.structures.models.AAStructureBindingModel; | |
33 | ||
34 | public interface JalviewStructureDisplayI | |
35 | { | |
36 | ||
37 | AAStructureBindingModel getBinding(); | |
38 | ||
39 | /** | |
40 | * @return true if there is an active GUI handling a structure display | |
41 | */ | |
42 | boolean isVisible(); | |
43 | ||
44 | /** | |
45 | * enable or disable the structure display - note this might just hide or show | |
46 | * a GUI element, but not actually reset the display | |
47 | * | |
48 | * @param b | |
49 | */ | |
50 | void setVisible(boolean b); | |
51 | ||
52 | /** | |
53 | * free up any external resources that were used by this display and collect | |
54 | * garbage | |
55 | */ | |
56 | void dispose(); | |
57 | ||
58 | /** | |
59 | * Shutdown any Jalview structure viewing processes started by this display | |
60 | * | |
61 | * @param closeExternalViewer | |
62 | * if true, force close any linked external viewer process | |
63 | */ | |
64 | void closeViewer(boolean closeExternalViewer); | |
65 | ||
66 | /** | |
67 | * Check if the external viewer is still running | |
68 | */ | |
69 | boolean stillRunning(); | |
70 | ||
71 | /** | |
72 | * | |
73 | * @return true if all background sequence/structure binding threads have | |
74 | * completed for this viewer instance | |
75 | */ | |
76 | boolean hasMapping(); | |
77 | ||
78 | /** | |
79 | * Checks if the PDB file is already loaded in this viewer, if so just adds | |
80 | * mappings as necessary and answers true, else answers false. This supports | |
81 | * the use case of adding additional chains of the same structure to a viewer. | |
82 | * | |
83 | * @param seq | |
84 | * @param chains | |
85 | * @param apanel | |
86 | * @param pdbId | |
87 | * @return | |
88 | */ | |
89 | boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains, | |
90 | AlignmentViewPanel apanel, String pdbId); | |
91 | ||
92 | /** | |
93 | * Adds one or more chains (sequences) of a PDB structure to this structure | |
94 | * viewer | |
95 | * | |
96 | * @param pdbentry | |
97 | * @param seq | |
98 | * @param chains | |
99 | * @param apanel | |
100 | * @param pdbId | |
101 | * @return | |
102 | */ | |
103 | void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq, | |
104 | String[] chains, AlignmentViewPanel apanel, String pdbId); | |
105 | ||
106 | /** | |
107 | * refresh GUI after reconfiguring structure(s) and alignment panels | |
108 | */ | |
109 | void updateTitleAndMenus(); | |
110 | ||
111 | /** | |
112 | * Answers true if the viewer should attempt to align any added structures, | |
113 | * else false | |
114 | * | |
115 | * @return | |
116 | */ | |
117 | boolean isAlignAddedStructures(); | |
118 | ||
119 | /** | |
120 | * Sets the flag for whether added structures should be aligned | |
121 | * | |
122 | * @param alignAdded | |
123 | */ | |
124 | void setAlignAddedStructures(boolean alignAdded); | |
125 | ||
126 | /** | |
127 | * Raise the panel to the top of the stack... | |
128 | */ | |
129 | void raiseViewer(); | |
130 | ||
131 | AlignmentViewPanel getAlignmentPanel(); | |
132 | ||
133 | /** | |
134 | * Answers true if the given alignment view is used to colour structures by | |
135 | * sequence, false if not | |
136 | * | |
137 | * @param ap | |
138 | * @return | |
139 | */ | |
140 | boolean isUsedForColourBy(AlignmentViewPanel ap); | |
141 | ||
142 | /** | |
143 | * If implemented, shows a command line console in the structure viewer | |
144 | * | |
145 | * @param show | |
146 | * true to show, false to hide | |
147 | */ | |
148 | void showConsole(boolean show); | |
149 | ||
150 | /** | |
151 | * Remove references to the given alignment view for this structure viewer | |
152 | * | |
153 | * @param avp | |
154 | */ | |
155 | void removeAlignmentPanel(AlignmentViewPanel avp); | |
156 | ||
157 | /** | |
158 | * Updates the progress bar if there is one. Call stopProgressBar with the | |
159 | * returned handle to remove the message. | |
160 | * | |
161 | * @param msg | |
162 | * @return handle | |
163 | */ | |
164 | long startProgressBar(String msg); | |
165 | ||
166 | /** | |
167 | * Ends the progress bar with the specified handle, leaving a message (if not | |
168 | * null) on the status bar | |
169 | * | |
170 | * @param msg | |
171 | * @param handle | |
172 | */ | |
173 | void stopProgressBar(String msg, long handle); | |
174 | ||
175 | /** | |
176 | * | |
177 | * @return true if the actions menu is shown for this viewer | |
178 | */ | |
179 | boolean hasViewerActionsMenu(); | |
180 | ||
181 | String getViewId(); | |
182 | ||
183 | StructureViewer.ViewerType getViewerType(); | |
184 | ||
185 | boolean isUsedforaligment(AlignmentViewPanel ap); | |
186 | ||
187 | boolean isColouredByViewer(); | |
188 | ||
189 | int getHeight(); | |
190 | ||
191 | int getWidth(); | |
192 | ||
193 | int getY(); | |
194 | ||
195 | File saveSession(); | |
196 | ||
197 | /** | |
198 | * | |
199 | * @return heteroatoms in a form suitable for display and passing to command | |
200 | * generator to display hetatms | |
201 | */ | |
202 | 0 | default List<String> getHetatms() |
203 | { | |
204 | 0 | return Collections.EMPTY_LIST; |
205 | } | |
206 | ||
207 | } |