2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.api.structures;
23 import jalview.api.AlignmentViewPanel;
24 import jalview.datamodel.PDBEntry;
25 import jalview.datamodel.SequenceI;
26 import jalview.structures.models.AAStructureBindingModel;
28 public interface JalviewStructureDisplayI
31 AAStructureBindingModel getBinding();
34 * @return true if there is an active GUI handling a structure display
39 * enable or disable the structure display - note this might just hide or show
40 * a GUI element, but not actually reset the display
44 void setVisible(boolean b);
47 * free up any external resources that were used by this display and collect
53 * Shutdown any Jalview structure viewing processes started by this display
55 * @param closeExternalViewer
56 * if true, force close any linked external viewer process
58 void closeViewer(boolean closeExternalViewer);
62 * @return true if all background sequence/structure binding threads have
63 * completed for this viewer instance
68 * Checks if the PDB file is already loaded in this viewer, if so just adds
69 * mappings as necessary and answers true, else answers false. This supports
70 * the use case of adding additional chains of the same structure to a viewer.
78 boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
79 AlignmentViewPanel apanel, String pdbId);
82 * Adds one or more chains (sequences) of a PDB structure to this structure
92 void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
93 String[] chains, AlignmentViewPanel apanel, String pdbId);
96 * refresh GUI after reconfiguring structure(s) and alignment panels
98 void updateTitleAndMenus();
101 * Answers true if the viewer should attempt to align any added structures,
106 boolean isAlignAddedStructures();
109 * Sets the flag for whether added structures should be aligned
113 void setAlignAddedStructures(boolean alignAdded);
116 * Raise the panel to the top of the stack...
120 AlignmentViewPanel getAlignmentPanel();
123 * Answers true if the given alignment view is used to colour structures by
124 * sequence, false if not
129 boolean isUsedForColourBy(AlignmentViewPanel ap);
132 * If implemented, shows a command line console in the structure viewer
135 * true to show, false to hide
137 void showConsole(boolean show);
140 * Remove references to the given alignment view for this structure viewer
144 void removeAlignmentPanel(AlignmentViewPanel avp);
147 * Updates the progress bar if there is one. Call stopProgressBar with the
148 * returned handle to remove the message.
153 long startProgressBar(String msg);
156 * Ends the progress bar with the specified handle, leaving a message (if not
157 * null) on the status bar
162 void stopProgressBar(String msg, long handle);