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.schemes.ColourSchemeI;
27 import jalview.structures.models.AAStructureBindingModel;
29 public interface JalviewStructureDisplayI
32 AAStructureBindingModel getBinding();
35 * @return true if there is an active GUI handling a structure display
40 * enable or disable the structure display - note this might just hide or show
41 * a GUI element, but not actually reset the display
45 void setVisible(boolean b);
48 * free up any external resources that were used by this display and collect
54 * Shutdown any Jalview structure viewing processes started by this display
56 * @param closeExternalViewer
57 * if true, force close any linked external viewer process
59 void closeViewer(boolean closeExternalViewer);
62 * apply a colourscheme to the structures in the viewer
66 void setJalviewColourScheme(ColourSchemeI colourScheme);
70 * @return true if all background sequence/structure binding threads have
71 * completed for this viewer instance
76 * Checks if the PDB file is already loaded in this viewer, if so just adds
77 * mappings as necessary and answers true, else answers false. This supports
78 * the use case of adding additional chains of the same structure to a viewer.
86 boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
87 AlignmentViewPanel apanel, String pdbId);
90 * Adds one or more chains (sequences) of a PDB structure to this structure
100 void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
101 String[] chains, AlignmentViewPanel apanel, String pdbId);
104 * refresh GUI after reconfiguring structure(s) and alignment panels
106 void updateTitleAndMenus();
109 * Answers true if the viewer should attempt to align any added structures,
114 boolean isAlignAddedStructures();
117 * Sets the flag for whether added structures should be aligned
121 void setAlignAddedStructures(boolean alignAdded);
124 * Raise the panel to the top of the stack...