Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewStructureDisplayI	34	1	1	0.00%	Show methods

Class JalviewStructureDisplayI

Class JalviewStructureDisplayI	Line # 34	Total Statements 1	Complexity 1	TOTAL Coverage 0.00%
getHetatms() : List<String>   getHetatms() : List<String>	202202	1.01	1.01	0.0 0.00%

 

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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
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 1
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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
202	0	default List<String> getHetatms()...
203		{
204	0	return Collections.EMPTY_LIST;
205		}
206
207		}