Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
JalviewStructureDisplayI	33	1	1	0.00%	Show methods

Class JalviewStructureDisplayI

Class JalviewStructureDisplayI	Line # 33	Total Statements 1	Complexity 1	TOTAL Coverage 0.00%
getHetatms() : List<String>   getHetatms() : List<String>	208208	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.StructureViewer;
31		import jalview.structures.models.AAStructureBindingModel;
32
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 1
33		public interface JalviewStructureDisplayI
34		{
35
36		AAStructureBindingModel getBinding();
37
38		/**
39		* @return true if there is an active GUI handling a structure display
40		*/
41		boolean isVisible();
42
43		/**
44		* enable or disable the structure display - note this might just hide or show
45		* a GUI element, but not actually reset the display
46		*
47		* @param b
48		*/
49		void setVisible(boolean b);
50
51		/**
52		* free up any external resources that were used by this display and collect
53		* garbage
54		*/
55		void dispose();
56
57		/**
58		* Shutdown any Jalview structure viewing processes started by this display
59		*
60		* @param closeExternalViewer
61		* if true, force close any linked external viewer process
62		*/
63		void closeViewer(boolean closeExternalViewer);
64
65		/**
66		* Check if the external viewer is still running
67		*/
68		boolean stillRunning();
69
70		/**
71		*
72		* @return true if all background sequence/structure binding threads have
73		* completed for this viewer instance
74		*/
75		boolean hasMapping();
76
77		/**
78		* Checks if the PDB file is already loaded in this viewer, if so just adds
79		* mappings as necessary and answers true, else answers false. This supports
80		* the use case of adding additional chains of the same structure to a viewer.
81		*
82		* @param seq
83		* @param chains
84		* @param apanel
85		* @param pdbId
86		* @return
87		*/
88		boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
89		AlignmentViewPanel apanel, String pdbId);
90
91		/**
92		* Adds one or more chains (sequences) of a PDB structure to this structure
93		* viewer
94		*
95		* @param pdbentry
96		* @param seq
97		* @param chains
98		* @param apanel
99		* @param pdbId
100		* @return
101		*/
102		void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
103		String[] chains, AlignmentViewPanel apanel, String pdbId);
104
105		/**
106		* refresh GUI after reconfiguring structure(s) and alignment panels
107		*/
108		void updateTitleAndMenus();
109
110		/**
111		* Answers true if the viewer should attempt to align any added structures,
112		* else false
113		*
114		* @return
115		*/
116		boolean isAlignAddedStructures();
117
118		/**
119		* Sets the flag for whether added structures should be aligned
120		*
121		* @param alignAdded
122		*/
123		void setAlignAddedStructures(boolean alignAdded);
124
125		/**
126		* Raise the panel to the top of the stack...
127		*/
128		void raiseViewer();
129
130		AlignmentViewPanel getAlignmentPanel();
131
132		/**
133		* Answers true if the given alignment view is used to colour structures by
134		* sequence, false if not
135		*
136		* @param ap
137		* @return
138		*/
139		boolean isUsedForColourBy(AlignmentViewPanel ap);
140
141		/**
142		* If implemented, shows a command line console in the structure viewer
143		*
144		* @param show
145		* true to show, false to hide
146		*/
147		void showConsole(boolean show);
148
149		/**
150		* Remove references to the given alignment view for this structure viewer
151		*
152		* @param avp
153		*/
154		void removeAlignmentPanel(AlignmentViewPanel avp);
155
156		/**
157		* Updates the progress bar if there is one. Call stopProgressBar with the
158		* returned handle to remove the message.
159		*
160		* @param msg
161		* @return handle
162		*/
163		long startProgressBar(String msg);
164
165		/**
166		* Ends the progress bar with the specified handle, leaving a message (if not
167		* null) on the status bar
168		*
169		* @param msg
170		* @param handle
171		*/
172		void stopProgressBar(String msg, long handle);
173
174		/**
175		*
176		* @return true if the actions menu is shown for this viewer
177		*/
178		boolean hasViewerActionsMenu();
179
180		/**
181		* Show all chains in the structure viewer
182		*/
183		public void showAllChains();
184
185		String getViewId();
186
187		StructureViewer.ViewerType getViewerType();
188
189		boolean isUsedforaligment(AlignmentViewPanel ap);
190
191		boolean isColouredByViewer();
192
193		int getHeight();
194
195		int getWidth();
196
197		int getX();
198
199		int getY();
200
201		File saveSession();
202
203		/**
204		*
205		* @return heteroatoms in a form suitable for display and passing to command
206		* generator to display hetatms
207		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
208	0	default List<String> getHetatms()...
209		{
210	0	return Collections.EMPTY_LIST;
211		}
212
213		/**
214		* Set a permanent viewer title. Can be changed by calling setPermanentTitle
215		* again.
216		*/
217		public void setPermanentTitle(String title);
218
219		/**
220		* Get the actual title displayed on the JInternalFrame
221		*/
222		public String getActualTitle();
223
224		/**
225		* Get the string we think should be used as the title for this viewer
226		* (permanent or dynamic)
227		*/
228		public String getViewerTitle();
229		}