Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SplitFrame	76	292	121	0.3601789836%	Show methods

Class SplitFrame

Class SplitFrame	Line # 76	Total Statements 292	Complexity 121	TOTAL Coverage 0.3601789836%
SplitFrame(GAlignFrame,GAlignFrame)   SplitFrame(GAlignFrame,GAlignFrame)	9797	2.02	1.01	1.0 1.0100%
init() : void   init() : void	106106	16.016	3.03	0.9 0.990%
fitHeightToDesktop(int) : int   fitHeightToDesktop(int) : int	150150	5.05	2.02	0.85714287 0.8571428785.7%
addCommandListeners() : void   addCommandListeners() : void	168168	3.03	1.01	1.0 1.0100%
adjustLayout() : void   adjustLayout() : void	181181	14.014	8.08	0.7307692 0.730769273.1%
adjustInitialLayout() : void   adjustInitialLayout() : void	221221	30.030	4.04	0.9166667 0.916666791.7%
internalFrameClosed(InternalFrameEvent) : void   internalFrameClosed(InternalFrameEvent) : void	296296	1.01	1.01	1.0 1.0100%
addCloseFrameListener() : void   addCloseFrameListener() : void	292292	1.01	1.01	1.0 1.0100%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	313313	5.05	3.03	0.0 0.00%
keyReleased(KeyEvent) : void   keyReleased(KeyEvent) : void	333333	4.04	2.02	0.0 0.00%
addKeyListener() : void   addKeyListener() : void	308308	1.01	1.01	1.0 1.0100%
overrideKey(KeyEvent,AlignFrame) : boolean   overrideKey(KeyEvent,AlignFrame) : boolean	362362	19.019	7.07	0.0 0.00%
addKeyBindings() : void   addKeyBindings() : void	400400	2.02	1.01	1.0 1.0100%
overrideImplementedKeyBindings() : void   overrideImplementedKeyBindings() : void	411411	5.05	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	433433	1.01	1.01	0.0 0.00%
overrideCloseView() : void   overrideCloseView() : void	423423	4.04	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	454454	1.01	1.01	0.0 0.00%
overrideNewView() : void   overrideNewView() : void	445445	3.03	1.01	1.0 1.0100%
overrideDelegatedKeyBindings() : void   overrideDelegatedKeyBindings() : void	468468	3.03	2.02	0.8 0.880%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	498498	4.04	3.03	0.0 0.00%
overrideKeyBinding(Entry<KeyStroke, JMenuItem>) : void   overrideKeyBinding(Entry<KeyStroke, JMenuItem>) : void	491491	4.04	1.01	1.0 1.0100%
overrideKeyBinding(KeyStroke,AbstractAction) : void   overrideKeyBinding(KeyStroke,AbstractAction) : void	519519	2.02	1.01	1.0 1.0100%
newView_actionPerformed() : void   newView_actionPerformed() : void	536536	15.015	2.02	0.0 0.00%
closeView_actionPerformed() : void   closeView_actionPerformed() : void	583583	8.08	2.02	0.0 0.00%
close() : void   close() : void	603603	4.04	2.02	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	624624	1.01	1.01	0.0 0.00%
overrideExpandViews() : void   overrideExpandViews() : void	619619	3.03	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	641641	1.01	1.01	0.0 0.00%
overrideGatherViews() : void   overrideGatherViews() : void	636636	3.03	1.01	1.0 1.0100%
overrideMenuItem(KeyStroke,AbstractAction) : void   overrideMenuItem(KeyStroke,AbstractAction) : void	657657	2.02	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	685685	1.01	1.01	0.0 0.00%
overrideMenuItem(KeyStroke,AbstractAction,JComponent) : void   overrideMenuItem(KeyStroke,AbstractAction,JComponent) : void	671671	6.06	3.03	0.8 0.880%
expandViews_actionPerformed() : void   expandViews_actionPerformed() : void	699699	1.01	1.01	0.0 0.00%
gatherViews_actionPerformed() : void   gatherViews_actionPerformed() : void	708708	1.01	1.01	0.0 0.00%
getComplement(Object) : AlignmentI   getComplement(Object) : AlignmentI	716716	5.05	3.03	0.0 0.00%
getComplementTitle(Object) : String   getComplementTitle(Object) : String	733733	5.05	3.03	0.0 0.00%
setComplementVisible(Object,boolean) : void   setComplementVisible(Object,boolean) : void	750750	5.05	3.03	0.0 0.00%
getAlignFrames() : List<AlignFrame>   getAlignFrames() : List<AlignFrame>	773773	1.01	1.01	0.0 0.00%
getComplementAlignFrame(AlignViewControllerGuiI) : AlignFrame   getComplementAlignFrame(AlignViewControllerGuiI) : AlignFrame	780780	5.05	3.03	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	810810	4.04	3.03	0.0 0.00%
overrideFind() : void   overrideFind() : void	801801	3.03	1.01	1.0 1.0100%
setSelected(boolean) : void   setSelected(boolean) : void	827827	7.07	5.05	0.53846157 0.5384615753.8%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	868868	6.06	7.07	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	902902	3.03	2.02	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	919919	6.06	3.03	0.0 0.00%
internalFrameClosed(javax.swing.event.InternalFrameEvent) : void   internalFrameClosed(javax.swing.event.InternalFrameEvent) : void	10001000	8.08	3.03	0.0 0.00%
addFeatureSettingsUI(FeatureSettingsControllerGuiI) : void   addFeatureSettingsUI(FeatureSettingsControllerGuiI) : void	856856	39.039	8.08	0.0 0.00%
createDummyTabs() : void   createDummyTabs() : void	10381038	3.03	2.02	0.0 0.00%
replaceWithDummyTab(FeatureSettingsControllerI) : void   replaceWithDummyTab(FeatureSettingsControllerI) : void	10471047	9.09	5.05	0.0 0.00%
closeFeatureSettings(FeatureSettingsControllerI,boolean) : void   closeFeatureSettings(FeatureSettingsControllerI,boolean) : void	10741074	6.06	4.04	0.0 0.00%
isFeatureSettingsOpen() : boolean   isFeatureSettingsOpen() : boolean	10981098	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.34451902	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.26845637	jalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResiduejalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResidue	1PASS
	0.015659954	jalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumnjalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumn	1PASS

 

Source view

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.gui;
22
23		import java.awt.BorderLayout;
24		import java.awt.Component;
25		import java.awt.Dimension;
26		import java.awt.event.ActionEvent;
27		import java.awt.event.ActionListener;
28		import java.awt.event.KeyAdapter;
29		import java.awt.event.KeyEvent;
30		import java.awt.event.KeyListener;
31		import java.beans.PropertyVetoException;
32		import java.util.Arrays;
33		import java.util.List;
34		import java.util.Map.Entry;
35
36		import javax.swing.AbstractAction;
37		import javax.swing.InputMap;
38		import javax.swing.JButton;
39		import javax.swing.JComponent;
40		import javax.swing.JDesktopPane;
41		import javax.swing.JInternalFrame;
42		import javax.swing.JLayeredPane;
43		import javax.swing.JMenuItem;
44		import javax.swing.JPanel;
45		import javax.swing.JTabbedPane;
46		import javax.swing.KeyStroke;
47		import javax.swing.event.ChangeEvent;
48		import javax.swing.event.ChangeListener;
49		import javax.swing.event.InternalFrameAdapter;
50		import javax.swing.event.InternalFrameEvent;
51
52		import jalview.api.AlignViewControllerGuiI;
53		import jalview.api.FeatureSettingsControllerI;
54		import jalview.api.SplitContainerI;
55		import jalview.controller.FeatureSettingsControllerGuiI;
56		import jalview.datamodel.AlignmentI;
57		import jalview.jbgui.GAlignFrame;
58		import jalview.jbgui.GSplitFrame;
59		import jalview.structure.StructureSelectionManager;
60		import jalview.util.MessageManager;
61		import jalview.util.Platform;
62		import jalview.viewmodel.AlignmentViewport;
63
64		/**
65		* An internal frame on the desktop that hosts a horizontally split view of
66		* linked DNA and Protein alignments. Additional views can be created in linked
67		* pairs, expanded to separate split frames, or regathered into a single frame.
68		* <p>
69		* (Some) operations on each alignment are automatically mirrored on the other.
70		* These include mouseover (highlighting), sequence and column selection,
71		* sequence ordering and sorting, and grouping, colouring and sorting by tree.
72		*
73		* @author gmcarstairs
74		*
75		*/
		36% Uncovered Elements: 286 (447) Complexity: 121 Complexity Density: 0.41
76		public class SplitFrame extends GSplitFrame implements SplitContainerI
77		{
78		private static final int WINDOWS_INSETS_WIDTH = 28; // tbc
79
80		private static final int MAC_INSETS_WIDTH = 28;
81
82		private static final int WINDOWS_INSETS_HEIGHT = 50; // tbc
83
84		private static final int MAC_INSETS_HEIGHT = 50;
85
86		private static final int DESKTOP_DECORATORS_HEIGHT = 65;
87
88		private static final long serialVersionUID = 1L;
89
90		/**
91		* geometry for Feature Settings Holder
92		*/
93		private static final int FS_MIN_WIDTH = 400;
94
95		private static final int FS_MIN_HEIGHT = 400;
96
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
97	3	public SplitFrame(GAlignFrame top, GAlignFrame bottom)...
98		{
99	3	super(top, bottom);
100	3	init();
101		}
102
103		/**
104		* Initialise this frame.
105		*/
		90% Uncovered Elements: 2 (20) Complexity: 3 Complexity Density: 0.19
106	3	protected void init()...
107		{
108	3	getTopFrame().setSplitFrame(this);
109	3	getBottomFrame().setSplitFrame(this);
110	3	getTopFrame().setVisible(true);
111	3	getBottomFrame().setVisible(true);
112
113	3	((AlignFrame) getTopFrame()).getViewport().setCodingComplement(
114		((AlignFrame) getBottomFrame()).getViewport());
115
116		/*
117		* estimate width and height of SplitFrame; this.getInsets() doesn't seem to
118		* give the full additional size (a few pixels short)
119		*/
120	3	int widthFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_WIDTH
121		: WINDOWS_INSETS_WIDTH;
122	3	int heightFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT
123		: WINDOWS_INSETS_HEIGHT;
124	3	int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge;
125	3	int height = ((AlignFrame) getTopFrame()).getHeight()
126		+ ((AlignFrame) getBottomFrame()).getHeight() + DIVIDER_SIZE
127		+ heightFudge;
128	3	height = fitHeightToDesktop(height);
129	3	setSize(width, height);
130
131	3	adjustLayout();
132
133	3	addCloseFrameListener();
134
135	3	addKeyListener();
136
137	3	addKeyBindings();
138
139	3	addCommandListeners();
140		}
141
142		/**
143		* Reduce the height if too large to fit in the Desktop. Also adjust the
144		* divider location in proportion.
145		*
146		* @param height
147		* in pixels
148		* @return original or reduced height
149		*/
		85.7% Uncovered Elements: 1 (7) Complexity: 2 Complexity Density: 0.4
150	3	public int fitHeightToDesktop(int height)...
151		{
152		// allow about 65 pixels for Desktop decorators on Windows
153
154	3	int newHeight = Math.min(height,
155		Desktop.instance.getHeight() - DESKTOP_DECORATORS_HEIGHT);
156	3	if (newHeight != height)
157		{
158	3	int oldDividerLocation = getDividerLocation();
159	3	setDividerLocation(oldDividerLocation * newHeight / height);
160		}
161	3	return newHeight;
162		}
163
164		/**
165		* Set the top and bottom frames to listen to each others Commands (e.g. Edit,
166		* Order).
167		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
168	3	protected void addCommandListeners()...
169		{
170		// TODO if CommandListener is only ever 1:1 for complementary views,
171		// may change broadcast pattern to direct messaging (more efficient)
172	3	final StructureSelectionManager ssm = StructureSelectionManager
173		.getStructureSelectionManager(Desktop.instance);
174	3	ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
175	3	ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
176		}
177
178		/**
179		* Do any tweaking and twerking of the layout wanted.
180		*/
		73.1% Uncovered Elements: 7 (26) Complexity: 8 Complexity Density: 0.57
181	3	public void adjustLayout()...
182		{
183	3	final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
184	3	final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
185
186		/*
187		* Ensure sequence ids are the same width so sequences line up
188		*/
189	3	int w1 = topViewport.getIdWidth();
190	3	int w2 = bottomViewport.getIdWidth();
191	3	int w3 = Math.max(w1, w2);
192	3	topViewport.setIdWidth(w3);
193	3	bottomViewport.setIdWidth(w3);
194
195		/*
196		* Scale protein to either 1 or 3 times character width of dna
197		*/
198	3	final AlignmentI topAlignment = topViewport.getAlignment();
199	3	final AlignmentI bottomAlignment = bottomViewport.getAlignment();
200	3	AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
201	0	: (bottomAlignment.isNucleotide() ? bottomViewport : null);
202	3	AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
203	3	: (!bottomAlignment.isNucleotide() ? bottomViewport : null);
204	3	if (protein != null && cdna != null)
205		{
206	3	int scale = protein.isScaleProteinAsCdna() ? 3 : 1;
207	3	protein.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
208		}
209		}
210
211		/**
212		* Adjusts the divider for a sensible split of the real estate (for example,
213		* when many transcripts are shown with a single protein). This should only be
214		* called after the split pane has been laid out (made visible) so it has a
215		* height. The aim is to avoid unnecessary vertical scroll bars, while
216		* ensuring that at least 2 sequences are visible in each panel.
217		* <p>
218		* Once laid out, the user may choose to customise as they wish, so this
219		* method is not called again after the initial layout.
220		*/
		91.7% Uncovered Elements: 3 (36) Complexity: 4 Complexity Density: 0.13
221	2	protected void adjustInitialLayout()...
222		{
223	2	AlignFrame topFrame = (AlignFrame) getTopFrame();
224	2	AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
225
226		/*
227		* recompute layout of top and bottom panels to reflect their
228		* actual (rather than requested) height
229		*/
230	2	topFrame.alignPanel.adjustAnnotationHeight();
231	2	bottomFrame.alignPanel.adjustAnnotationHeight();
232
233	2	final AlignViewport topViewport = topFrame.viewport;
234	2	final AlignViewport bottomViewport = bottomFrame.viewport;
235	2	final AlignmentI topAlignment = topViewport.getAlignment();
236	2	final AlignmentI bottomAlignment = bottomViewport.getAlignment();
237	2	boolean topAnnotations = topViewport.isShowAnnotation();
238	2	boolean bottomAnnotations = bottomViewport.isShowAnnotation();
239		// TODO need number of visible sequences here, not #sequences - how?
240	2	int topCount = topAlignment.getHeight();
241	2	int bottomCount = bottomAlignment.getHeight();
242	2	int topCharHeight = topViewport.getViewStyle().getCharHeight();
243	2	int bottomCharHeight = bottomViewport.getViewStyle().getCharHeight();
244
245		/*
246		* calculate the minimum ratio that leaves at least the height
247		* of two sequences (after rounding) visible in the top panel
248		*/
249	2	int topPanelHeight = topFrame.getHeight();
250	2	int bottomPanelHeight = bottomFrame.getHeight();
251	2	int topSequencesHeight = topFrame.alignPanel.getSeqPanel().seqCanvas
252		.getHeight();
253	2	int topPanelMinHeight = topPanelHeight
254		- Math.max(0, topSequencesHeight - 3 * topCharHeight);
255	2	double totalHeight = (double) topPanelHeight + bottomPanelHeight;
256	2	double minRatio = topPanelMinHeight / totalHeight;
257
258		/*
259		* calculate the maximum ratio that leaves at least the height
260		* of two sequences (after rounding) visible in the bottom panel
261		*/
262	2	int bottomSequencesHeight = bottomFrame.alignPanel.getSeqPanel().seqCanvas
263		.getHeight();
264	2	int bottomPanelMinHeight = bottomPanelHeight
265		- Math.max(0, bottomSequencesHeight - 3 * bottomCharHeight);
266	2	double maxRatio = (totalHeight - bottomPanelMinHeight) / totalHeight;
267
268		/*
269		* estimate ratio of (topFrameContent / bottomFrameContent)
270		*/
271	2	int insets = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT
272		: WINDOWS_INSETS_HEIGHT;
273		// allow 3 'rows' for scale, scrollbar, status bar
274	2	int topHeight = insets + (3 + topCount) * topCharHeight
275	2	+ (topAnnotations ? topViewport.calcPanelHeight() : 0);
276	2	int bottomHeight = insets + (3 + bottomCount) * bottomCharHeight
277	2	+ (bottomAnnotations ? bottomViewport.calcPanelHeight() : 0);
278	2	double ratio = ((double) topHeight)
279		/ (double) (topHeight + bottomHeight);
280
281		/*
282		* limit ratio to avoid concealing all sequences
283		*/
284	2	ratio = Math.min(ratio, maxRatio);
285	2	ratio = Math.max(ratio, minRatio);
286	2	setRelativeDividerLocation(ratio);
287		}
288
289		/**
290		* Add a listener to tidy up when the frame is closed.
291		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
292	3	protected void addCloseFrameListener()...
293		{
294	3	addInternalFrameListener(new InternalFrameAdapter()
295		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
296	2	@Override...
297		public void internalFrameClosed(InternalFrameEvent evt)
298		{
299	2	close();
300		};
301		});
302		}
303
304		/**
305		* Add a key listener that delegates to whichever split component the mouse is
306		* in (or does nothing if neither).
307		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
308	3	protected void addKeyListener()...
309		{
310	3	addKeyListener(new KeyAdapter()
311		{
312
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
313	0	@Override...
314		public void keyPressed(KeyEvent e)
315		{
316	0	AlignFrame af = (AlignFrame) getFrameAtMouse();
317
318		/*
319		* Intercept and override any keys here if wanted.
320		*/
321	0	if (!overrideKey(e, af))
322		{
323	0	if (af != null)
324		{
325	0	for (KeyListener kl : af.getKeyListeners())
326		{
327	0	kl.keyPressed(e);
328		}
329		}
330		}
331		}
332
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
333	0	@Override...
334		public void keyReleased(KeyEvent e)
335		{
336	0	Component c = getFrameAtMouse();
337	0	if (c != null)
338		{
339	0	for (KeyListener kl : c.getKeyListeners())
340		{
341	0	kl.keyReleased(e);
342		}
343		}
344		}
345
346		});
347		}
348
349		/**
350		* Returns true if the key event is overriden and actioned (or ignored) here,
351		* else returns false, indicating it should be delegated to the AlignFrame's
352		* usual handler.
353		* <p>
354		* We can't handle Cmd-Key combinations here, instead this is done by
355		* overriding key bindings.
356		*
357		* @see addKeyOverrides
358		* @param e
359		* @param af
360		* @return
361		*/
		0% Uncovered Elements: 23 (23) Complexity: 7 Complexity Density: 0.37
362	0	protected boolean overrideKey(KeyEvent e, AlignFrame af)...
363		{
364	0	boolean actioned = false;
365	0	int keyCode = e.getKeyCode();
366	0	switch (keyCode)
367		{
368	0	case KeyEvent.VK_DOWN:
369	0	if (e.isAltDown() || !af.viewport.cursorMode)
370		{
371		/*
372		* Key down (or Alt-key-down in cursor mode) - move selected sequences
373		*/
374	0	((AlignFrame) getTopFrame()).moveSelectedSequences(false);
375	0	((AlignFrame) getBottomFrame()).moveSelectedSequences(false);
376	0	actioned = true;
377	0	e.consume();
378		}
379	0	break;
380	0	case KeyEvent.VK_UP:
381	0	if (e.isAltDown() || !af.viewport.cursorMode)
382		{
383		/*
384		* Key up (or Alt-key-up in cursor mode) - move selected sequences
385		*/
386	0	((AlignFrame) getTopFrame()).moveSelectedSequences(true);
387	0	((AlignFrame) getBottomFrame()).moveSelectedSequences(true);
388	0	actioned = true;
389	0	e.consume();
390		}
391	0	break;
392	0	default:
393		}
394	0	return actioned;
395		}
396
397		/**
398		* Set key bindings (recommended for Swing over key accelerators).
399		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
400	3	private void addKeyBindings()...
401		{
402	3	overrideDelegatedKeyBindings();
403
404	3	overrideImplementedKeyBindings();
405		}
406
407		/**
408		* Override key bindings with alternative action methods implemented in this
409		* class.
410		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
411	3	protected void overrideImplementedKeyBindings()...
412		{
413	3	overrideFind();
414	3	overrideNewView();
415	3	overrideCloseView();
416	3	overrideExpandViews();
417	3	overrideGatherViews();
418		}
419
420		/**
421		* Replace Cmd-W close view action with our version.
422		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
423	3	protected void overrideCloseView()...
424		{
425	3	AbstractAction action;
426		/*
427		* Ctrl-W / Cmd-W - close view or window
428		*/
429	3	KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W,
430		jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
431	3	action = new AbstractAction()
432		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
433	0	@Override...
434		public void actionPerformed(ActionEvent e)
435		{
436	0	closeView_actionPerformed();
437		}
438		};
439	3	overrideKeyBinding(key_cmdW, action);
440		}
441
442		/**
443		* Replace Cmd-T new view action with our version.
444		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
445	3	protected void overrideNewView()...
446		{
447		/*
448		* Ctrl-T / Cmd-T open new view
449		*/
450	3	KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T,
451		jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
452	3	AbstractAction action = new AbstractAction()
453		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
454	0	@Override...
455		public void actionPerformed(ActionEvent e)
456		{
457	0	newView_actionPerformed();
458		}
459		};
460	3	overrideKeyBinding(key_cmdT, action);
461		}
462
463		/**
464		* For now, delegates key events to the corresponding key accelerator for the
465		* AlignFrame that the mouse is in. Hopefully can be simplified in future if
466		* AlignFrame is changed to use key bindings rather than accelerators.
467		*/
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.67
468	3	protected void overrideDelegatedKeyBindings()...
469		{
470	3	if (getTopFrame() instanceof AlignFrame)
471		{
472		/*
473		* Get all accelerator keys in the top frame (the bottom should be
474		* identical) and override each one.
475		*/
476	3	for (Entry<KeyStroke, JMenuItem> acc : ((AlignFrame) getTopFrame())
477		.getAccelerators().entrySet())
478		{
479	78	overrideKeyBinding(acc);
480		}
481		}
482		}
483
484		/**
485		* Overrides an AlignFrame key accelerator with our version which delegates to
486		* the action listener in whichever frame has the mouse (and does nothing if
487		* neither has).
488		*
489		* @param acc
490		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
491	78	private void overrideKeyBinding(Entry<KeyStroke, JMenuItem> acc)...
492		{
493	78	final KeyStroke ks = acc.getKey();
494	78	InputMap inputMap = this.getInputMap(JComponent.WHEN_FOCUSED);
495	78	inputMap.put(ks, ks);
496	78	this.getActionMap().put(ks, new AbstractAction()
497		{
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
498	0	@Override...
499		public void actionPerformed(ActionEvent e)
500		{
501	0	Component c = getFrameAtMouse();
502	0	if (c != null && c instanceof AlignFrame)
503		{
504	0	for (ActionListener a : ((AlignFrame) c).getAccelerators().get(ks)
505		.getActionListeners())
506		{
507	0	a.actionPerformed(null);
508		}
509		}
510		}
511		});
512		}
513
514		/**
515		* Replace an accelerator key's action with the specified action.
516		*
517		* @param ks
518		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
519	9	protected void overrideKeyBinding(KeyStroke ks, AbstractAction action)...
520		{
521	9	this.getActionMap().put(ks, action);
522	9	overrideMenuItem(ks, action);
523		}
524
525		/**
526		* Create and link new views (with matching names) in both panes.
527		* <p>
528		* Note this is _not_ multiple tabs, each hosting a split pane view, rather it
529		* is a single split pane with each split holding multiple tabs which are
530		* linked in pairs.
531		* <p>
532		* TODO implement instead with a tabbed holder in the SplitView, each tab
533		* holding a single JSplitPane. Would avoid a duplicated tab, at the cost of
534		* some additional coding.
535		*/
		0% Uncovered Elements: 17 (17) Complexity: 2 Complexity Density: 0.13
536	0	protected void newView_actionPerformed()...
537		{
538	0	AlignFrame topFrame = (AlignFrame) getTopFrame();
539	0	AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
540	0	final boolean scaleProteinAsCdna = topFrame.viewport
541		.isScaleProteinAsCdna();
542
543	0	AlignmentPanel newTopPanel = topFrame.newView(null, true);
544	0	AlignmentPanel newBottomPanel = bottomFrame.newView(null, true);
545
546		/*
547		* This currently (for the first new view only) leaves the top pane on tab 0
548		* but the bottom on tab 1. This results from 'setInitialTabVisible' echoing
549		* from the bottom back to the first frame. Next line is a fudge to work
550		* around this. TODO find a better way.
551		*/
552	0	if (topFrame.getTabIndex() != bottomFrame.getTabIndex())
553		{
554	0	topFrame.setDisplayedView(newTopPanel);
555		}
556
557	0	newBottomPanel.av.setViewName(newTopPanel.av.getViewName());
558	0	newTopPanel.av.setCodingComplement(newBottomPanel.av);
559
560		/*
561		* These lines can be removed once scaleProteinAsCdna is added to element
562		* Viewport in jalview.xsd, as Jalview2XML.copyAlignPanel will then take
563		* care of it
564		*/
565	0	newTopPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
566	0	newBottomPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
567
568		/*
569		* Line up id labels etc
570		*/
571	0	adjustLayout();
572
573	0	final StructureSelectionManager ssm = StructureSelectionManager
574		.getStructureSelectionManager(Desktop.instance);
575	0	ssm.addCommandListener(newTopPanel.av);
576	0	ssm.addCommandListener(newBottomPanel.av);
577		}
578
579		/**
580		* Close the currently selected view in both panes. If there is only one view,
581		* close this split frame.
582		*/
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.25
583	0	protected void closeView_actionPerformed()...
584		{
585	0	int viewCount = ((AlignFrame) getTopFrame()).getAlignPanels().size();
586	0	if (viewCount < 2)
587		{
588	0	close();
589	0	return;
590		}
591
592	0	AlignmentPanel topPanel = ((AlignFrame) getTopFrame()).alignPanel;
593	0	AlignmentPanel bottomPanel = ((AlignFrame) getBottomFrame()).alignPanel;
594
595	0	((AlignFrame) getTopFrame()).closeView(topPanel);
596	0	((AlignFrame) getBottomFrame()).closeView(bottomPanel);
597
598		}
599
600		/**
601		* Close child frames and this split frame.
602		*/
		100% Uncovered Elements: 0 (4) Complexity: 2 Complexity Density: 0.5
603	2	public void close()...
604		{
605	2	((AlignFrame) getTopFrame()).closeMenuItem_actionPerformed(true);
606	2	((AlignFrame) getBottomFrame()).closeMenuItem_actionPerformed(true);
607	2	try
608		{
609	2	this.setClosed(true);
610		} catch (PropertyVetoException e)
611		{
612		// ignore
613		}
614		}
615
616		/**
617		* Replace AlignFrame 'expand views' action with SplitFrame version.
618		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
619	3	protected void overrideExpandViews()...
620		{
621	3	KeyStroke key_X = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
622	3	AbstractAction action = new AbstractAction()
623		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
624	0	@Override...
625		public void actionPerformed(ActionEvent e)
626		{
627	0	expandViews_actionPerformed();
628		}
629		};
630	3	overrideMenuItem(key_X, action);
631		}
632
633		/**
634		* Replace AlignFrame 'gather views' action with SplitFrame version.
635		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
636	3	protected void overrideGatherViews()...
637		{
638	3	KeyStroke key_G = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
639	3	AbstractAction action = new AbstractAction()
640		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
641	0	@Override...
642		public void actionPerformed(ActionEvent e)
643		{
644	0	gatherViews_actionPerformed();
645		}
646		};
647	3	overrideMenuItem(key_G, action);
648		}
649
650		/**
651		* Override the menu action associated with the keystroke in the child frames,
652		* replacing it with the given action.
653		*
654		* @param ks
655		* @param action
656		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
657	15	private void overrideMenuItem(KeyStroke ks, AbstractAction action)...
658		{
659	15	overrideMenuItem(ks, action, getTopFrame());
660	15	overrideMenuItem(ks, action, getBottomFrame());
661		}
662
663		/**
664		* Override the menu action associated with the keystroke in one child frame,
665		* replacing it with the given action. Mwahahahaha.
666		*
667		* @param key
668		* @param action
669		* @param comp
670		*/
		80% Uncovered Elements: 2 (10) Complexity: 3 Complexity Density: 0.5
671	30	private void overrideMenuItem(KeyStroke key, final AbstractAction action,...
672		JComponent comp)
673		{
674	30	if (comp instanceof AlignFrame)
675		{
676	30	JMenuItem mi = ((AlignFrame) comp).getAccelerators().get(key);
677	30	if (mi != null)
678		{
679	30	for (ActionListener al : mi.getActionListeners())
680		{
681	30	mi.removeActionListener(al);
682		}
683	30	mi.addActionListener(new ActionListener()
684		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
685	0	@Override...
686		public void actionPerformed(ActionEvent e)
687		{
688	0	action.actionPerformed(e);
689		}
690		});
691		}
692		}
693		}
694
695		/**
696		* Expand any multiple views (which are always in pairs) into separate split
697		* frames.
698		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
699	0	protected void expandViews_actionPerformed()...
700		{
701	0	Desktop.instance.explodeViews(this);
702		}
703
704		/**
705		* Gather any other SplitFrame views of this alignment back in as multiple
706		* (pairs of) views in this SplitFrame.
707		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
708	0	protected void gatherViews_actionPerformed()...
709		{
710	0	Desktop.instance.gatherViews(this);
711		}
712
713		/**
714		* Returns the alignment in the complementary frame to the one given.
715		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
716	0	@Override...
717		public AlignmentI getComplement(Object alignFrame)
718		{
719	0	if (alignFrame == this.getTopFrame())
720		{
721	0	return ((AlignFrame) getBottomFrame()).viewport.getAlignment();
722		}
723	0	else if (alignFrame == this.getBottomFrame())
724		{
725	0	return ((AlignFrame) getTopFrame()).viewport.getAlignment();
726		}
727	0	return null;
728		}
729
730		/**
731		* Returns the title of the complementary frame to the one given.
732		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
733	0	@Override...
734		public String getComplementTitle(Object alignFrame)
735		{
736	0	if (alignFrame == this.getTopFrame())
737		{
738	0	return ((AlignFrame) getBottomFrame()).getTitle();
739		}
740	0	else if (alignFrame == this.getBottomFrame())
741		{
742	0	return ((AlignFrame) getTopFrame()).getTitle();
743		}
744	0	return null;
745		}
746
747		/**
748		* Set the 'other half' to hidden / revealed.
749		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
750	0	@Override...
751		public void setComplementVisible(Object alignFrame, boolean show)
752		{
753		/*
754		* Hiding the AlignPanel suppresses unnecessary repaints
755		*/
756	0	if (alignFrame == getTopFrame())
757		{
758	0	((AlignFrame) getBottomFrame()).alignPanel.setVisible(show);
759		}
760	0	else if (alignFrame == getBottomFrame())
761		{
762	0	((AlignFrame) getTopFrame()).alignPanel.setVisible(show);
763		}
764	0	super.setComplementVisible(alignFrame, show);
765		}
766
767		/**
768		* return the AlignFrames held by this container
769		*
770		* @return { Top alignFrame (Usually CDS), Bottom AlignFrame (Usually
771		* Protein)}
772		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
773	0	public List<AlignFrame> getAlignFrames()...
774		{
775	0	return Arrays
776		.asList(new AlignFrame[]
777		{ (AlignFrame) getTopFrame(), (AlignFrame) getBottomFrame() });
778		}
779
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
780	0	@Override...
781		public AlignFrame getComplementAlignFrame(
782		AlignViewControllerGuiI alignFrame)
783		{
784	0	if (getTopFrame() == alignFrame)
785		{
786	0	return (AlignFrame) getBottomFrame();
787		}
788	0	if (getBottomFrame() == alignFrame)
789		{
790	0	return (AlignFrame) getTopFrame();
791		}
792		// we didn't know anything about this frame...
793	0	return null;
794		}
795
796		/**
797		* Replace Cmd-F Find action with our version. This is necessary because the
798		* 'default' Finder searches in the first AlignFrame it finds. We need it to
799		* search in the half of the SplitFrame that has the mouse.
800		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
801	3	protected void overrideFind()...
802		{
803		/*
804		* Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
805		*/
806	3	KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F,
807		jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx(), false);
808	3	AbstractAction action = new AbstractAction()
809		{
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
810	0	@Override...
811		public void actionPerformed(ActionEvent e)
812		{
813	0	Component c = getFrameAtMouse();
814	0	if (c != null && c instanceof AlignFrame)
815		{
816	0	AlignFrame af = (AlignFrame) c;
817	0	new Finder(af.viewport, af.alignPanel);
818		}
819		}
820		};
821	3	overrideKeyBinding(key_cmdF, action);
822		}
823
824		/**
825		* Override to do nothing if triggered from one of the child frames
826		*/
		53.8% Uncovered Elements: 6 (13) Complexity: 5 Complexity Density: 0.71
827	11	@Override...
828		public void setSelected(boolean selected) throws PropertyVetoException
829		{
830	11	JDesktopPane desktopPane = getDesktopPane();
831	11	JInternalFrame fr = desktopPane == null ? null
832		: desktopPane.getSelectedFrame();
833	11	if (fr == getTopFrame() || fr == getBottomFrame())
834		{
835		/*
836		* patch for JAL-3288 (deselecting top/bottom frame closes popup menu);
837		* it may be possible to remove this method in future
838		* if the underlying Java behaviour changes
839		*/
840	0	if (selected)
841		{
842	0	moveToFront();
843		}
844	0	return;
845		}
846	11	super.setSelected(selected);
847		}
848
849		/**
850		* holds the frame for feature settings, so Protein and DNA tabs can be managed
851		*/
852		JInternalFrame featureSettingsUI;
853
854		JTabbedPane featureSettingsPanels;
855
		0% Uncovered Elements: 51 (51) Complexity: 8 Complexity Density: 0.21
856	0	@Override...
857		public void addFeatureSettingsUI(
858		FeatureSettingsControllerGuiI featureSettings)
859		{
860	0	boolean showInternalFrame = false;
861	0	if (featureSettingsUI == null || featureSettingsPanels == null)
862		{
863	0	showInternalFrame = true;
864	0	featureSettingsPanels = new JTabbedPane();
865	0	featureSettingsPanels.addChangeListener(new ChangeListener()
866		{
867
		0% Uncovered Elements: 10 (10) Complexity: 7 Complexity Density: 1.17
868	0	@Override...
869		public void stateChanged(ChangeEvent e)
870		{
871	0	if (e.getSource() != featureSettingsPanels
872		|| featureSettingsUI == null
873		|| featureSettingsUI.isClosed()
874		|| !featureSettingsUI.isVisible())
875		{
876		// not our tabbed pane
877	0	return;
878		}
879	0	int tab = featureSettingsPanels.getSelectedIndex();
880	0	if (tab < 0 || featureSettingsPanels
881		.getSelectedComponent() instanceof FeatureSettingsControllerGuiI)
882		{
883		// no tab selected or already showing a feature settings GUI
884	0	return;
885		}
886	0	getAlignFrames().get(tab).showFeatureSettingsUI();
887		}
888		});
889	0	featureSettingsUI = new JInternalFrame(MessageManager.getString(
890		"label.sequence_feature_settings_for_CDS_and_Protein"));
891	0	featureSettingsPanels.setOpaque(true);
892
893	0	JPanel dialog = new JPanel();
894	0	dialog.setOpaque(true);
895	0	dialog.setLayout(new BorderLayout());
896	0	dialog.add(featureSettingsPanels, BorderLayout.CENTER);
897	0	JPanel buttons = new JPanel();
898	0	JButton ok = new JButton(MessageManager.getString("action.ok"));
899	0	ok.addActionListener(new ActionListener()
900		{
901
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
902	0	@Override...
903		public void actionPerformed(ActionEvent e)
904		{
905	0	try
906		{
907	0	featureSettingsUI.setClosed(true);
908		} catch (PropertyVetoException pv)
909		{
910	0	pv.printStackTrace();
911		}
912		}
913		});
914	0	JButton cancel = new JButton(
915		MessageManager.getString("action.cancel"));
916	0	cancel.addActionListener(new ActionListener()
917		{
918
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
919	0	@Override...
920		public void actionPerformed(ActionEvent e)
921		{
922	0	try
923		{
924	0	for (Component fspanel : featureSettingsPanels.getComponents())
925		{
926	0	if (fspanel instanceof FeatureSettingsControllerGuiI)
927		{
928	0	((FeatureSettingsControllerGuiI) fspanel).revert();
929		}
930		}
931	0	featureSettingsUI.setClosed(true);
932		} catch (Exception pv)
933		{
934	0	pv.printStackTrace();
935		}
936		}
937		});
938	0	buttons.add(ok);
939	0	buttons.add(cancel);
940	0	dialog.add(buttons, BorderLayout.SOUTH);
941	0	featureSettingsUI.setContentPane(dialog);
942	0	createDummyTabs();
943		}
944	0	if (featureSettingsPanels
945		.indexOfTabComponent((Component) featureSettings) > -1)
946		{
947		// just show the feature settings !
948	0	featureSettingsPanels
949		.setSelectedComponent((Component) featureSettings);
950	0	return;
951		}
952		// otherwise replace the dummy tab with the given feature settings
953	0	int pos = getAlignFrames().indexOf(featureSettings.getAlignframe());
954		// if pos==-1 then alignFrame isn't managed by this splitframe
955	0	if (pos == 0)
956		{
957	0	featureSettingsPanels.removeTabAt(0);
958	0	featureSettingsPanels.insertTab(tabName[0], null,
959		(Component) featureSettings,
960		MessageManager.formatMessage(
961		"label.sequence_feature_settings_for", tabName[0]),
962		0);
963		}
964	0	if (pos == 1)
965		{
966	0	featureSettingsPanels.removeTabAt(1);
967	0	featureSettingsPanels.insertTab(tabName[1], null,
968		(Component) featureSettings,
969		MessageManager.formatMessage(
970		"label.sequence_feature_settings_for", tabName[1]),
971		1);
972		}
973	0	featureSettingsPanels.setSelectedComponent((Component) featureSettings);
974
975		// TODO: JAL-3535 - construct a feature settings title including names of
976		// currently selected CDS and Protein names
977
978	0	if (showInternalFrame)
979		{
980	0	if (Platform.isAMacAndNotJS())
981		{
982	0	Desktop.addInternalFrame(featureSettingsUI,
983		MessageManager.getString(
984		"label.sequence_feature_settings_for_CDS_and_Protein"),
985		600, 480);
986		}
987		else
988		{
989	0	Desktop.addInternalFrame(featureSettingsUI,
990		MessageManager.getString(
991		"label.sequence_feature_settings_for_CDS_and_Protein"),
992		600, 450);
993		}
994	0	featureSettingsUI
995		.setMinimumSize(new Dimension(FS_MIN_WIDTH, FS_MIN_HEIGHT));
996
997	0	featureSettingsUI.addInternalFrameListener(
998		new javax.swing.event.InternalFrameAdapter()
999		{
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
1000	0	@Override...
1001		public void internalFrameClosed(
1002		javax.swing.event.InternalFrameEvent evt)
1003		{
1004	0	for (int tab = 0; tab < featureSettingsPanels
1005		.getTabCount();)
1006		{
1007	0	FeatureSettingsControllerGuiI fsettings = (FeatureSettingsControllerGuiI) featureSettingsPanels
1008		.getTabComponentAt(tab);
1009	0	if (fsettings != null)
1010		{
1011	0	featureSettingsPanels.removeTabAt(tab);
1012	0	fsettings.featureSettings_isClosed();
1013		}
1014		else
1015		{
1016	0	tab++;
1017		}
1018		}
1019	0	featureSettingsPanels = null;
1020	0	featureSettingsUI = null;
1021		};
1022		});
1023	0	featureSettingsUI.setLayer(JLayeredPane.PALETTE_LAYER);
1024		}
1025		}
1026
1027		/**
1028		* tab names for feature settings
1029		*/
1030		private String[] tabName = new String[] {
1031		MessageManager.getString("label.CDS"),
1032		MessageManager.getString("label.protein") };
1033
1034		/**
1035		* create placeholder tabs which materialise the feature settings for a given
1036		* view. Also reinitialises any tabs containing stale feature settings
1037		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
1038	0	private void createDummyTabs()...
1039		{
1040	0	for (int tabIndex = 0; tabIndex < 2; tabIndex++)
1041		{
1042	0	JPanel dummyTab = new JPanel();
1043	0	featureSettingsPanels.addTab(tabName[tabIndex], dummyTab);
1044		}
1045		}
1046
		0% Uncovered Elements: 15 (15) Complexity: 5 Complexity Density: 0.56
1047	0	private void replaceWithDummyTab(FeatureSettingsControllerI toClose)...
1048		{
1049	0	Component dummyTab = null;
1050	0	for (int tabIndex = 0; tabIndex < 2; tabIndex++)
1051		{
1052	0	if (featureSettingsPanels.getTabCount() > tabIndex)
1053		{
1054	0	dummyTab = featureSettingsPanels.getTabComponentAt(tabIndex);
1055	0	if (dummyTab instanceof FeatureSettingsControllerGuiI
1056		&& !dummyTab.isVisible())
1057		{
1058	0	featureSettingsPanels.removeTabAt(tabIndex);
1059		// close the feature Settings tab
1060	0	((FeatureSettingsControllerGuiI) dummyTab)
1061		.featureSettings_isClosed();
1062		// create a dummy tab in its place
1063	0	dummyTab = new JPanel();
1064	0	featureSettingsPanels.insertTab(tabName[tabIndex], null, dummyTab,
1065		MessageManager.formatMessage(
1066		"label.sequence_feature_settings_for",
1067		tabName[tabIndex]),
1068		tabIndex);
1069		}
1070		}
1071		}
1072		}
1073
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
1074	0	@Override...
1075		public void closeFeatureSettings(
1076		FeatureSettingsControllerI featureSettings,
1077		boolean closeContainingFrame)
1078		{
1079	0	if (featureSettingsUI != null)
1080		{
1081	0	if (closeContainingFrame)
1082		{
1083	0	try
1084		{
1085	0	featureSettingsUI.setClosed(true);
1086		} catch (Exception x)
1087		{
1088		}
1089	0	featureSettingsUI = null;
1090		}
1091		else
1092		{
1093	0	replaceWithDummyTab(featureSettings);
1094		}
1095		}
1096		}
1097
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1098	0	@Override...
1099		public boolean isFeatureSettingsOpen()
1100		{
1101	0	return featureSettingsUI != null && !featureSettingsUI.isClosed();
1102		}
1103		}