Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SplitFrame	76	296	122	0.357615935.8%	Show methods

Class SplitFrame

Class SplitFrame	Line # 76	Total Statements 296	Complexity 122	TOTAL Coverage 0.357615935.8%
SplitFrame(GAlignFrame,GAlignFrame)   SplitFrame(GAlignFrame,GAlignFrame)	9797	2.02	1.01	1.0 1.0100%
init() : void   init() : void	106106	17.017	3.03	0.9047619 0.904761990.5%
fitHeightToDesktop(int) : int   fitHeightToDesktop(int) : int	151151	5.05	2.02	0.85714287 0.8571428785.7%
addCommandListeners() : void   addCommandListeners() : void	169169	3.03	1.01	1.0 1.0100%
adjustLayout() : void   adjustLayout() : void	182182	14.014	8.08	0.7307692 0.730769273.1%
adjustInitialLayout() : void   adjustInitialLayout() : void	222222	30.030	4.04	0.9166667 0.916666791.7%
internalFrameClosed(InternalFrameEvent) : void   internalFrameClosed(InternalFrameEvent) : void	297297	1.01	1.01	1.0 1.0100%
addCloseFrameListener() : void   addCloseFrameListener() : void	293293	1.01	1.01	1.0 1.0100%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	314314	5.05	3.03	0.0 0.00%
keyReleased(KeyEvent) : void   keyReleased(KeyEvent) : void	334334	4.04	2.02	0.0 0.00%
addKeyListener() : void   addKeyListener() : void	309309	1.01	1.01	1.0 1.0100%
overrideKey(KeyEvent,AlignFrame) : boolean   overrideKey(KeyEvent,AlignFrame) : boolean	363363	19.019	7.07	0.0 0.00%
addKeyBindings() : void   addKeyBindings() : void	401401	2.02	1.01	1.0 1.0100%
overrideImplementedKeyBindings() : void   overrideImplementedKeyBindings() : void	412412	5.05	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	436436	1.01	1.01	0.0 0.00%
overrideCloseView() : void   overrideCloseView() : void	424424	4.04	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	459459	1.01	1.01	0.0 0.00%
overrideNewView() : void   overrideNewView() : void	448448	3.03	1.01	1.0 1.0100%
overrideDelegatedKeyBindings() : void   overrideDelegatedKeyBindings() : void	473473	3.03	2.02	0.8 0.880%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	503503	4.04	3.03	0.0 0.00%
overrideKeyBinding(Entry<KeyStroke, JMenuItem>) : void   overrideKeyBinding(Entry<KeyStroke, JMenuItem>) : void	496496	4.04	1.01	1.0 1.0100%
overrideKeyBinding(KeyStroke,AbstractAction) : void   overrideKeyBinding(KeyStroke,AbstractAction) : void	524524	2.02	1.01	1.0 1.0100%
newView_actionPerformed() : void   newView_actionPerformed() : void	541541	15.015	2.02	0.0 0.00%
closeView_actionPerformed() : void   closeView_actionPerformed() : void	588588	8.08	2.02	0.0 0.00%
close() : void   close() : void	608608	4.04	2.02	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	629629	1.01	1.01	0.0 0.00%
overrideExpandViews() : void   overrideExpandViews() : void	624624	3.03	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	646646	1.01	1.01	0.0 0.00%
overrideGatherViews() : void   overrideGatherViews() : void	641641	3.03	1.01	1.0 1.0100%
overrideMenuItem(KeyStroke,AbstractAction) : void   overrideMenuItem(KeyStroke,AbstractAction) : void	662662	2.02	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	690690	1.01	1.01	0.0 0.00%
overrideMenuItem(KeyStroke,AbstractAction,JComponent) : void   overrideMenuItem(KeyStroke,AbstractAction,JComponent) : void	676676	6.06	3.03	0.8 0.880%
expandViews_actionPerformed() : void   expandViews_actionPerformed() : void	704704	1.01	1.01	0.0 0.00%
gatherViews_actionPerformed() : void   gatherViews_actionPerformed() : void	713713	1.01	1.01	0.0 0.00%
getComplement(Object) : AlignmentI   getComplement(Object) : AlignmentI	721721	5.05	3.03	0.0 0.00%
getComplementTitle(Object) : String   getComplementTitle(Object) : String	738738	5.05	3.03	0.0 0.00%
setComplementVisible(Object,boolean) : void   setComplementVisible(Object,boolean) : void	755755	5.05	3.03	0.0 0.00%
getAlignFrames() : List<AlignFrame>   getAlignFrames() : List<AlignFrame>	778778	1.01	1.01	0.0 0.00%
getComplementAlignFrame(AlignViewControllerGuiI) : AlignFrame   getComplementAlignFrame(AlignViewControllerGuiI) : AlignFrame	785785	5.05	3.03	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	817817	6.06	4.04	0.0 0.00%
overrideFind() : void   overrideFind() : void	806806	3.03	1.01	1.0 1.0100%
setSelected(boolean) : void   setSelected(boolean) : void	838838	7.07	5.05	0.53846157 0.5384615753.8%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	880880	6.06	7.07	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	915915	3.03	2.02	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	932932	6.06	3.03	0.0 0.00%
internalFrameClosed(javax.swing.event.InternalFrameEvent) : void   internalFrameClosed(javax.swing.event.InternalFrameEvent) : void	10131013	8.08	3.03	0.0 0.00%
addFeatureSettingsUI(FeatureSettingsControllerGuiI) : void   addFeatureSettingsUI(FeatureSettingsControllerGuiI) : void	868868	40.040	8.08	0.0 0.00%
createDummyTabs() : void   createDummyTabs() : void	10511051	3.03	2.02	0.0 0.00%
replaceWithDummyTab(FeatureSettingsControllerI) : void   replaceWithDummyTab(FeatureSettingsControllerI) : void	10601060	9.09	5.05	0.0 0.00%
closeFeatureSettings(FeatureSettingsControllerI,boolean) : void   closeFeatureSettings(FeatureSettingsControllerI,boolean) : void	10871087	6.06	4.04	0.0 0.00%
isFeatureSettingsOpen() : boolean   isFeatureSettingsOpen() : boolean	11111111	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.34216335	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.26710817	jalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResiduejalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResidue	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		*/
		35.8% Uncovered Elements: 291 (453) Complexity: 122 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		*/
		90.5% Uncovered Elements: 2 (21) Complexity: 3 Complexity Density: 0.18
106	3	protected void init()...
107		{
108	3	setFrameIcon(null);
109	3	getTopFrame().setSplitFrame(this);
110	3	getBottomFrame().setSplitFrame(this);
111	3	getTopFrame().setVisible(true);
112	3	getBottomFrame().setVisible(true);
113
114	3	((AlignFrame) getTopFrame()).getViewport().setCodingComplement(
115		((AlignFrame) getBottomFrame()).getViewport());
116
117		/*
118		* estimate width and height of SplitFrame; this.getInsets() doesn't seem to
119		* give the full additional size (a few pixels short)
120		*/
121	3	int widthFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_WIDTH
122		: WINDOWS_INSETS_WIDTH;
123	3	int heightFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT
124		: WINDOWS_INSETS_HEIGHT;
125	3	int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge;
126	3	int height = ((AlignFrame) getTopFrame()).getHeight()
127		+ ((AlignFrame) getBottomFrame()).getHeight() + DIVIDER_SIZE
128		+ heightFudge;
129	3	height = fitHeightToDesktop(height);
130	3	setSize(width, height);
131
132	3	adjustLayout();
133
134	3	addCloseFrameListener();
135
136	3	addKeyListener();
137
138	3	addKeyBindings();
139
140	3	addCommandListeners();
141		}
142
143		/**
144		* Reduce the height if too large to fit in the Desktop. Also adjust the
145		* divider location in proportion.
146		*
147		* @param height
148		* in pixels
149		* @return original or reduced height
150		*/
		85.7% Uncovered Elements: 1 (7) Complexity: 2 Complexity Density: 0.4
151	3	public int fitHeightToDesktop(int height)...
152		{
153		// allow about 65 pixels for Desktop decorators on Windows
154
155	3	int newHeight = Math.min(height,
156		Desktop.instance.getHeight() - DESKTOP_DECORATORS_HEIGHT);
157	3	if (newHeight != height)
158		{
159	3	int oldDividerLocation = getDividerLocation();
160	3	setDividerLocation(oldDividerLocation * newHeight / height);
161		}
162	3	return newHeight;
163		}
164
165		/**
166		* Set the top and bottom frames to listen to each others Commands (e.g. Edit,
167		* Order).
168		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
169	3	protected void addCommandListeners()...
170		{
171		// TODO if CommandListener is only ever 1:1 for complementary views,
172		// may change broadcast pattern to direct messaging (more efficient)
173	3	final StructureSelectionManager ssm = StructureSelectionManager
174		.getStructureSelectionManager(Desktop.instance);
175	3	ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
176	3	ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
177		}
178
179		/**
180		* Do any tweaking and twerking of the layout wanted.
181		*/
		73.1% Uncovered Elements: 7 (26) Complexity: 8 Complexity Density: 0.57
182	3	public void adjustLayout()...
183		{
184	3	final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
185	3	final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
186
187		/*
188		* Ensure sequence ids are the same width so sequences line up
189		*/
190	3	int w1 = topViewport.getIdWidth();
191	3	int w2 = bottomViewport.getIdWidth();
192	3	int w3 = Math.max(w1, w2);
193	3	topViewport.setIdWidth(w3);
194	3	bottomViewport.setIdWidth(w3);
195
196		/*
197		* Scale protein to either 1 or 3 times character width of dna
198		*/
199	3	final AlignmentI topAlignment = topViewport.getAlignment();
200	3	final AlignmentI bottomAlignment = bottomViewport.getAlignment();
201	3	AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
202	0	: (bottomAlignment.isNucleotide() ? bottomViewport : null);
203	3	AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
204	3	: (!bottomAlignment.isNucleotide() ? bottomViewport : null);
205	3	if (protein != null && cdna != null)
206		{
207	3	int scale = protein.isScaleProteinAsCdna() ? 3 : 1;
208	3	protein.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
209		}
210		}
211
212		/**
213		* Adjusts the divider for a sensible split of the real estate (for example,
214		* when many transcripts are shown with a single protein). This should only be
215		* called after the split pane has been laid out (made visible) so it has a
216		* height. The aim is to avoid unnecessary vertical scroll bars, while
217		* ensuring that at least 2 sequences are visible in each panel.
218		* <p>
219		* Once laid out, the user may choose to customise as they wish, so this
220		* method is not called again after the initial layout.
221		*/
		91.7% Uncovered Elements: 3 (36) Complexity: 4 Complexity Density: 0.13
222	2	protected void adjustInitialLayout()...
223		{
224	2	AlignFrame topFrame = (AlignFrame) getTopFrame();
225	2	AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
226
227		/*
228		* recompute layout of top and bottom panels to reflect their
229		* actual (rather than requested) height
230		*/
231	2	topFrame.alignPanel.adjustAnnotationHeight();
232	2	bottomFrame.alignPanel.adjustAnnotationHeight();
233
234	2	final AlignViewport topViewport = topFrame.viewport;
235	2	final AlignViewport bottomViewport = bottomFrame.viewport;
236	2	final AlignmentI topAlignment = topViewport.getAlignment();
237	2	final AlignmentI bottomAlignment = bottomViewport.getAlignment();
238	2	boolean topAnnotations = topViewport.isShowAnnotation();
239	2	boolean bottomAnnotations = bottomViewport.isShowAnnotation();
240		// TODO need number of visible sequences here, not #sequences - how?
241	2	int topCount = topAlignment.getHeight();
242	2	int bottomCount = bottomAlignment.getHeight();
243	2	int topCharHeight = topViewport.getViewStyle().getCharHeight();
244	2	int bottomCharHeight = bottomViewport.getViewStyle().getCharHeight();
245
246		/*
247		* calculate the minimum ratio that leaves at least the height
248		* of two sequences (after rounding) visible in the top panel
249		*/
250	2	int topPanelHeight = topFrame.getHeight();
251	2	int bottomPanelHeight = bottomFrame.getHeight();
252	2	int topSequencesHeight = topFrame.alignPanel.getSeqPanel().seqCanvas
253		.getHeight();
254	2	int topPanelMinHeight = topPanelHeight
255		- Math.max(0, topSequencesHeight - 3 * topCharHeight);
256	2	double totalHeight = (double) topPanelHeight + bottomPanelHeight;
257	2	double minRatio = topPanelMinHeight / totalHeight;
258
259		/*
260		* calculate the maximum ratio that leaves at least the height
261		* of two sequences (after rounding) visible in the bottom panel
262		*/
263	2	int bottomSequencesHeight = bottomFrame.alignPanel
264		.getSeqPanel().seqCanvas.getHeight();
265	2	int bottomPanelMinHeight = bottomPanelHeight
266		- Math.max(0, bottomSequencesHeight - 3 * bottomCharHeight);
267	2	double maxRatio = (totalHeight - bottomPanelMinHeight) / totalHeight;
268
269		/*
270		* estimate ratio of (topFrameContent / bottomFrameContent)
271		*/
272	2	int insets = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT
273		: WINDOWS_INSETS_HEIGHT;
274		// allow 3 'rows' for scale, scrollbar, status bar
275	2	int topHeight = insets + (3 + topCount) * topCharHeight
276	2	+ (topAnnotations ? topViewport.calcPanelHeight() : 0);
277	2	int bottomHeight = insets + (3 + bottomCount) * bottomCharHeight
278	2	+ (bottomAnnotations ? bottomViewport.calcPanelHeight() : 0);
279	2	double ratio = ((double) topHeight)
280		/ (double) (topHeight + bottomHeight);
281
282		/*
283		* limit ratio to avoid concealing all sequences
284		*/
285	2	ratio = Math.min(ratio, maxRatio);
286	2	ratio = Math.max(ratio, minRatio);
287	2	setRelativeDividerLocation(ratio);
288		}
289
290		/**
291		* Add a listener to tidy up when the frame is closed.
292		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
293	3	protected void addCloseFrameListener()...
294		{
295	3	addInternalFrameListener(new InternalFrameAdapter()
296		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
297	3	@Override...
298		public void internalFrameClosed(InternalFrameEvent evt)
299		{
300	3	close();
301		};
302		});
303		}
304
305		/**
306		* Add a key listener that delegates to whichever split component the mouse is
307		* in (or does nothing if neither).
308		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
309	3	protected void addKeyListener()...
310		{
311	3	addKeyListener(new KeyAdapter()
312		{
313
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
314	0	@Override...
315		public void keyPressed(KeyEvent e)
316		{
317	0	AlignFrame af = (AlignFrame) getFrameAtMouse();
318
319		/*
320		* Intercept and override any keys here if wanted.
321		*/
322	0	if (!overrideKey(e, af))
323		{
324	0	if (af != null)
325		{
326	0	for (KeyListener kl : af.getKeyListeners())
327		{
328	0	kl.keyPressed(e);
329		}
330		}
331		}
332		}
333
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
334	0	@Override...
335		public void keyReleased(KeyEvent e)
336		{
337	0	Component c = getFrameAtMouse();
338	0	if (c != null)
339		{
340	0	for (KeyListener kl : c.getKeyListeners())
341		{
342	0	kl.keyReleased(e);
343		}
344		}
345		}
346
347		});
348		}
349
350		/**
351		* Returns true if the key event is overriden and actioned (or ignored) here,
352		* else returns false, indicating it should be delegated to the AlignFrame's
353		* usual handler.
354		* <p>
355		* We can't handle Cmd-Key combinations here, instead this is done by
356		* overriding key bindings.
357		*
358		* @see addKeyOverrides
359		* @param e
360		* @param af
361		* @return
362		*/
		0% Uncovered Elements: 23 (23) Complexity: 7 Complexity Density: 0.37
363	0	protected boolean overrideKey(KeyEvent e, AlignFrame af)...
364		{
365	0	boolean actioned = false;
366	0	int keyCode = e.getKeyCode();
367	0	switch (keyCode)
368		{
369	0	case KeyEvent.VK_DOWN:
370	0	if (e.isAltDown() || !af.viewport.cursorMode)
371		{
372		/*
373		* Key down (or Alt-key-down in cursor mode) - move selected sequences
374		*/
375	0	((AlignFrame) getTopFrame()).moveSelectedSequences(false);
376	0	((AlignFrame) getBottomFrame()).moveSelectedSequences(false);
377	0	actioned = true;
378	0	e.consume();
379		}
380	0	break;
381	0	case KeyEvent.VK_UP:
382	0	if (e.isAltDown() || !af.viewport.cursorMode)
383		{
384		/*
385		* Key up (or Alt-key-up in cursor mode) - move selected sequences
386		*/
387	0	((AlignFrame) getTopFrame()).moveSelectedSequences(true);
388	0	((AlignFrame) getBottomFrame()).moveSelectedSequences(true);
389	0	actioned = true;
390	0	e.consume();
391		}
392	0	break;
393	0	default:
394		}
395	0	return actioned;
396		}
397
398		/**
399		* Set key bindings (recommended for Swing over key accelerators).
400		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
401	3	private void addKeyBindings()...
402		{
403	3	overrideDelegatedKeyBindings();
404
405	3	overrideImplementedKeyBindings();
406		}
407
408		/**
409		* Override key bindings with alternative action methods implemented in this
410		* class.
411		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
412	3	protected void overrideImplementedKeyBindings()...
413		{
414	3	overrideFind();
415	3	overrideNewView();
416	3	overrideCloseView();
417	3	overrideExpandViews();
418	3	overrideGatherViews();
419		}
420
421		/**
422		* Replace Cmd-W close view action with our version.
423		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
424	3	protected void overrideCloseView()...
425		{
426	3	AbstractAction action;
427		/*
428		* Ctrl-W / Cmd-W - close view or window
429		*/
430	3	KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W,
431		jalview.util.ShortcutKeyMaskExWrapper
432		.getMenuShortcutKeyMaskEx(),
433		false);
434	3	action = new AbstractAction()
435		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
436	0	@Override...
437		public void actionPerformed(ActionEvent e)
438		{
439	0	closeView_actionPerformed();
440		}
441		};
442	3	overrideKeyBinding(key_cmdW, action);
443		}
444
445		/**
446		* Replace Cmd-T new view action with our version.
447		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
448	3	protected void overrideNewView()...
449		{
450		/*
451		* Ctrl-T / Cmd-T open new view
452		*/
453	3	KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T,
454		jalview.util.ShortcutKeyMaskExWrapper
455		.getMenuShortcutKeyMaskEx(),
456		false);
457	3	AbstractAction action = new AbstractAction()
458		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
459	0	@Override...
460		public void actionPerformed(ActionEvent e)
461		{
462	0	newView_actionPerformed();
463		}
464		};
465	3	overrideKeyBinding(key_cmdT, action);
466		}
467
468		/**
469		* For now, delegates key events to the corresponding key accelerator for the
470		* AlignFrame that the mouse is in. Hopefully can be simplified in future if
471		* AlignFrame is changed to use key bindings rather than accelerators.
472		*/
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.67
473	3	protected void overrideDelegatedKeyBindings()...
474		{
475	3	if (getTopFrame() instanceof AlignFrame)
476		{
477		/*
478		* Get all accelerator keys in the top frame (the bottom should be
479		* identical) and override each one.
480		*/
481	3	for (Entry<KeyStroke, JMenuItem> acc : ((AlignFrame) getTopFrame())
482		.getAccelerators().entrySet())
483		{
484	81	overrideKeyBinding(acc);
485		}
486		}
487		}
488
489		/**
490		* Overrides an AlignFrame key accelerator with our version which delegates to
491		* the action listener in whichever frame has the mouse (and does nothing if
492		* neither has).
493		*
494		* @param acc
495		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
496	81	private void overrideKeyBinding(Entry<KeyStroke, JMenuItem> acc)...
497		{
498	81	final KeyStroke ks = acc.getKey();
499	81	InputMap inputMap = this.getInputMap(JComponent.WHEN_FOCUSED);
500	81	inputMap.put(ks, ks);
501	81	this.getActionMap().put(ks, new AbstractAction()
502		{
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
503	0	@Override...
504		public void actionPerformed(ActionEvent e)
505		{
506	0	Component c = getFrameAtMouse();
507	0	if (c != null && c instanceof AlignFrame)
508		{
509	0	for (ActionListener a : ((AlignFrame) c).getAccelerators().get(ks)
510		.getActionListeners())
511		{
512	0	a.actionPerformed(null);
513		}
514		}
515		}
516		});
517		}
518
519		/**
520		* Replace an accelerator key's action with the specified action.
521		*
522		* @param ks
523		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
524	9	protected void overrideKeyBinding(KeyStroke ks, AbstractAction action)...
525		{
526	9	this.getActionMap().put(ks, action);
527	9	overrideMenuItem(ks, action);
528		}
529
530		/**
531		* Create and link new views (with matching names) in both panes.
532		* <p>
533		* Note this is _not_ multiple tabs, each hosting a split pane view, rather it
534		* is a single split pane with each split holding multiple tabs which are
535		* linked in pairs.
536		* <p>
537		* TODO implement instead with a tabbed holder in the SplitView, each tab
538		* holding a single JSplitPane. Would avoid a duplicated tab, at the cost of
539		* some additional coding.
540		*/
		0% Uncovered Elements: 17 (17) Complexity: 2 Complexity Density: 0.13
541	0	protected void newView_actionPerformed()...
542		{
543	0	AlignFrame topFrame = (AlignFrame) getTopFrame();
544	0	AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
545	0	final boolean scaleProteinAsCdna = topFrame.viewport
546		.isScaleProteinAsCdna();
547
548	0	AlignmentPanel newTopPanel = topFrame.newView(null, true);
549	0	AlignmentPanel newBottomPanel = bottomFrame.newView(null, true);
550
551		/*
552		* This currently (for the first new view only) leaves the top pane on tab 0
553		* but the bottom on tab 1. This results from 'setInitialTabVisible' echoing
554		* from the bottom back to the first frame. Next line is a fudge to work
555		* around this. TODO find a better way.
556		*/
557	0	if (topFrame.getTabIndex() != bottomFrame.getTabIndex())
558		{
559	0	topFrame.setDisplayedView(newTopPanel);
560		}
561
562	0	newBottomPanel.av.setViewName(newTopPanel.av.getViewName());
563	0	newTopPanel.av.setCodingComplement(newBottomPanel.av);
564
565		/*
566		* These lines can be removed once scaleProteinAsCdna is added to element
567		* Viewport in jalview.xsd, as Jalview2XML.copyAlignPanel will then take
568		* care of it
569		*/
570	0	newTopPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
571	0	newBottomPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
572
573		/*
574		* Line up id labels etc
575		*/
576	0	adjustLayout();
577
578	0	final StructureSelectionManager ssm = StructureSelectionManager
579		.getStructureSelectionManager(Desktop.instance);
580	0	ssm.addCommandListener(newTopPanel.av);
581	0	ssm.addCommandListener(newBottomPanel.av);
582		}
583
584		/**
585		* Close the currently selected view in both panes. If there is only one view,
586		* close this split frame.
587		*/
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.25
588	0	protected void closeView_actionPerformed()...
589		{
590	0	int viewCount = ((AlignFrame) getTopFrame()).getAlignPanels().size();
591	0	if (viewCount < 2)
592		{
593	0	close();
594	0	return;
595		}
596
597	0	AlignmentPanel topPanel = ((AlignFrame) getTopFrame()).alignPanel;
598	0	AlignmentPanel bottomPanel = ((AlignFrame) getBottomFrame()).alignPanel;
599
600	0	((AlignFrame) getTopFrame()).closeView(topPanel);
601	0	((AlignFrame) getBottomFrame()).closeView(bottomPanel);
602
603		}
604
605		/**
606		* Close child frames and this split frame.
607		*/
		100% Uncovered Elements: 0 (4) Complexity: 2 Complexity Density: 0.5
608	3	public void close()...
609		{
610	3	((AlignFrame) getTopFrame()).closeMenuItem_actionPerformed(true);
611	3	((AlignFrame) getBottomFrame()).closeMenuItem_actionPerformed(true);
612	3	try
613		{
614	3	this.setClosed(true);
615		} catch (PropertyVetoException e)
616		{
617		// ignore
618		}
619		}
620
621		/**
622		* Replace AlignFrame 'expand views' action with SplitFrame version.
623		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
624	3	protected void overrideExpandViews()...
625		{
626	3	KeyStroke key_X = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
627	3	AbstractAction action = new AbstractAction()
628		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
629	0	@Override...
630		public void actionPerformed(ActionEvent e)
631		{
632	0	expandViews_actionPerformed();
633		}
634		};
635	3	overrideMenuItem(key_X, action);
636		}
637
638		/**
639		* Replace AlignFrame 'gather views' action with SplitFrame version.
640		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
641	3	protected void overrideGatherViews()...
642		{
643	3	KeyStroke key_G = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
644	3	AbstractAction action = new AbstractAction()
645		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
646	0	@Override...
647		public void actionPerformed(ActionEvent e)
648		{
649	0	gatherViews_actionPerformed();
650		}
651		};
652	3	overrideMenuItem(key_G, action);
653		}
654
655		/**
656		* Override the menu action associated with the keystroke in the child frames,
657		* replacing it with the given action.
658		*
659		* @param ks
660		* @param action
661		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
662	15	private void overrideMenuItem(KeyStroke ks, AbstractAction action)...
663		{
664	15	overrideMenuItem(ks, action, getTopFrame());
665	15	overrideMenuItem(ks, action, getBottomFrame());
666		}
667
668		/**
669		* Override the menu action associated with the keystroke in one child frame,
670		* replacing it with the given action. Mwahahahaha.
671		*
672		* @param key
673		* @param action
674		* @param comp
675		*/
		80% Uncovered Elements: 2 (10) Complexity: 3 Complexity Density: 0.5
676	30	private void overrideMenuItem(KeyStroke key, final AbstractAction action,...
677		JComponent comp)
678		{
679	30	if (comp instanceof AlignFrame)
680		{
681	30	JMenuItem mi = ((AlignFrame) comp).getAccelerators().get(key);
682	30	if (mi != null)
683		{
684	30	for (ActionListener al : mi.getActionListeners())
685		{
686	30	mi.removeActionListener(al);
687		}
688	30	mi.addActionListener(new ActionListener()
689		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
690	0	@Override...
691		public void actionPerformed(ActionEvent e)
692		{
693	0	action.actionPerformed(e);
694		}
695		});
696		}
697		}
698		}
699
700		/**
701		* Expand any multiple views (which are always in pairs) into separate split
702		* frames.
703		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
704	0	protected void expandViews_actionPerformed()...
705		{
706	0	Desktop.instance.explodeViews(this);
707		}
708
709		/**
710		* Gather any other SplitFrame views of this alignment back in as multiple
711		* (pairs of) views in this SplitFrame.
712		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
713	0	protected void gatherViews_actionPerformed()...
714		{
715	0	Desktop.instance.gatherViews(this);
716		}
717
718		/**
719		* Returns the alignment in the complementary frame to the one given.
720		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
721	0	@Override...
722		public AlignmentI getComplement(Object alignFrame)
723		{
724	0	if (alignFrame == this.getTopFrame())
725		{
726	0	return ((AlignFrame) getBottomFrame()).viewport.getAlignment();
727		}
728	0	else if (alignFrame == this.getBottomFrame())
729		{
730	0	return ((AlignFrame) getTopFrame()).viewport.getAlignment();
731		}
732	0	return null;
733		}
734
735		/**
736		* Returns the title of the complementary frame to the one given.
737		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
738	0	@Override...
739		public String getComplementTitle(Object alignFrame)
740		{
741	0	if (alignFrame == this.getTopFrame())
742		{
743	0	return ((AlignFrame) getBottomFrame()).getTitle();
744		}
745	0	else if (alignFrame == this.getBottomFrame())
746		{
747	0	return ((AlignFrame) getTopFrame()).getTitle();
748		}
749	0	return null;
750		}
751
752		/**
753		* Set the 'other half' to hidden / revealed.
754		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
755	0	@Override...
756		public void setComplementVisible(Object alignFrame, boolean show)
757		{
758		/*
759		* Hiding the AlignPanel suppresses unnecessary repaints
760		*/
761	0	if (alignFrame == getTopFrame())
762		{
763	0	((AlignFrame) getBottomFrame()).alignPanel.setVisible(show);
764		}
765	0	else if (alignFrame == getBottomFrame())
766		{
767	0	((AlignFrame) getTopFrame()).alignPanel.setVisible(show);
768		}
769	0	super.setComplementVisible(alignFrame, show);
770		}
771
772		/**
773		* return the AlignFrames held by this container
774		*
775		* @return { Top alignFrame (Usually CDS), Bottom AlignFrame (Usually
776		* Protein)}
777		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
778	0	public List<AlignFrame> getAlignFrames()...
779		{
780	0	return Arrays
781		.asList(new AlignFrame[]
782		{ (AlignFrame) getTopFrame(), (AlignFrame) getBottomFrame() });
783		}
784
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
785	0	@Override...
786		public AlignFrame getComplementAlignFrame(
787		AlignViewControllerGuiI alignFrame)
788		{
789	0	if (getTopFrame() == alignFrame)
790		{
791	0	return (AlignFrame) getBottomFrame();
792		}
793	0	if (getBottomFrame() == alignFrame)
794		{
795	0	return (AlignFrame) getTopFrame();
796		}
797		// we didn't know anything about this frame...
798	0	return null;
799		}
800
801		/**
802		* Replace Cmd-F Find action with our version. This is necessary because the
803		* 'default' Finder searches in the first AlignFrame it finds. We need it to
804		* search in the half of the SplitFrame that has the mouse.
805		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
806	3	protected void overrideFind()...
807		{
808		/*
809		* Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
810		*/
811	3	KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F,
812		jalview.util.ShortcutKeyMaskExWrapper
813		.getMenuShortcutKeyMaskEx(),
814		false);
815	3	AbstractAction action = new AbstractAction()
816		{
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
817	0	@Override...
818		public void actionPerformed(ActionEvent e)
819		{
820	0	Component c = getFrameAtMouse();
821	0	if (c != null && c instanceof AlignFrame)
822		{
823	0	AlignFrame af = (AlignFrame) c;
824	0	boolean dna = af.getViewport().getAlignment().isNucleotide();
825	0	String scope = MessageManager.getString("label.in") + " "
826	0	+ (dna ? MessageManager.getString("label.nucleotide")
827		: MessageManager.getString("label.protein"));
828	0	new Finder(af.alignPanel, true, scope);
829		}
830		}
831		};
832	3	overrideKeyBinding(key_cmdF, action);
833		}
834
835		/**
836		* Override to do nothing if triggered from one of the child frames
837		*/
		53.8% Uncovered Elements: 6 (13) Complexity: 5 Complexity Density: 0.71
838	11	@Override...
839		public void setSelected(boolean selected) throws PropertyVetoException
840		{
841	11	JDesktopPane desktopPane = getDesktopPane();
842	11	JInternalFrame fr = desktopPane == null ? null
843		: desktopPane.getSelectedFrame();
844	11	if (fr == getTopFrame() || fr == getBottomFrame())
845		{
846		/*
847		* patch for JAL-3288 (deselecting top/bottom frame closes popup menu);
848		* it may be possible to remove this method in future
849		* if the underlying Java behaviour changes
850		*/
851	0	if (selected)
852		{
853	0	moveToFront();
854		}
855	0	return;
856		}
857	11	super.setSelected(selected);
858		}
859
860		/**
861		* holds the frame for feature settings, so Protein and DNA tabs can be
862		* managed
863		*/
864		JInternalFrame featureSettingsUI;
865
866		JTabbedPane featureSettingsPanels;
867
		0% Uncovered Elements: 52 (52) Complexity: 8 Complexity Density: 0.2
868	0	@Override...
869		public void addFeatureSettingsUI(
870		FeatureSettingsControllerGuiI featureSettings)
871		{
872	0	boolean showInternalFrame = false;
873	0	if (featureSettingsUI == null || featureSettingsPanels == null)
874		{
875	0	showInternalFrame = true;
876	0	featureSettingsPanels = new JTabbedPane();
877	0	featureSettingsPanels.addChangeListener(new ChangeListener()
878		{
879
		0% Uncovered Elements: 10 (10) Complexity: 7 Complexity Density: 1.17
880	0	@Override...
881		public void stateChanged(ChangeEvent e)
882		{
883	0	if (e.getSource() != featureSettingsPanels
884		|| featureSettingsUI == null
885		|| featureSettingsUI.isClosed()
886		|| !featureSettingsUI.isVisible())
887		{
888		// not our tabbed pane
889	0	return;
890		}
891	0	int tab = featureSettingsPanels.getSelectedIndex();
892	0	if (tab < 0 || featureSettingsPanels
893		.getSelectedComponent() instanceof FeatureSettingsControllerGuiI)
894		{
895		// no tab selected or already showing a feature settings GUI
896	0	return;
897		}
898	0	getAlignFrames().get(tab).showFeatureSettingsUI();
899		}
900		});
901	0	featureSettingsUI = new JInternalFrame(MessageManager.getString(
902		"label.sequence_feature_settings_for_CDS_and_Protein"));
903	0	featureSettingsUI.setFrameIcon(null);
904	0	featureSettingsPanels.setOpaque(true);
905
906	0	JPanel dialog = new JPanel();
907	0	dialog.setOpaque(true);
908	0	dialog.setLayout(new BorderLayout());
909	0	dialog.add(featureSettingsPanels, BorderLayout.CENTER);
910	0	JPanel buttons = new JPanel();
911	0	JButton ok = new JButton(MessageManager.getString("action.ok"));
912	0	ok.addActionListener(new ActionListener()
913		{
914
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
915	0	@Override...
916		public void actionPerformed(ActionEvent e)
917		{
918	0	try
919		{
920	0	featureSettingsUI.setClosed(true);
921		} catch (PropertyVetoException pv)
922		{
923	0	pv.printStackTrace();
924		}
925		}
926		});
927	0	JButton cancel = new JButton(
928		MessageManager.getString("action.cancel"));
929	0	cancel.addActionListener(new ActionListener()
930		{
931
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
932	0	@Override...
933		public void actionPerformed(ActionEvent e)
934		{
935	0	try
936		{
937	0	for (Component fspanel : featureSettingsPanels.getComponents())
938		{
939	0	if (fspanel instanceof FeatureSettingsControllerGuiI)
940		{
941	0	((FeatureSettingsControllerGuiI) fspanel).revert();
942		}
943		}
944	0	featureSettingsUI.setClosed(true);
945		} catch (Exception pv)
946		{
947	0	pv.printStackTrace();
948		}
949		}
950		});
951	0	buttons.add(ok);
952	0	buttons.add(cancel);
953	0	dialog.add(buttons, BorderLayout.SOUTH);
954	0	featureSettingsUI.setContentPane(dialog);
955	0	createDummyTabs();
956		}
957	0	if (featureSettingsPanels
958		.indexOfTabComponent((Component) featureSettings) > -1)
959		{
960		// just show the feature settings !
961	0	featureSettingsPanels
962		.setSelectedComponent((Component) featureSettings);
963	0	return;
964		}
965		// otherwise replace the dummy tab with the given feature settings
966	0	int pos = getAlignFrames().indexOf(featureSettings.getAlignframe());
967		// if pos==-1 then alignFrame isn't managed by this splitframe
968	0	if (pos == 0)
969		{
970	0	featureSettingsPanels.removeTabAt(0);
971	0	featureSettingsPanels.insertTab(tabName[0], null,
972		(Component) featureSettings,
973		MessageManager.formatMessage(
974		"label.sequence_feature_settings_for", tabName[0]),
975		0);
976		}
977	0	if (pos == 1)
978		{
979	0	featureSettingsPanels.removeTabAt(1);
980	0	featureSettingsPanels.insertTab(tabName[1], null,
981		(Component) featureSettings,
982		MessageManager.formatMessage(
983		"label.sequence_feature_settings_for", tabName[1]),
984		1);
985		}
986	0	featureSettingsPanels.setSelectedComponent((Component) featureSettings);
987
988		// TODO: JAL-3535 - construct a feature settings title including names of
989		// currently selected CDS and Protein names
990
991	0	if (showInternalFrame)
992		{
993	0	if (Platform.isAMacAndNotJS())
994		{
995	0	Desktop.addInternalFrame(featureSettingsUI,
996		MessageManager.getString(
997		"label.sequence_feature_settings_for_CDS_and_Protein"),
998		600, 480);
999		}
1000		else
1001		{
1002	0	Desktop.addInternalFrame(featureSettingsUI,
1003		MessageManager.getString(
1004		"label.sequence_feature_settings_for_CDS_and_Protein"),
1005		600, 450);
1006		}
1007	0	featureSettingsUI
1008		.setMinimumSize(new Dimension(FS_MIN_WIDTH, FS_MIN_HEIGHT));
1009
1010	0	featureSettingsUI.addInternalFrameListener(
1011		new javax.swing.event.InternalFrameAdapter()
1012		{
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
1013	0	@Override...
1014		public void internalFrameClosed(
1015		javax.swing.event.InternalFrameEvent evt)
1016		{
1017	0	for (int tab = 0; tab < featureSettingsPanels
1018		.getTabCount();)
1019		{
1020	0	FeatureSettingsControllerGuiI fsettings = (FeatureSettingsControllerGuiI) featureSettingsPanels
1021		.getTabComponentAt(tab);
1022	0	if (fsettings != null)
1023		{
1024	0	featureSettingsPanels.removeTabAt(tab);
1025	0	fsettings.featureSettings_isClosed();
1026		}
1027		else
1028		{
1029	0	tab++;
1030		}
1031		}
1032	0	featureSettingsPanels = null;
1033	0	featureSettingsUI = null;
1034		};
1035		});
1036	0	featureSettingsUI.setLayer(JLayeredPane.PALETTE_LAYER);
1037		}
1038		}
1039
1040		/**
1041		* tab names for feature settings
1042		*/
1043		private String[] tabName = new String[] {
1044		MessageManager.getString("label.CDS"),
1045		MessageManager.getString("label.protein") };
1046
1047		/**
1048		* create placeholder tabs which materialise the feature settings for a given
1049		* view. Also reinitialises any tabs containing stale feature settings
1050		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
1051	0	private void createDummyTabs()...
1052		{
1053	0	for (int tabIndex = 0; tabIndex < 2; tabIndex++)
1054		{
1055	0	JPanel dummyTab = new JPanel();
1056	0	featureSettingsPanels.addTab(tabName[tabIndex], dummyTab);
1057		}
1058		}
1059
		0% Uncovered Elements: 15 (15) Complexity: 5 Complexity Density: 0.56
1060	0	private void replaceWithDummyTab(FeatureSettingsControllerI toClose)...
1061		{
1062	0	Component dummyTab = null;
1063	0	for (int tabIndex = 0; tabIndex < 2; tabIndex++)
1064		{
1065	0	if (featureSettingsPanels.getTabCount() > tabIndex)
1066		{
1067	0	dummyTab = featureSettingsPanels.getTabComponentAt(tabIndex);
1068	0	if (dummyTab instanceof FeatureSettingsControllerGuiI
1069		&& !dummyTab.isVisible())
1070		{
1071	0	featureSettingsPanels.removeTabAt(tabIndex);
1072		// close the feature Settings tab
1073	0	((FeatureSettingsControllerGuiI) dummyTab)
1074		.featureSettings_isClosed();
1075		// create a dummy tab in its place
1076	0	dummyTab = new JPanel();
1077	0	featureSettingsPanels.insertTab(tabName[tabIndex], null, dummyTab,
1078		MessageManager.formatMessage(
1079		"label.sequence_feature_settings_for",
1080		tabName[tabIndex]),
1081		tabIndex);
1082		}
1083		}
1084		}
1085		}
1086
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
1087	0	@Override...
1088		public void closeFeatureSettings(
1089		FeatureSettingsControllerI featureSettings,
1090		boolean closeContainingFrame)
1091		{
1092	0	if (featureSettingsUI != null)
1093		{
1094	0	if (closeContainingFrame)
1095		{
1096	0	try
1097		{
1098	0	featureSettingsUI.setClosed(true);
1099		} catch (Exception x)
1100		{
1101		}
1102	0	featureSettingsUI = null;
1103		}
1104		else
1105		{
1106	0	replaceWithDummyTab(featureSettings);
1107		}
1108		}
1109		}
1110
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1111	0	@Override...
1112		public boolean isFeatureSettingsOpen()
1113		{
1114	0	return featureSettingsUI != null && !featureSettingsUI.isClosed();
1115		}
1116		}