Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SplitFrame	77	298	122	0.3604395736%	Show methods

Class SplitFrame

Class SplitFrame	Line # 77	Total Statements 298	Complexity 122	TOTAL Coverage 0.3604395736%
SplitFrame(GAlignFrame,GAlignFrame)   SplitFrame(GAlignFrame,GAlignFrame)	9898	2.02	1.01	1.0 1.0100%
init() : void   init() : void	107107	19.019	3.03	0.9130435 0.913043591.3%
fitHeightToDesktop(int) : int   fitHeightToDesktop(int) : int	156156	5.05	2.02	0.85714287 0.8571428785.7%
addCommandListeners() : void   addCommandListeners() : void	174174	3.03	1.01	1.0 1.0100%
adjustLayout() : void   adjustLayout() : void	187187	14.014	8.08	0.7307692 0.730769273.1%
adjustInitialLayout() : void   adjustInitialLayout() : void	227227	30.030	4.04	0.9166667 0.916666791.7%
internalFrameClosed(InternalFrameEvent) : void   internalFrameClosed(InternalFrameEvent) : void	302302	1.01	1.01	1.0 1.0100%
addCloseFrameListener() : void   addCloseFrameListener() : void	298298	1.01	1.01	1.0 1.0100%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	319319	5.05	3.03	0.0 0.00%
keyReleased(KeyEvent) : void   keyReleased(KeyEvent) : void	339339	4.04	2.02	0.0 0.00%
addKeyListener() : void   addKeyListener() : void	314314	1.01	1.01	1.0 1.0100%
overrideKey(KeyEvent,AlignFrame) : boolean   overrideKey(KeyEvent,AlignFrame) : boolean	368368	19.019	7.07	0.0 0.00%
addKeyBindings() : void   addKeyBindings() : void	406406	2.02	1.01	1.0 1.0100%
overrideImplementedKeyBindings() : void   overrideImplementedKeyBindings() : void	417417	5.05	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	439439	1.01	1.01	0.0 0.00%
overrideCloseView() : void   overrideCloseView() : void	429429	4.04	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	460460	1.01	1.01	0.0 0.00%
overrideNewView() : void   overrideNewView() : void	451451	3.03	1.01	1.0 1.0100%
overrideDelegatedKeyBindings() : void   overrideDelegatedKeyBindings() : void	474474	3.03	2.02	0.8 0.880%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	504504	4.04	3.03	0.0 0.00%
overrideKeyBinding(Entry<KeyStroke, JMenuItem>) : void   overrideKeyBinding(Entry<KeyStroke, JMenuItem>) : void	497497	4.04	1.01	1.0 1.0100%
overrideKeyBinding(KeyStroke,AbstractAction) : void   overrideKeyBinding(KeyStroke,AbstractAction) : void	525525	2.02	1.01	1.0 1.0100%
newView_actionPerformed() : void   newView_actionPerformed() : void	542542	15.015	2.02	0.0 0.00%
closeView_actionPerformed() : void   closeView_actionPerformed() : void	589589	8.08	2.02	0.0 0.00%
close() : void   close() : void	609609	4.04	2.02	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	630630	1.01	1.01	0.0 0.00%
overrideExpandViews() : void   overrideExpandViews() : void	625625	3.03	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	647647	1.01	1.01	0.0 0.00%
overrideGatherViews() : void   overrideGatherViews() : void	642642	3.03	1.01	1.0 1.0100%
overrideMenuItem(KeyStroke,AbstractAction) : void   overrideMenuItem(KeyStroke,AbstractAction) : void	663663	2.02	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	691691	1.01	1.01	0.0 0.00%
overrideMenuItem(KeyStroke,AbstractAction,JComponent) : void   overrideMenuItem(KeyStroke,AbstractAction,JComponent) : void	677677	6.06	3.03	0.8 0.880%
expandViews_actionPerformed() : void   expandViews_actionPerformed() : void	705705	1.01	1.01	0.0 0.00%
gatherViews_actionPerformed() : void   gatherViews_actionPerformed() : void	714714	1.01	1.01	0.0 0.00%
getComplement(Object) : AlignmentI   getComplement(Object) : AlignmentI	722722	5.05	3.03	0.0 0.00%
getComplementTitle(Object) : String   getComplementTitle(Object) : String	739739	5.05	3.03	0.0 0.00%
setComplementVisible(Object,boolean) : void   setComplementVisible(Object,boolean) : void	756756	5.05	3.03	0.0 0.00%
getAlignFrames() : List<AlignFrame>   getAlignFrames() : List<AlignFrame>	779779	1.01	1.01	0.0 0.00%
getComplementAlignFrame(AlignViewControllerGuiI) : AlignFrame   getComplementAlignFrame(AlignViewControllerGuiI) : AlignFrame	786786	5.05	3.03	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	816816	6.06	4.04	0.0 0.00%
overrideFind() : void   overrideFind() : void	807807	3.03	1.01	1.0 1.0100%
setSelected(boolean) : void   setSelected(boolean) : void	837837	7.07	5.05	0.53846157 0.5384615753.8%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	878878	6.06	7.07	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	913913	3.03	2.02	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	930930	6.06	3.03	0.0 0.00%
internalFrameClosed(javax.swing.event.InternalFrameEvent) : void   internalFrameClosed(javax.swing.event.InternalFrameEvent) : void	10111011	8.08	3.03	0.0 0.00%
addFeatureSettingsUI(FeatureSettingsControllerGuiI) : void   addFeatureSettingsUI(FeatureSettingsControllerGuiI) : void	866866	40.040	8.08	0.0 0.00%
createDummyTabs() : void   createDummyTabs() : void	10491049	3.03	2.02	0.0 0.00%
replaceWithDummyTab(FeatureSettingsControllerI) : void   replaceWithDummyTab(FeatureSettingsControllerI) : void	10581058	9.09	5.05	0.0 0.00%
closeFeatureSettings(FeatureSettingsControllerI,boolean) : void   closeFeatureSettings(FeatureSettingsControllerI,boolean) : void	10851085	6.06	4.04	0.0 0.00%
isFeatureSettingsOpen() : boolean   isFeatureSettingsOpen() : boolean	11091109	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.34505495	jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice	1PASS
	0.27032968	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 jalview.api.AlignViewportI;
24		import jalview.api.AlignViewControllerGuiI;
25		import jalview.api.FeatureSettingsControllerI;
26		import jalview.api.SplitContainerI;
27		import jalview.controller.FeatureSettingsControllerGuiI;
28		import jalview.datamodel.AlignmentI;
29		import jalview.jbgui.GAlignFrame;
30		import jalview.jbgui.GSplitFrame;
31		import jalview.structure.StructureSelectionManager;
32		import jalview.util.MessageManager;
33		import jalview.util.Platform;
34		import jalview.viewmodel.AlignmentViewport;
35		import java.awt.BorderLayout;
36		import java.awt.Component;
37		import java.awt.Dimension;
38		import java.awt.event.ActionEvent;
39		import java.awt.event.ActionListener;
40		import java.awt.event.KeyAdapter;
41		import java.awt.event.KeyEvent;
42		import java.awt.event.KeyListener;
43		import java.beans.PropertyVetoException;
44		import java.util.Arrays;
45		import java.util.List;
46		import java.util.Map.Entry;
47
48		import javax.swing.AbstractAction;
49		import javax.swing.InputMap;
50		import javax.swing.JButton;
51		import javax.swing.JComponent;
52		import javax.swing.JDesktopPane;
53		import javax.swing.JInternalFrame;
54		import javax.swing.JLayeredPane;
55		import javax.swing.JMenuItem;
56		import javax.swing.JPanel;
57		import javax.swing.JTabbedPane;
58		import javax.swing.KeyStroke;
59		import javax.swing.event.ChangeEvent;
60		import javax.swing.event.ChangeListener;
61		import javax.swing.event.InternalFrameAdapter;
62		import javax.swing.event.InternalFrameEvent;
63
64
65		/**
66		* An internal frame on the desktop that hosts a horizontally split view of
67		* linked DNA and Protein alignments. Additional views can be created in linked
68		* pairs, expanded to separate split frames, or regathered into a single frame.
69		* <p>
70		* (Some) operations on each alignment are automatically mirrored on the other.
71		* These include mouseover (highlighting), sequence and column selection,
72		* sequence ordering and sorting, and grouping, colouring and sorting by tree.
73		*
74		* @author gmcarstairs
75		*
76		*/
		36% Uncovered Elements: 291 (455) Complexity: 122 Complexity Density: 0.41
77		public class SplitFrame extends GSplitFrame implements SplitContainerI
78		{
79		private static final int WINDOWS_INSETS_WIDTH = 28; // tbc
80
81		private static final int MAC_INSETS_WIDTH = 28;
82
83		private static final int WINDOWS_INSETS_HEIGHT = 50; // tbc
84
85		private static final int MAC_INSETS_HEIGHT = 50;
86
87		private static final int DESKTOP_DECORATORS_HEIGHT = 65;
88
89		private static final long serialVersionUID = 1L;
90
91		/**
92		* geometry for Feature Settings Holder
93		*/
94		private static final int FS_MIN_WIDTH = 400;
95
96		private static final int FS_MIN_HEIGHT = 400;
97
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
98	3	public SplitFrame(GAlignFrame top, GAlignFrame bottom)...
99		{
100	3	super(top, bottom);
101	3	init();
102		}
103
104		/**
105		* Initialise this frame.
106		*/
		91.3% Uncovered Elements: 2 (23) Complexity: 3 Complexity Density: 0.16
107	3	protected void init()...
108		{
109	3	setFrameIcon(null);
110	3	getTopFrame().setSplitFrame(this);
111	3	getBottomFrame().setSplitFrame(this);
112	3	getTopFrame().setVisible(true);
113	3	getBottomFrame().setVisible(true);
114
115	3	((AlignFrame) getTopFrame()).getViewport().setCodingComplement(
116		((AlignFrame) getBottomFrame()).getViewport());
117
118		/*
119		* estimate width and height of SplitFrame; this.getInsets() doesn't seem to
120		* give the full additional size (a few pixels short)
121		*/
122	3	int widthFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_WIDTH
123		: WINDOWS_INSETS_WIDTH;
124	3	int heightFudge = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT
125		: WINDOWS_INSETS_HEIGHT;
126	3	int width = ((AlignFrame) getTopFrame()).getWidth() + widthFudge;
127	3	int height = ((AlignFrame) getTopFrame()).getHeight()
128		+ ((AlignFrame) getBottomFrame()).getHeight() + DIVIDER_SIZE
129		+ heightFudge;
130	3	height = fitHeightToDesktop(height);
131	3	setSize(width, height);
132
133	3	adjustLayout();
134
135	3	addCloseFrameListener();
136
137	3	addKeyListener();
138
139	3	addKeyBindings();
140
141	3	addCommandListeners();
142
143		// ensure all workers are added
144	3	((AlignFrame) getTopFrame()).getViewport().updateConsensus(((AlignFrame) getTopFrame()).alignPanel);
145	3	((AlignFrame) getBottomFrame()).getViewport().updateConsensus(((AlignFrame) getBottomFrame()).alignPanel);
146		}
147
148		/**
149		* Reduce the height if too large to fit in the Desktop. Also adjust the
150		* divider location in proportion.
151		*
152		* @param height
153		* in pixels
154		* @return original or reduced height
155		*/
		85.7% Uncovered Elements: 1 (7) Complexity: 2 Complexity Density: 0.4
156	3	public int fitHeightToDesktop(int height)...
157		{
158		// allow about 65 pixels for Desktop decorators on Windows
159
160	3	int newHeight = Math.min(height,
161		Desktop.getInstance().getHeight() - DESKTOP_DECORATORS_HEIGHT);
162	3	if (newHeight != height)
163		{
164	3	int oldDividerLocation = getDividerLocation();
165	3	setDividerLocation(oldDividerLocation * newHeight / height);
166		}
167	3	return newHeight;
168		}
169
170		/**
171		* Set the top and bottom frames to listen to each others Commands (e.g. Edit,
172		* Order).
173		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
174	3	protected void addCommandListeners()...
175		{
176		// TODO if CommandListener is only ever 1:1 for complementary views,
177		// may change broadcast pattern to direct messaging (more efficient)
178	3	final StructureSelectionManager ssm = StructureSelectionManager
179		.getStructureSelectionManager(Desktop.getInstance());
180	3	ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
181	3	ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
182		}
183
184		/**
185		* Do any tweaking and twerking of the layout wanted.
186		*/
		73.1% Uncovered Elements: 7 (26) Complexity: 8 Complexity Density: 0.57
187	3	public void adjustLayout()...
188		{
189	3	final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
190	3	final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
191
192		/*
193		* Ensure sequence ids are the same width so sequences line up
194		*/
195	3	int w1 = topViewport.getIdWidth();
196	3	int w2 = bottomViewport.getIdWidth();
197	3	int w3 = Math.max(w1, w2);
198	3	topViewport.setIdWidth(w3);
199	3	bottomViewport.setIdWidth(w3);
200
201		/*
202		* Scale protein to either 1 or 3 times character width of dna
203		*/
204	3	final AlignmentI topAlignment = topViewport.getAlignment();
205	3	final AlignmentI bottomAlignment = bottomViewport.getAlignment();
206	3	AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
207	0	: (bottomAlignment.isNucleotide() ? bottomViewport : null);
208	3	AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
209	3	: (!bottomAlignment.isNucleotide() ? bottomViewport : null);
210	3	if (protein != null && cdna != null)
211		{
212	3	int scale = protein.isScaleProteinAsCdna() ? 3 : 1;
213	3	protein.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
214		}
215		}
216
217		/**
218		* Adjusts the divider for a sensible split of the real estate (for example,
219		* when many transcripts are shown with a single protein). This should only be
220		* called after the split pane has been laid out (made visible) so it has a
221		* height. The aim is to avoid unnecessary vertical scroll bars, while
222		* ensuring that at least 2 sequences are visible in each panel.
223		* <p>
224		* Once laid out, the user may choose to customise as they wish, so this
225		* method is not called again after the initial layout.
226		*/
		91.7% Uncovered Elements: 3 (36) Complexity: 4 Complexity Density: 0.13
227	2	protected void adjustInitialLayout()...
228		{
229	2	AlignFrame topFrame = (AlignFrame) getTopFrame();
230	2	AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
231
232		/*
233		* recompute layout of top and bottom panels to reflect their
234		* actual (rather than requested) height
235		*/
236	2	topFrame.alignPanel.adjustAnnotationHeight();
237	2	bottomFrame.alignPanel.adjustAnnotationHeight();
238
239	2	final AlignViewportI topViewport = topFrame.viewport;
240	2	final AlignViewportI bottomViewport = bottomFrame.viewport;
241	2	final AlignmentI topAlignment = topViewport.getAlignment();
242	2	final AlignmentI bottomAlignment = bottomViewport.getAlignment();
243	2	boolean topAnnotations = topViewport.isShowAnnotation();
244	2	boolean bottomAnnotations = bottomViewport.isShowAnnotation();
245		// TODO need number of visible sequences here, not #sequences - how?
246	2	int topCount = topAlignment.getHeight();
247	2	int bottomCount = bottomAlignment.getHeight();
248	2	int topCharHeight = topViewport.getViewStyle().getCharHeight();
249	2	int bottomCharHeight = bottomViewport.getViewStyle().getCharHeight();
250
251		/*
252		* calculate the minimum ratio that leaves at least the height
253		* of two sequences (after rounding) visible in the top panel
254		*/
255	2	int topPanelHeight = topFrame.getHeight();
256	2	int bottomPanelHeight = bottomFrame.getHeight();
257	2	int topSequencesHeight = topFrame.alignPanel.getSeqPanel().seqCanvas
258		.getHeight();
259	2	int topPanelMinHeight = topPanelHeight
260		- Math.max(0, topSequencesHeight - 3 * topCharHeight);
261	2	double totalHeight = (double) topPanelHeight + bottomPanelHeight;
262	2	double minRatio = topPanelMinHeight / totalHeight;
263
264		/*
265		* calculate the maximum ratio that leaves at least the height
266		* of two sequences (after rounding) visible in the bottom panel
267		*/
268	2	int bottomSequencesHeight = bottomFrame.alignPanel.getSeqPanel().seqCanvas
269		.getHeight();
270	2	int bottomPanelMinHeight = bottomPanelHeight
271		- Math.max(0, bottomSequencesHeight - 3 * bottomCharHeight);
272	2	double maxRatio = (totalHeight - bottomPanelMinHeight) / totalHeight;
273
274		/*
275		* estimate ratio of (topFrameContent / bottomFrameContent)
276		*/
277	2	int insets = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT
278		: WINDOWS_INSETS_HEIGHT;
279		// allow 3 'rows' for scale, scrollbar, status bar
280	2	int topHeight = insets + (3 + topCount) * topCharHeight
281	2	+ (topAnnotations ? topViewport.calcPanelHeight() : 0);
282	2	int bottomHeight = insets + (3 + bottomCount) * bottomCharHeight
283	2	+ (bottomAnnotations ? bottomViewport.calcPanelHeight() : 0);
284	2	double ratio = ((double) topHeight)
285		/ (double) (topHeight + bottomHeight);
286
287		/*
288		* limit ratio to avoid concealing all sequences
289		*/
290	2	ratio = Math.min(ratio, maxRatio);
291	2	ratio = Math.max(ratio, minRatio);
292	2	setRelativeDividerLocation(ratio);
293		}
294
295		/**
296		* Add a listener to tidy up when the frame is closed.
297		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
298	3	protected void addCloseFrameListener()...
299		{
300	3	addInternalFrameListener(new InternalFrameAdapter()
301		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
302	3	@Override...
303		public void internalFrameClosed(InternalFrameEvent evt)
304		{
305	3	close();
306		};
307		});
308		}
309
310		/**
311		* Add a key listener that delegates to whichever split component the mouse is
312		* in (or does nothing if neither).
313		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
314	3	protected void addKeyListener()...
315		{
316	3	addKeyListener(new KeyAdapter()
317		{
318
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
319	0	@Override...
320		public void keyPressed(KeyEvent e)
321		{
322	0	AlignFrame af = (AlignFrame) getFrameAtMouse();
323
324		/*
325		* Intercept and override any keys here if wanted.
326		*/
327	0	if (!overrideKey(e, af))
328		{
329	0	if (af != null)
330		{
331	0	for (KeyListener kl : af.getKeyListeners())
332		{
333	0	kl.keyPressed(e);
334		}
335		}
336		}
337		}
338
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
339	0	@Override...
340		public void keyReleased(KeyEvent e)
341		{
342	0	Component c = getFrameAtMouse();
343	0	if (c != null)
344		{
345	0	for (KeyListener kl : c.getKeyListeners())
346		{
347	0	kl.keyReleased(e);
348		}
349		}
350		}
351
352		});
353		}
354
355		/**
356		* Returns true if the key event is overriden and actioned (or ignored) here,
357		* else returns false, indicating it should be delegated to the AlignFrame's
358		* usual handler.
359		* <p>
360		* We can't handle Cmd-Key combinations here, instead this is done by
361		* overriding key bindings.
362		*
363		* @see addKeyOverrides
364		* @param e
365		* @param af
366		* @return
367		*/
		0% Uncovered Elements: 23 (23) Complexity: 7 Complexity Density: 0.37
368	0	protected boolean overrideKey(KeyEvent e, AlignFrame af)...
369		{
370	0	boolean actioned = false;
371	0	int keyCode = e.getKeyCode();
372	0	switch (keyCode)
373		{
374	0	case KeyEvent.VK_DOWN:
375	0	if (e.isAltDown() || !af.viewport.cursorMode)
376		{
377		/*
378		* Key down (or Alt-key-down in cursor mode) - move selected sequences
379		*/
380	0	((AlignFrame) getTopFrame()).moveSelectedSequences(false);
381	0	((AlignFrame) getBottomFrame()).moveSelectedSequences(false);
382	0	actioned = true;
383	0	e.consume();
384		}
385	0	break;
386	0	case KeyEvent.VK_UP:
387	0	if (e.isAltDown() || !af.viewport.cursorMode)
388		{
389		/*
390		* Key up (or Alt-key-up in cursor mode) - move selected sequences
391		*/
392	0	((AlignFrame) getTopFrame()).moveSelectedSequences(true);
393	0	((AlignFrame) getBottomFrame()).moveSelectedSequences(true);
394	0	actioned = true;
395	0	e.consume();
396		}
397	0	break;
398	0	default:
399		}
400	0	return actioned;
401		}
402
403		/**
404		* Set key bindings (recommended for Swing over key accelerators).
405		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
406	3	private void addKeyBindings()...
407		{
408	3	overrideDelegatedKeyBindings();
409
410	3	overrideImplementedKeyBindings();
411		}
412
413		/**
414		* Override key bindings with alternative action methods implemented in this
415		* class.
416		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
417	3	protected void overrideImplementedKeyBindings()...
418		{
419	3	overrideFind();
420	3	overrideNewView();
421	3	overrideCloseView();
422	3	overrideExpandViews();
423	3	overrideGatherViews();
424		}
425
426		/**
427		* Replace Cmd-W close view action with our version.
428		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
429	3	protected void overrideCloseView()...
430		{
431	3	AbstractAction action;
432		/*
433		* Ctrl-W / Cmd-W - close view or window
434		*/
435	3	KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W,
436		Platform.SHORTCUT_KEY_MASK, false);
437	3	action = new AbstractAction()
438		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
439	0	@Override...
440		public void actionPerformed(ActionEvent e)
441		{
442	0	closeView_actionPerformed();
443		}
444		};
445	3	overrideKeyBinding(key_cmdW, action);
446		}
447
448		/**
449		* Replace Cmd-T new view action with our version.
450		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
451	3	protected void overrideNewView()...
452		{
453		/*
454		* Ctrl-T / Cmd-T open new view
455		*/
456	3	KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T,
457		Platform.SHORTCUT_KEY_MASK, false);
458	3	AbstractAction action = new AbstractAction()
459		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
460	0	@Override...
461		public void actionPerformed(ActionEvent e)
462		{
463	0	newView_actionPerformed();
464		}
465		};
466	3	overrideKeyBinding(key_cmdT, action);
467		}
468
469		/**
470		* For now, delegates key events to the corresponding key accelerator for the
471		* AlignFrame that the mouse is in. Hopefully can be simplified in future if
472		* AlignFrame is changed to use key bindings rather than accelerators.
473		*/
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.67
474	3	protected void overrideDelegatedKeyBindings()...
475		{
476	3	if (getTopFrame() instanceof AlignFrame)
477		{
478		/*
479		* Get all accelerator keys in the top frame (the bottom should be
480		* identical) and override each one.
481		*/
482	3	for (Entry<KeyStroke, JMenuItem> acc : ((AlignFrame) getTopFrame())
483		.getAccelerators().entrySet())
484		{
485	81	overrideKeyBinding(acc);
486		}
487		}
488		}
489
490		/**
491		* Overrides an AlignFrame key accelerator with our version which delegates to
492		* the action listener in whichever frame has the mouse (and does nothing if
493		* neither has).
494		*
495		* @param acc
496		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
497	81	private void overrideKeyBinding(Entry<KeyStroke, JMenuItem> acc)...
498		{
499	81	final KeyStroke ks = acc.getKey();
500	81	InputMap inputMap = this.getInputMap(JComponent.WHEN_FOCUSED);
501	81	inputMap.put(ks, ks);
502	81	this.getActionMap().put(ks, new AbstractAction()
503		{
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
504	0	@Override...
505		public void actionPerformed(ActionEvent e)
506		{
507	0	Component c = getFrameAtMouse();
508	0	if (c != null && c instanceof AlignFrame)
509		{
510	0	for (ActionListener a : ((AlignFrame) c).getAccelerators().get(ks)
511		.getActionListeners())
512		{
513	0	a.actionPerformed(null);
514		}
515		}
516		}
517		});
518		}
519
520		/**
521		* Replace an accelerator key's action with the specified action.
522		*
523		* @param ks
524		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
525	9	protected void overrideKeyBinding(KeyStroke ks, AbstractAction action)...
526		{
527	9	this.getActionMap().put(ks, action);
528	9	overrideMenuItem(ks, action);
529		}
530
531		/**
532		* Create and link new views (with matching names) in both panes.
533		* <p>
534		* Note this is _not_ multiple tabs, each hosting a split pane view, rather it
535		* is a single split pane with each split holding multiple tabs which are
536		* linked in pairs.
537		* <p>
538		* TODO implement instead with a tabbed holder in the SplitView, each tab
539		* holding a single JSplitPane. Would avoid a duplicated tab, at the cost of
540		* some additional coding.
541		*/
		0% Uncovered Elements: 17 (17) Complexity: 2 Complexity Density: 0.13
542	0	protected void newView_actionPerformed()...
543		{
544	0	AlignFrame topFrame = (AlignFrame) getTopFrame();
545	0	AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
546	0	final boolean scaleProteinAsCdna = topFrame.viewport
547		.isScaleProteinAsCdna();
548
549	0	AlignmentPanel newTopPanel = topFrame.newView(null, true);
550	0	AlignmentPanel newBottomPanel = bottomFrame.newView(null, true);
551
552		/*
553		* This currently (for the first new view only) leaves the top pane on tab 0
554		* but the bottom on tab 1. This results from 'setInitialTabVisible' echoing
555		* from the bottom back to the first frame. Next line is a fudge to work
556		* around this. TODO find a better way.
557		*/
558	0	if (topFrame.getTabIndex() != bottomFrame.getTabIndex())
559		{
560	0	topFrame.setDisplayedView(newTopPanel);
561		}
562
563	0	newBottomPanel.av.setViewName(newTopPanel.av.getViewName());
564	0	newTopPanel.av.setCodingComplement(newBottomPanel.av);
565
566		/*
567		* These lines can be removed once scaleProteinAsCdna is added to element
568		* Viewport in jalview.xsd, as Jalview2XML.copyAlignPanel will then take
569		* care of it
570		*/
571	0	newTopPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
572	0	newBottomPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
573
574		/*
575		* Line up id labels etc
576		*/
577	0	adjustLayout();
578
579	0	final StructureSelectionManager ssm = StructureSelectionManager
580		.getStructureSelectionManager(Desktop.getInstance());
581	0	ssm.addCommandListener(newTopPanel.av);
582	0	ssm.addCommandListener(newBottomPanel.av);
583		}
584
585		/**
586		* Close the currently selected view in both panes. If there is only one view,
587		* close this split frame.
588		*/
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.25
589	0	protected void closeView_actionPerformed()...
590		{
591	0	int viewCount = ((AlignFrame) getTopFrame()).getAlignPanels().size();
592	0	if (viewCount < 2)
593		{
594	0	close();
595	0	return;
596		}
597
598	0	AlignmentPanel topPanel = ((AlignFrame) getTopFrame()).alignPanel;
599	0	AlignmentPanel bottomPanel = ((AlignFrame) getBottomFrame()).alignPanel;
600
601	0	((AlignFrame) getTopFrame()).closeView(topPanel);
602	0	((AlignFrame) getBottomFrame()).closeView(bottomPanel);
603
604		}
605
606		/**
607		* Close child frames and this split frame.
608		*/
		100% Uncovered Elements: 0 (4) Complexity: 2 Complexity Density: 0.5
609	3	public void close()...
610		{
611	3	((AlignFrame) getTopFrame()).closeMenuItem_actionPerformed(true);
612	3	((AlignFrame) getBottomFrame()).closeMenuItem_actionPerformed(true);
613	3	try
614		{
615	3	this.setClosed(true);
616		} catch (PropertyVetoException e)
617		{
618		// ignore
619		}
620		}
621
622		/**
623		* Replace AlignFrame 'expand views' action with SplitFrame version.
624		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
625	3	protected void overrideExpandViews()...
626		{
627	3	KeyStroke key_X = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
628	3	AbstractAction action = new AbstractAction()
629		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
630	0	@Override...
631		public void actionPerformed(ActionEvent e)
632		{
633	0	expandViews_actionPerformed();
634		}
635		};
636	3	overrideMenuItem(key_X, action);
637		}
638
639		/**
640		* Replace AlignFrame 'gather views' action with SplitFrame version.
641		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
642	3	protected void overrideGatherViews()...
643		{
644	3	KeyStroke key_G = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
645	3	AbstractAction action = new AbstractAction()
646		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
647	0	@Override...
648		public void actionPerformed(ActionEvent e)
649		{
650	0	gatherViews_actionPerformed();
651		}
652		};
653	3	overrideMenuItem(key_G, action);
654		}
655
656		/**
657		* Override the menu action associated with the keystroke in the child frames,
658		* replacing it with the given action.
659		*
660		* @param ks
661		* @param action
662		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
663	15	private void overrideMenuItem(KeyStroke ks, AbstractAction action)...
664		{
665	15	overrideMenuItem(ks, action, getTopFrame());
666	15	overrideMenuItem(ks, action, getBottomFrame());
667		}
668
669		/**
670		* Override the menu action associated with the keystroke in one child frame,
671		* replacing it with the given action. Mwahahahaha.
672		*
673		* @param key
674		* @param action
675		* @param comp
676		*/
		80% Uncovered Elements: 2 (10) Complexity: 3 Complexity Density: 0.5
677	30	private void overrideMenuItem(KeyStroke key, final AbstractAction action,...
678		JComponent comp)
679		{
680	30	if (comp instanceof AlignFrame)
681		{
682	30	JMenuItem mi = ((AlignFrame) comp).getAccelerators().get(key);
683	30	if (mi != null)
684		{
685	30	for (ActionListener al : mi.getActionListeners())
686		{
687	30	mi.removeActionListener(al);
688		}
689	30	mi.addActionListener(new ActionListener()
690		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
691	0	@Override...
692		public void actionPerformed(ActionEvent e)
693		{
694	0	action.actionPerformed(e);
695		}
696		});
697		}
698		}
699		}
700
701		/**
702		* Expand any multiple views (which are always in pairs) into separate split
703		* frames.
704		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
705	0	protected void expandViews_actionPerformed()...
706		{
707	0	Desktop.getInstance().explodeViews(this);
708		}
709
710		/**
711		* Gather any other SplitFrame views of this alignment back in as multiple
712		* (pairs of) views in this SplitFrame.
713		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
714	0	protected void gatherViews_actionPerformed()...
715		{
716	0	Desktop.getInstance().gatherViews(this);
717		}
718
719		/**
720		* Returns the alignment in the complementary frame to the one given.
721		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
722	0	@Override...
723		public AlignmentI getComplement(Object alignFrame)
724		{
725	0	if (alignFrame == this.getTopFrame())
726		{
727	0	return ((AlignFrame) getBottomFrame()).viewport.getAlignment();
728		}
729	0	else if (alignFrame == this.getBottomFrame())
730		{
731	0	return ((AlignFrame) getTopFrame()).viewport.getAlignment();
732		}
733	0	return null;
734		}
735
736		/**
737		* Returns the title of the complementary frame to the one given.
738		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
739	0	@Override...
740		public String getComplementTitle(Object alignFrame)
741		{
742	0	if (alignFrame == this.getTopFrame())
743		{
744	0	return ((AlignFrame) getBottomFrame()).getTitle();
745		}
746	0	else if (alignFrame == this.getBottomFrame())
747		{
748	0	return ((AlignFrame) getTopFrame()).getTitle();
749		}
750	0	return null;
751		}
752
753		/**
754		* Set the 'other half' to hidden / revealed.
755		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
756	0	@Override...
757		public void setComplementVisible(Object alignFrame, boolean show)
758		{
759		/*
760		* Hiding the AlignPanel suppresses unnecessary repaints
761		*/
762	0	if (alignFrame == getTopFrame())
763		{
764	0	((AlignFrame) getBottomFrame()).alignPanel.setVisible(show);
765		}
766	0	else if (alignFrame == getBottomFrame())
767		{
768	0	((AlignFrame) getTopFrame()).alignPanel.setVisible(show);
769		}
770	0	super.setComplementVisible(alignFrame, show);
771		}
772
773		/**
774		* return the AlignFrames held by this container
775		*
776		* @return { Top alignFrame (Usually CDS), Bottom AlignFrame (Usually
777		* Protein)}
778		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
779	0	public List<AlignFrame> getAlignFrames()...
780		{
781	0	return Arrays
782		.asList(new AlignFrame[]
783		{ (AlignFrame) getTopFrame(), (AlignFrame) getBottomFrame() });
784		}
785
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
786	0	@Override...
787		public AlignFrame getComplementAlignFrame(
788		AlignViewControllerGuiI alignFrame)
789		{
790	0	if (getTopFrame() == alignFrame)
791		{
792	0	return (AlignFrame) getBottomFrame();
793		}
794	0	if (getBottomFrame() == alignFrame)
795		{
796	0	return (AlignFrame) getTopFrame();
797		}
798		// we didn't know anything about this frame...
799	0	return null;
800		}
801
802		/**
803		* Replace Cmd-F Find action with our version. This is necessary because the
804		* 'default' Finder searches in the first AlignFrame it finds. We need it to
805		* search in the half of the SplitFrame that has the mouse.
806		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
807	3	protected void overrideFind()...
808		{
809		/*
810		* Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
811		*/
812	3	KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F,
813		Platform.SHORTCUT_KEY_MASK, false);
814	3	AbstractAction action = new AbstractAction()
815		{
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
816	0	@Override...
817		public void actionPerformed(ActionEvent e)
818		{
819	0	Component c = getFrameAtMouse();
820	0	if (c != null && c instanceof AlignFrame)
821		{
822	0	AlignFrame af = (AlignFrame) c;
823	0	boolean dna = af.getViewport().getAlignment().isNucleotide();
824	0	String scope = MessageManager.getString("label.in") + " "
825	0	+ (dna ? MessageManager.getString("label.nucleotide")
826		: MessageManager.getString("label.protein"));
827	0	new Finder(af.alignPanel, true, scope);
828		}
829		}
830		};
831	3	overrideKeyBinding(key_cmdF, action);
832		}
833
834		/**
835		* Override to do nothing if triggered from one of the child frames
836		*/
		53.8% Uncovered Elements: 6 (13) Complexity: 5 Complexity Density: 0.71
837	11	@Override...
838		public void setSelected(boolean selected) throws PropertyVetoException
839		{
840	11	JDesktopPane desktopPane = getDesktopPane();
841	11	JInternalFrame fr = desktopPane == null ? null
842		: desktopPane.getSelectedFrame();
843	11	if (fr == getTopFrame() || fr == getBottomFrame())
844		{
845		/*
846		* patch for JAL-3288 (deselecting top/bottom frame closes popup menu);
847		* it may be possible to remove this method in future
848		* if the underlying Java behaviour changes
849		*/
850	0	if (selected)
851		{
852	0	moveToFront();
853		}
854	0	return;
855		}
856	11	super.setSelected(selected);
857		}
858
859		/**
860		* holds the frame for feature settings, so Protein and DNA tabs can be managed
861		*/
862		JInternalFrame featureSettingsUI;
863
864		JTabbedPane featureSettingsPanels;
865
		0% Uncovered Elements: 52 (52) Complexity: 8 Complexity Density: 0.2
866	0	@Override...
867		public void addFeatureSettingsUI(
868		FeatureSettingsControllerGuiI featureSettings)
869		{
870	0	boolean showInternalFrame = false;
871	0	if (featureSettingsUI == null || featureSettingsPanels == null)
872		{
873	0	showInternalFrame = true;
874	0	featureSettingsPanels = new JTabbedPane();
875	0	featureSettingsPanels.addChangeListener(new ChangeListener()
876		{
877
		0% Uncovered Elements: 10 (10) Complexity: 7 Complexity Density: 1.17
878	0	@Override...
879		public void stateChanged(ChangeEvent e)
880		{
881	0	if (e.getSource() != featureSettingsPanels
882		|| featureSettingsUI == null
883		|| featureSettingsUI.isClosed()
884		|| !featureSettingsUI.isVisible())
885		{
886		// not our tabbed pane
887	0	return;
888		}
889	0	int tab = featureSettingsPanels.getSelectedIndex();
890	0	if (tab < 0 || featureSettingsPanels
891		.getSelectedComponent() instanceof FeatureSettingsControllerGuiI)
892		{
893		// no tab selected or already showing a feature settings GUI
894	0	return;
895		}
896	0	getAlignFrames().get(tab).showFeatureSettingsUI();
897		}
898		});
899	0	featureSettingsUI = new JInternalFrame(MessageManager.getString(
900		"label.sequence_feature_settings_for_CDS_and_Protein"));
901	0	featureSettingsUI.setFrameIcon(null);
902	0	featureSettingsPanels.setOpaque(true);
903
904	0	JPanel dialog = new JPanel();
905	0	dialog.setOpaque(true);
906	0	dialog.setLayout(new BorderLayout());
907	0	dialog.add(featureSettingsPanels, BorderLayout.CENTER);
908	0	JPanel buttons = new JPanel();
909	0	JButton ok = new JButton(MessageManager.getString("action.ok"));
910	0	ok.addActionListener(new ActionListener()
911		{
912
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
913	0	@Override...
914		public void actionPerformed(ActionEvent e)
915		{
916	0	try
917		{
918	0	featureSettingsUI.setClosed(true);
919		} catch (PropertyVetoException pv)
920		{
921	0	pv.printStackTrace();
922		}
923		}
924		});
925	0	JButton cancel = new JButton(
926		MessageManager.getString("action.cancel"));
927	0	cancel.addActionListener(new ActionListener()
928		{
929
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
930	0	@Override...
931		public void actionPerformed(ActionEvent e)
932		{
933	0	try
934		{
935	0	for (Component fspanel : featureSettingsPanels.getComponents())
936		{
937	0	if (fspanel instanceof FeatureSettingsControllerGuiI)
938		{
939	0	((FeatureSettingsControllerGuiI) fspanel).revert();
940		}
941		}
942	0	featureSettingsUI.setClosed(true);
943		} catch (Exception pv)
944		{
945	0	pv.printStackTrace();
946		}
947		}
948		});
949	0	buttons.add(ok);
950	0	buttons.add(cancel);
951	0	dialog.add(buttons, BorderLayout.SOUTH);
952	0	featureSettingsUI.setContentPane(dialog);
953	0	createDummyTabs();
954		}
955	0	if (featureSettingsPanels
956		.indexOfTabComponent((Component) featureSettings) > -1)
957		{
958		// just show the feature settings !
959	0	featureSettingsPanels
960		.setSelectedComponent((Component) featureSettings);
961	0	return;
962		}
963		// otherwise replace the dummy tab with the given feature settings
964	0	int pos = getAlignFrames().indexOf(featureSettings.getAlignframe());
965		// if pos==-1 then alignFrame isn't managed by this splitframe
966	0	if (pos == 0)
967		{
968	0	featureSettingsPanels.removeTabAt(0);
969	0	featureSettingsPanels.insertTab(tabName[0], null,
970		(Component) featureSettings,
971		MessageManager.formatMessage(
972		"label.sequence_feature_settings_for", tabName[0]),
973		0);
974		}
975	0	if (pos == 1)
976		{
977	0	featureSettingsPanels.removeTabAt(1);
978	0	featureSettingsPanels.insertTab(tabName[1], null,
979		(Component) featureSettings,
980		MessageManager.formatMessage(
981		"label.sequence_feature_settings_for", tabName[1]),
982		1);
983		}
984	0	featureSettingsPanels.setSelectedComponent((Component) featureSettings);
985
986		// TODO: JAL-3535 - construct a feature settings title including names of
987		// currently selected CDS and Protein names
988
989	0	if (showInternalFrame)
990		{
991	0	if (Platform.isAMacAndNotJS())
992		{
993	0	Desktop.addInternalFrame(featureSettingsUI,
994		MessageManager.getString(
995		"label.sequence_feature_settings_for_CDS_and_Protein"),
996		600, 480);
997		}
998		else
999		{
1000	0	Desktop.addInternalFrame(featureSettingsUI,
1001		MessageManager.getString(
1002		"label.sequence_feature_settings_for_CDS_and_Protein"),
1003		600, 450);
1004		}
1005	0	featureSettingsUI
1006		.setMinimumSize(new Dimension(FS_MIN_WIDTH, FS_MIN_HEIGHT));
1007
1008	0	featureSettingsUI.addInternalFrameListener(
1009		new javax.swing.event.InternalFrameAdapter()
1010		{
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
1011	0	@Override...
1012		public void internalFrameClosed(
1013		javax.swing.event.InternalFrameEvent evt)
1014		{
1015	0	for (int tab = 0; tab < featureSettingsPanels
1016		.getTabCount();)
1017		{
1018	0	FeatureSettingsControllerGuiI fsettings = (FeatureSettingsControllerGuiI) featureSettingsPanels
1019		.getTabComponentAt(tab);
1020	0	if (fsettings != null)
1021		{
1022	0	featureSettingsPanels.removeTabAt(tab);
1023	0	fsettings.featureSettings_isClosed();
1024		}
1025		else
1026		{
1027	0	tab++;
1028		}
1029		}
1030	0	featureSettingsPanels = null;
1031	0	featureSettingsUI = null;
1032		};
1033		});
1034	0	featureSettingsUI.setLayer(JLayeredPane.PALETTE_LAYER);
1035		}
1036		}
1037
1038		/**
1039		* tab names for feature settings
1040		*/
1041		private String[] tabName = new String[] {
1042		MessageManager.getString("label.CDS"),
1043		MessageManager.getString("label.protein") };
1044
1045		/**
1046		* create placeholder tabs which materialise the feature settings for a given
1047		* view. Also reinitialises any tabs containing stale feature settings
1048		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
1049	0	private void createDummyTabs()...
1050		{
1051	0	for (int tabIndex = 0; tabIndex < 2; tabIndex++)
1052		{
1053	0	JPanel dummyTab = new JPanel();
1054	0	featureSettingsPanels.addTab(tabName[tabIndex], dummyTab);
1055		}
1056		}
1057
		0% Uncovered Elements: 15 (15) Complexity: 5 Complexity Density: 0.56
1058	0	private void replaceWithDummyTab(FeatureSettingsControllerI toClose)...
1059		{
1060	0	Component dummyTab = null;
1061	0	for (int tabIndex = 0; tabIndex < 2; tabIndex++)
1062		{
1063	0	if (featureSettingsPanels.getTabCount() > tabIndex)
1064		{
1065	0	dummyTab = featureSettingsPanels.getTabComponentAt(tabIndex);
1066	0	if (dummyTab instanceof FeatureSettingsControllerGuiI
1067		&& !dummyTab.isVisible())
1068		{
1069	0	featureSettingsPanels.removeTabAt(tabIndex);
1070		// close the feature Settings tab
1071	0	((FeatureSettingsControllerGuiI) dummyTab)
1072		.featureSettings_isClosed();
1073		// create a dummy tab in its place
1074	0	dummyTab = new JPanel();
1075	0	featureSettingsPanels.insertTab(tabName[tabIndex], null, dummyTab,
1076		MessageManager.formatMessage(
1077		"label.sequence_feature_settings_for",
1078		tabName[tabIndex]),
1079		tabIndex);
1080		}
1081		}
1082		}
1083		}
1084
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
1085	0	@Override...
1086		public void closeFeatureSettings(
1087		FeatureSettingsControllerI featureSettings,
1088		boolean closeContainingFrame)
1089		{
1090	0	if (featureSettingsUI != null)
1091		{
1092	0	if (closeContainingFrame)
1093		{
1094	0	try
1095		{
1096	0	featureSettingsUI.setClosed(true);
1097		} catch (Exception x)
1098		{
1099		}
1100	0	featureSettingsUI = null;
1101		}
1102		else
1103		{
1104	0	replaceWithDummyTab(featureSettings);
1105		}
1106		}
1107		}
1108
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1109	0	@Override...
1110		public boolean isFeatureSettingsOpen()
1111		{
1112	0	return featureSettingsUI != null && !featureSettingsUI.isClosed();
1113		}
1114		}