Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SplitFrame	77	296	122	0.357615935.8%	Show methods

Class SplitFrame

Class SplitFrame	Line # 77	Total Statements 296	Complexity 122	TOTAL Coverage 0.357615935.8%
SplitFrame(GAlignFrame,GAlignFrame)   SplitFrame(GAlignFrame,GAlignFrame)	9898	2.02	1.01	1.0 1.0100%
init() : void   init() : void	107107	17.017	3.03	0.9047619 0.904761990.5%
fitHeightToDesktop(int) : int   fitHeightToDesktop(int) : int	152152	5.05	2.02	0.85714287 0.8571428785.7%
addCommandListeners() : void   addCommandListeners() : void	170170	3.03	1.01	1.0 1.0100%
adjustLayout() : void   adjustLayout() : void	183183	14.014	8.08	0.7307692 0.730769273.1%
adjustInitialLayout() : void   adjustInitialLayout() : void	223223	30.030	4.04	0.9166667 0.916666791.7%
internalFrameClosed(InternalFrameEvent) : void   internalFrameClosed(InternalFrameEvent) : void	298298	1.01	1.01	1.0 1.0100%
addCloseFrameListener() : void   addCloseFrameListener() : void	294294	1.01	1.01	1.0 1.0100%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	315315	5.05	3.03	0.0 0.00%
keyReleased(KeyEvent) : void   keyReleased(KeyEvent) : void	335335	4.04	2.02	0.0 0.00%
addKeyListener() : void   addKeyListener() : void	310310	1.01	1.01	1.0 1.0100%
overrideKey(KeyEvent,AlignFrame) : boolean   overrideKey(KeyEvent,AlignFrame) : boolean	364364	19.019	7.07	0.0 0.00%
addKeyBindings() : void   addKeyBindings() : void	402402	2.02	1.01	1.0 1.0100%
overrideImplementedKeyBindings() : void   overrideImplementedKeyBindings() : void	413413	5.05	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	435435	1.01	1.01	0.0 0.00%
overrideCloseView() : void   overrideCloseView() : void	425425	4.04	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	456456	1.01	1.01	0.0 0.00%
overrideNewView() : void   overrideNewView() : void	447447	3.03	1.01	1.0 1.0100%
overrideDelegatedKeyBindings() : void   overrideDelegatedKeyBindings() : void	470470	3.03	2.02	0.8 0.880%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	500500	4.04	3.03	0.0 0.00%
overrideKeyBinding(Entry<KeyStroke, JMenuItem>) : void   overrideKeyBinding(Entry<KeyStroke, JMenuItem>) : void	493493	4.04	1.01	1.0 1.0100%
overrideKeyBinding(KeyStroke,AbstractAction) : void   overrideKeyBinding(KeyStroke,AbstractAction) : void	521521	2.02	1.01	1.0 1.0100%
newView_actionPerformed() : void   newView_actionPerformed() : void	538538	15.015	2.02	0.0 0.00%
closeView_actionPerformed() : void   closeView_actionPerformed() : void	585585	8.08	2.02	0.0 0.00%
close() : void   close() : void	605605	4.04	2.02	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	626626	1.01	1.01	0.0 0.00%
overrideExpandViews() : void   overrideExpandViews() : void	621621	3.03	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	643643	1.01	1.01	0.0 0.00%
overrideGatherViews() : void   overrideGatherViews() : void	638638	3.03	1.01	1.0 1.0100%
overrideMenuItem(KeyStroke,AbstractAction) : void   overrideMenuItem(KeyStroke,AbstractAction) : void	659659	2.02	1.01	1.0 1.0100%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	687687	1.01	1.01	0.0 0.00%
overrideMenuItem(KeyStroke,AbstractAction,JComponent) : void   overrideMenuItem(KeyStroke,AbstractAction,JComponent) : void	673673	6.06	3.03	0.8 0.880%
expandViews_actionPerformed() : void   expandViews_actionPerformed() : void	701701	1.01	1.01	0.0 0.00%
gatherViews_actionPerformed() : void   gatherViews_actionPerformed() : void	710710	1.01	1.01	0.0 0.00%
getComplement(Object) : AlignmentI   getComplement(Object) : AlignmentI	718718	5.05	3.03	0.0 0.00%
getComplementTitle(Object) : String   getComplementTitle(Object) : String	735735	5.05	3.03	0.0 0.00%
setComplementVisible(Object,boolean) : void   setComplementVisible(Object,boolean) : void	752752	5.05	3.03	0.0 0.00%
getAlignFrames() : List<AlignFrame>   getAlignFrames() : List<AlignFrame>	775775	1.01	1.01	0.0 0.00%
getComplementAlignFrame(AlignViewControllerGuiI) : AlignFrame   getComplementAlignFrame(AlignViewControllerGuiI) : AlignFrame	782782	5.05	3.03	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	812812	6.06	4.04	0.0 0.00%
overrideFind() : void   overrideFind() : void	803803	3.03	1.01	1.0 1.0100%
setSelected(boolean) : void   setSelected(boolean) : void	833833	7.07	5.05	0.53846157 0.5384615753.8%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	874874	6.06	7.07	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	909909	3.03	2.02	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	926926	6.06	3.03	0.0 0.00%
internalFrameClosed(javax.swing.event.InternalFrameEvent) : void   internalFrameClosed(javax.swing.event.InternalFrameEvent) : void	10071007	8.08	3.03	0.0 0.00%
addFeatureSettingsUI(FeatureSettingsControllerGuiI) : void   addFeatureSettingsUI(FeatureSettingsControllerGuiI) : void	862862	40.040	8.08	0.0 0.00%
createDummyTabs() : void   createDummyTabs() : void	10451045	3.03	2.02	0.0 0.00%
replaceWithDummyTab(FeatureSettingsControllerI) : void   replaceWithDummyTab(FeatureSettingsControllerI) : void	10541054	9.09	5.05	0.0 0.00%
closeFeatureSettings(FeatureSettingsControllerI,boolean) : void   closeFeatureSettings(FeatureSettingsControllerI,boolean) : void	10811081	6.06	4.04	0.0 0.00%
isFeatureSettingsOpen() : boolean   isFeatureSettingsOpen() : boolean	11051105	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 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		*/
		35.8% Uncovered Elements: 291 (453) 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		*/
		90.5% Uncovered Elements: 2 (21) Complexity: 3 Complexity Density: 0.18
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
144		/**
145		* Reduce the height if too large to fit in the Desktop. Also adjust the
146		* divider location in proportion.
147		*
148		* @param height
149		* in pixels
150		* @return original or reduced height
151		*/
		85.7% Uncovered Elements: 1 (7) Complexity: 2 Complexity Density: 0.4
152	3	public int fitHeightToDesktop(int height)...
153		{
154		// allow about 65 pixels for Desktop decorators on Windows
155
156	3	int newHeight = Math.min(height,
157		Desktop.getInstance().getHeight() - DESKTOP_DECORATORS_HEIGHT);
158	3	if (newHeight != height)
159		{
160	3	int oldDividerLocation = getDividerLocation();
161	3	setDividerLocation(oldDividerLocation * newHeight / height);
162		}
163	3	return newHeight;
164		}
165
166		/**
167		* Set the top and bottom frames to listen to each others Commands (e.g. Edit,
168		* Order).
169		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
170	3	protected void addCommandListeners()...
171		{
172		// TODO if CommandListener is only ever 1:1 for complementary views,
173		// may change broadcast pattern to direct messaging (more efficient)
174	3	final StructureSelectionManager ssm = StructureSelectionManager
175		.getStructureSelectionManager(Desktop.getInstance());
176	3	ssm.addCommandListener(((AlignFrame) getTopFrame()).getViewport());
177	3	ssm.addCommandListener(((AlignFrame) getBottomFrame()).getViewport());
178		}
179
180		/**
181		* Do any tweaking and twerking of the layout wanted.
182		*/
		73.1% Uncovered Elements: 7 (26) Complexity: 8 Complexity Density: 0.57
183	3	public void adjustLayout()...
184		{
185	3	final AlignViewport topViewport = ((AlignFrame) getTopFrame()).viewport;
186	3	final AlignViewport bottomViewport = ((AlignFrame) getBottomFrame()).viewport;
187
188		/*
189		* Ensure sequence ids are the same width so sequences line up
190		*/
191	3	int w1 = topViewport.getIdWidth();
192	3	int w2 = bottomViewport.getIdWidth();
193	3	int w3 = Math.max(w1, w2);
194	3	topViewport.setIdWidth(w3);
195	3	bottomViewport.setIdWidth(w3);
196
197		/*
198		* Scale protein to either 1 or 3 times character width of dna
199		*/
200	3	final AlignmentI topAlignment = topViewport.getAlignment();
201	3	final AlignmentI bottomAlignment = bottomViewport.getAlignment();
202	3	AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
203	0	: (bottomAlignment.isNucleotide() ? bottomViewport : null);
204	3	AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
205	3	: (!bottomAlignment.isNucleotide() ? bottomViewport : null);
206	3	if (protein != null && cdna != null)
207		{
208	3	int scale = protein.isScaleProteinAsCdna() ? 3 : 1;
209	3	protein.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
210		}
211		}
212
213		/**
214		* Adjusts the divider for a sensible split of the real estate (for example,
215		* when many transcripts are shown with a single protein). This should only be
216		* called after the split pane has been laid out (made visible) so it has a
217		* height. The aim is to avoid unnecessary vertical scroll bars, while
218		* ensuring that at least 2 sequences are visible in each panel.
219		* <p>
220		* Once laid out, the user may choose to customise as they wish, so this
221		* method is not called again after the initial layout.
222		*/
		91.7% Uncovered Elements: 3 (36) Complexity: 4 Complexity Density: 0.13
223	2	protected void adjustInitialLayout()...
224		{
225	2	AlignFrame topFrame = (AlignFrame) getTopFrame();
226	2	AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
227
228		/*
229		* recompute layout of top and bottom panels to reflect their
230		* actual (rather than requested) height
231		*/
232	2	topFrame.alignPanel.adjustAnnotationHeight();
233	2	bottomFrame.alignPanel.adjustAnnotationHeight();
234
235	2	final AlignViewportI topViewport = topFrame.viewport;
236	2	final AlignViewportI bottomViewport = bottomFrame.viewport;
237	2	final AlignmentI topAlignment = topViewport.getAlignment();
238	2	final AlignmentI bottomAlignment = bottomViewport.getAlignment();
239	2	boolean topAnnotations = topViewport.isShowAnnotation();
240	2	boolean bottomAnnotations = bottomViewport.isShowAnnotation();
241		// TODO need number of visible sequences here, not #sequences - how?
242	2	int topCount = topAlignment.getHeight();
243	2	int bottomCount = bottomAlignment.getHeight();
244	2	int topCharHeight = topViewport.getViewStyle().getCharHeight();
245	2	int bottomCharHeight = bottomViewport.getViewStyle().getCharHeight();
246
247		/*
248		* calculate the minimum ratio that leaves at least the height
249		* of two sequences (after rounding) visible in the top panel
250		*/
251	2	int topPanelHeight = topFrame.getHeight();
252	2	int bottomPanelHeight = bottomFrame.getHeight();
253	2	int topSequencesHeight = topFrame.alignPanel.getSeqPanel().seqCanvas
254		.getHeight();
255	2	int topPanelMinHeight = topPanelHeight
256		- Math.max(0, topSequencesHeight - 3 * topCharHeight);
257	2	double totalHeight = (double) topPanelHeight + bottomPanelHeight;
258	2	double minRatio = topPanelMinHeight / totalHeight;
259
260		/*
261		* calculate the maximum ratio that leaves at least the height
262		* of two sequences (after rounding) visible in the bottom panel
263		*/
264	2	int bottomSequencesHeight = bottomFrame.alignPanel.getSeqPanel().seqCanvas
265		.getHeight();
266	2	int bottomPanelMinHeight = bottomPanelHeight
267		- Math.max(0, bottomSequencesHeight - 3 * bottomCharHeight);
268	2	double maxRatio = (totalHeight - bottomPanelMinHeight) / totalHeight;
269
270		/*
271		* estimate ratio of (topFrameContent / bottomFrameContent)
272		*/
273	2	int insets = Platform.isAMacAndNotJS() ? MAC_INSETS_HEIGHT
274		: WINDOWS_INSETS_HEIGHT;
275		// allow 3 'rows' for scale, scrollbar, status bar
276	2	int topHeight = insets + (3 + topCount) * topCharHeight
277	2	+ (topAnnotations ? topViewport.calcPanelHeight() : 0);
278	2	int bottomHeight = insets + (3 + bottomCount) * bottomCharHeight
279	2	+ (bottomAnnotations ? bottomViewport.calcPanelHeight() : 0);
280	2	double ratio = ((double) topHeight)
281		/ (double) (topHeight + bottomHeight);
282
283		/*
284		* limit ratio to avoid concealing all sequences
285		*/
286	2	ratio = Math.min(ratio, maxRatio);
287	2	ratio = Math.max(ratio, minRatio);
288	2	setRelativeDividerLocation(ratio);
289		}
290
291		/**
292		* Add a listener to tidy up when the frame is closed.
293		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
294	3	protected void addCloseFrameListener()...
295		{
296	3	addInternalFrameListener(new InternalFrameAdapter()
297		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
298	3	@Override...
299		public void internalFrameClosed(InternalFrameEvent evt)
300		{
301	3	close();
302		};
303		});
304		}
305
306		/**
307		* Add a key listener that delegates to whichever split component the mouse is
308		* in (or does nothing if neither).
309		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
310	3	protected void addKeyListener()...
311		{
312	3	addKeyListener(new KeyAdapter()
313		{
314
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
315	0	@Override...
316		public void keyPressed(KeyEvent e)
317		{
318	0	AlignFrame af = (AlignFrame) getFrameAtMouse();
319
320		/*
321		* Intercept and override any keys here if wanted.
322		*/
323	0	if (!overrideKey(e, af))
324		{
325	0	if (af != null)
326		{
327	0	for (KeyListener kl : af.getKeyListeners())
328		{
329	0	kl.keyPressed(e);
330		}
331		}
332		}
333		}
334
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
335	0	@Override...
336		public void keyReleased(KeyEvent e)
337		{
338	0	Component c = getFrameAtMouse();
339	0	if (c != null)
340		{
341	0	for (KeyListener kl : c.getKeyListeners())
342		{
343	0	kl.keyReleased(e);
344		}
345		}
346		}
347
348		});
349		}
350
351		/**
352		* Returns true if the key event is overriden and actioned (or ignored) here,
353		* else returns false, indicating it should be delegated to the AlignFrame's
354		* usual handler.
355		* <p>
356		* We can't handle Cmd-Key combinations here, instead this is done by
357		* overriding key bindings.
358		*
359		* @see addKeyOverrides
360		* @param e
361		* @param af
362		* @return
363		*/
		0% Uncovered Elements: 23 (23) Complexity: 7 Complexity Density: 0.37
364	0	protected boolean overrideKey(KeyEvent e, AlignFrame af)...
365		{
366	0	boolean actioned = false;
367	0	int keyCode = e.getKeyCode();
368	0	switch (keyCode)
369		{
370	0	case KeyEvent.VK_DOWN:
371	0	if (e.isAltDown() || !af.viewport.cursorMode)
372		{
373		/*
374		* Key down (or Alt-key-down in cursor mode) - move selected sequences
375		*/
376	0	((AlignFrame) getTopFrame()).moveSelectedSequences(false);
377	0	((AlignFrame) getBottomFrame()).moveSelectedSequences(false);
378	0	actioned = true;
379	0	e.consume();
380		}
381	0	break;
382	0	case KeyEvent.VK_UP:
383	0	if (e.isAltDown() || !af.viewport.cursorMode)
384		{
385		/*
386		* Key up (or Alt-key-up in cursor mode) - move selected sequences
387		*/
388	0	((AlignFrame) getTopFrame()).moveSelectedSequences(true);
389	0	((AlignFrame) getBottomFrame()).moveSelectedSequences(true);
390	0	actioned = true;
391	0	e.consume();
392		}
393	0	break;
394	0	default:
395		}
396	0	return actioned;
397		}
398
399		/**
400		* Set key bindings (recommended for Swing over key accelerators).
401		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
402	3	private void addKeyBindings()...
403		{
404	3	overrideDelegatedKeyBindings();
405
406	3	overrideImplementedKeyBindings();
407		}
408
409		/**
410		* Override key bindings with alternative action methods implemented in this
411		* class.
412		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
413	3	protected void overrideImplementedKeyBindings()...
414		{
415	3	overrideFind();
416	3	overrideNewView();
417	3	overrideCloseView();
418	3	overrideExpandViews();
419	3	overrideGatherViews();
420		}
421
422		/**
423		* Replace Cmd-W close view action with our version.
424		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
425	3	protected void overrideCloseView()...
426		{
427	3	AbstractAction action;
428		/*
429		* Ctrl-W / Cmd-W - close view or window
430		*/
431	3	KeyStroke key_cmdW = KeyStroke.getKeyStroke(KeyEvent.VK_W,
432		Platform.SHORTCUT_KEY_MASK, false);
433	3	action = new AbstractAction()
434		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
435	0	@Override...
436		public void actionPerformed(ActionEvent e)
437		{
438	0	closeView_actionPerformed();
439		}
440		};
441	3	overrideKeyBinding(key_cmdW, action);
442		}
443
444		/**
445		* Replace Cmd-T new view action with our version.
446		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
447	3	protected void overrideNewView()...
448		{
449		/*
450		* Ctrl-T / Cmd-T open new view
451		*/
452	3	KeyStroke key_cmdT = KeyStroke.getKeyStroke(KeyEvent.VK_T,
453		Platform.SHORTCUT_KEY_MASK, false);
454	3	AbstractAction action = new AbstractAction()
455		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
456	0	@Override...
457		public void actionPerformed(ActionEvent e)
458		{
459	0	newView_actionPerformed();
460		}
461		};
462	3	overrideKeyBinding(key_cmdT, action);
463		}
464
465		/**
466		* For now, delegates key events to the corresponding key accelerator for the
467		* AlignFrame that the mouse is in. Hopefully can be simplified in future if
468		* AlignFrame is changed to use key bindings rather than accelerators.
469		*/
		80% Uncovered Elements: 1 (5) Complexity: 2 Complexity Density: 0.67
470	3	protected void overrideDelegatedKeyBindings()...
471		{
472	3	if (getTopFrame() instanceof AlignFrame)
473		{
474		/*
475		* Get all accelerator keys in the top frame (the bottom should be
476		* identical) and override each one.
477		*/
478	3	for (Entry<KeyStroke, JMenuItem> acc : ((AlignFrame) getTopFrame())
479		.getAccelerators().entrySet())
480		{
481	81	overrideKeyBinding(acc);
482		}
483		}
484		}
485
486		/**
487		* Overrides an AlignFrame key accelerator with our version which delegates to
488		* the action listener in whichever frame has the mouse (and does nothing if
489		* neither has).
490		*
491		* @param acc
492		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
493	81	private void overrideKeyBinding(Entry<KeyStroke, JMenuItem> acc)...
494		{
495	81	final KeyStroke ks = acc.getKey();
496	81	InputMap inputMap = this.getInputMap(JComponent.WHEN_FOCUSED);
497	81	inputMap.put(ks, ks);
498	81	this.getActionMap().put(ks, new AbstractAction()
499		{
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
500	0	@Override...
501		public void actionPerformed(ActionEvent e)
502		{
503	0	Component c = getFrameAtMouse();
504	0	if (c != null && c instanceof AlignFrame)
505		{
506	0	for (ActionListener a : ((AlignFrame) c).getAccelerators().get(ks)
507		.getActionListeners())
508		{
509	0	a.actionPerformed(null);
510		}
511		}
512		}
513		});
514		}
515
516		/**
517		* Replace an accelerator key's action with the specified action.
518		*
519		* @param ks
520		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
521	9	protected void overrideKeyBinding(KeyStroke ks, AbstractAction action)...
522		{
523	9	this.getActionMap().put(ks, action);
524	9	overrideMenuItem(ks, action);
525		}
526
527		/**
528		* Create and link new views (with matching names) in both panes.
529		* <p>
530		* Note this is _not_ multiple tabs, each hosting a split pane view, rather it
531		* is a single split pane with each split holding multiple tabs which are
532		* linked in pairs.
533		* <p>
534		* TODO implement instead with a tabbed holder in the SplitView, each tab
535		* holding a single JSplitPane. Would avoid a duplicated tab, at the cost of
536		* some additional coding.
537		*/
		0% Uncovered Elements: 17 (17) Complexity: 2 Complexity Density: 0.13
538	0	protected void newView_actionPerformed()...
539		{
540	0	AlignFrame topFrame = (AlignFrame) getTopFrame();
541	0	AlignFrame bottomFrame = (AlignFrame) getBottomFrame();
542	0	final boolean scaleProteinAsCdna = topFrame.viewport
543		.isScaleProteinAsCdna();
544
545	0	AlignmentPanel newTopPanel = topFrame.newView(null, true);
546	0	AlignmentPanel newBottomPanel = bottomFrame.newView(null, true);
547
548		/*
549		* This currently (for the first new view only) leaves the top pane on tab 0
550		* but the bottom on tab 1. This results from 'setInitialTabVisible' echoing
551		* from the bottom back to the first frame. Next line is a fudge to work
552		* around this. TODO find a better way.
553		*/
554	0	if (topFrame.getTabIndex() != bottomFrame.getTabIndex())
555		{
556	0	topFrame.setDisplayedView(newTopPanel);
557		}
558
559	0	newBottomPanel.av.setViewName(newTopPanel.av.getViewName());
560	0	newTopPanel.av.setCodingComplement(newBottomPanel.av);
561
562		/*
563		* These lines can be removed once scaleProteinAsCdna is added to element
564		* Viewport in jalview.xsd, as Jalview2XML.copyAlignPanel will then take
565		* care of it
566		*/
567	0	newTopPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
568	0	newBottomPanel.av.setScaleProteinAsCdna(scaleProteinAsCdna);
569
570		/*
571		* Line up id labels etc
572		*/
573	0	adjustLayout();
574
575	0	final StructureSelectionManager ssm = StructureSelectionManager
576		.getStructureSelectionManager(Desktop.getInstance());
577	0	ssm.addCommandListener(newTopPanel.av);
578	0	ssm.addCommandListener(newBottomPanel.av);
579		}
580
581		/**
582		* Close the currently selected view in both panes. If there is only one view,
583		* close this split frame.
584		*/
		0% Uncovered Elements: 10 (10) Complexity: 2 Complexity Density: 0.25
585	0	protected void closeView_actionPerformed()...
586		{
587	0	int viewCount = ((AlignFrame) getTopFrame()).getAlignPanels().size();
588	0	if (viewCount < 2)
589		{
590	0	close();
591	0	return;
592		}
593
594	0	AlignmentPanel topPanel = ((AlignFrame) getTopFrame()).alignPanel;
595	0	AlignmentPanel bottomPanel = ((AlignFrame) getBottomFrame()).alignPanel;
596
597	0	((AlignFrame) getTopFrame()).closeView(topPanel);
598	0	((AlignFrame) getBottomFrame()).closeView(bottomPanel);
599
600		}
601
602		/**
603		* Close child frames and this split frame.
604		*/
		100% Uncovered Elements: 0 (4) Complexity: 2 Complexity Density: 0.5
605	3	public void close()...
606		{
607	3	((AlignFrame) getTopFrame()).closeMenuItem_actionPerformed(true);
608	3	((AlignFrame) getBottomFrame()).closeMenuItem_actionPerformed(true);
609	3	try
610		{
611	3	this.setClosed(true);
612		} catch (PropertyVetoException e)
613		{
614		// ignore
615		}
616		}
617
618		/**
619		* Replace AlignFrame 'expand views' action with SplitFrame version.
620		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
621	3	protected void overrideExpandViews()...
622		{
623	3	KeyStroke key_X = KeyStroke.getKeyStroke(KeyEvent.VK_X, 0, false);
624	3	AbstractAction action = new AbstractAction()
625		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
626	0	@Override...
627		public void actionPerformed(ActionEvent e)
628		{
629	0	expandViews_actionPerformed();
630		}
631		};
632	3	overrideMenuItem(key_X, action);
633		}
634
635		/**
636		* Replace AlignFrame 'gather views' action with SplitFrame version.
637		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
638	3	protected void overrideGatherViews()...
639		{
640	3	KeyStroke key_G = KeyStroke.getKeyStroke(KeyEvent.VK_G, 0, false);
641	3	AbstractAction action = new AbstractAction()
642		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
643	0	@Override...
644		public void actionPerformed(ActionEvent e)
645		{
646	0	gatherViews_actionPerformed();
647		}
648		};
649	3	overrideMenuItem(key_G, action);
650		}
651
652		/**
653		* Override the menu action associated with the keystroke in the child frames,
654		* replacing it with the given action.
655		*
656		* @param ks
657		* @param action
658		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
659	15	private void overrideMenuItem(KeyStroke ks, AbstractAction action)...
660		{
661	15	overrideMenuItem(ks, action, getTopFrame());
662	15	overrideMenuItem(ks, action, getBottomFrame());
663		}
664
665		/**
666		* Override the menu action associated with the keystroke in one child frame,
667		* replacing it with the given action. Mwahahahaha.
668		*
669		* @param key
670		* @param action
671		* @param comp
672		*/
		80% Uncovered Elements: 2 (10) Complexity: 3 Complexity Density: 0.5
673	30	private void overrideMenuItem(KeyStroke key, final AbstractAction action,...
674		JComponent comp)
675		{
676	30	if (comp instanceof AlignFrame)
677		{
678	30	JMenuItem mi = ((AlignFrame) comp).getAccelerators().get(key);
679	30	if (mi != null)
680		{
681	30	for (ActionListener al : mi.getActionListeners())
682		{
683	30	mi.removeActionListener(al);
684		}
685	30	mi.addActionListener(new ActionListener()
686		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
687	0	@Override...
688		public void actionPerformed(ActionEvent e)
689		{
690	0	action.actionPerformed(e);
691		}
692		});
693		}
694		}
695		}
696
697		/**
698		* Expand any multiple views (which are always in pairs) into separate split
699		* frames.
700		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
701	0	protected void expandViews_actionPerformed()...
702		{
703	0	Desktop.getInstance().explodeViews(this);
704		}
705
706		/**
707		* Gather any other SplitFrame views of this alignment back in as multiple
708		* (pairs of) views in this SplitFrame.
709		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
710	0	protected void gatherViews_actionPerformed()...
711		{
712	0	Desktop.getInstance().gatherViews(this);
713		}
714
715		/**
716		* Returns the alignment in the complementary frame to the one given.
717		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
718	0	@Override...
719		public AlignmentI getComplement(Object alignFrame)
720		{
721	0	if (alignFrame == this.getTopFrame())
722		{
723	0	return ((AlignFrame) getBottomFrame()).viewport.getAlignment();
724		}
725	0	else if (alignFrame == this.getBottomFrame())
726		{
727	0	return ((AlignFrame) getTopFrame()).viewport.getAlignment();
728		}
729	0	return null;
730		}
731
732		/**
733		* Returns the title of the complementary frame to the one given.
734		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
735	0	@Override...
736		public String getComplementTitle(Object alignFrame)
737		{
738	0	if (alignFrame == this.getTopFrame())
739		{
740	0	return ((AlignFrame) getBottomFrame()).getTitle();
741		}
742	0	else if (alignFrame == this.getBottomFrame())
743		{
744	0	return ((AlignFrame) getTopFrame()).getTitle();
745		}
746	0	return null;
747		}
748
749		/**
750		* Set the 'other half' to hidden / revealed.
751		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
752	0	@Override...
753		public void setComplementVisible(Object alignFrame, boolean show)
754		{
755		/*
756		* Hiding the AlignPanel suppresses unnecessary repaints
757		*/
758	0	if (alignFrame == getTopFrame())
759		{
760	0	((AlignFrame) getBottomFrame()).alignPanel.setVisible(show);
761		}
762	0	else if (alignFrame == getBottomFrame())
763		{
764	0	((AlignFrame) getTopFrame()).alignPanel.setVisible(show);
765		}
766	0	super.setComplementVisible(alignFrame, show);
767		}
768
769		/**
770		* return the AlignFrames held by this container
771		*
772		* @return { Top alignFrame (Usually CDS), Bottom AlignFrame (Usually
773		* Protein)}
774		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
775	0	public List<AlignFrame> getAlignFrames()...
776		{
777	0	return Arrays
778		.asList(new AlignFrame[]
779		{ (AlignFrame) getTopFrame(), (AlignFrame) getBottomFrame() });
780		}
781
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
782	0	@Override...
783		public AlignFrame getComplementAlignFrame(
784		AlignViewControllerGuiI alignFrame)
785		{
786	0	if (getTopFrame() == alignFrame)
787		{
788	0	return (AlignFrame) getBottomFrame();
789		}
790	0	if (getBottomFrame() == alignFrame)
791		{
792	0	return (AlignFrame) getTopFrame();
793		}
794		// we didn't know anything about this frame...
795	0	return null;
796		}
797
798		/**
799		* Replace Cmd-F Find action with our version. This is necessary because the
800		* 'default' Finder searches in the first AlignFrame it finds. We need it to
801		* search in the half of the SplitFrame that has the mouse.
802		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
803	3	protected void overrideFind()...
804		{
805		/*
806		* Ctrl-F / Cmd-F open Finder dialog, 'focused' on the right alignment
807		*/
808	3	KeyStroke key_cmdF = KeyStroke.getKeyStroke(KeyEvent.VK_F,
809		Platform.SHORTCUT_KEY_MASK, false);
810	3	AbstractAction action = new AbstractAction()
811		{
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
812	0	@Override...
813		public void actionPerformed(ActionEvent e)
814		{
815	0	Component c = getFrameAtMouse();
816	0	if (c != null && c instanceof AlignFrame)
817		{
818	0	AlignFrame af = (AlignFrame) c;
819	0	boolean dna = af.getViewport().getAlignment().isNucleotide();
820	0	String scope = MessageManager.getString("label.in") + " "
821	0	+ (dna ? MessageManager.getString("label.nucleotide")
822		: MessageManager.getString("label.protein"));
823	0	new Finder(af.alignPanel, true, scope);
824		}
825		}
826		};
827	3	overrideKeyBinding(key_cmdF, action);
828		}
829
830		/**
831		* Override to do nothing if triggered from one of the child frames
832		*/
		53.8% Uncovered Elements: 6 (13) Complexity: 5 Complexity Density: 0.71
833	11	@Override...
834		public void setSelected(boolean selected) throws PropertyVetoException
835		{
836	11	JDesktopPane desktopPane = getDesktopPane();
837	11	JInternalFrame fr = desktopPane == null ? null
838		: desktopPane.getSelectedFrame();
839	11	if (fr == getTopFrame() || fr == getBottomFrame())
840		{
841		/*
842		* patch for JAL-3288 (deselecting top/bottom frame closes popup menu);
843		* it may be possible to remove this method in future
844		* if the underlying Java behaviour changes
845		*/
846	0	if (selected)
847		{
848	0	moveToFront();
849		}
850	0	return;
851		}
852	11	super.setSelected(selected);
853		}
854
855		/**
856		* holds the frame for feature settings, so Protein and DNA tabs can be managed
857		*/
858		JInternalFrame featureSettingsUI;
859
860		JTabbedPane featureSettingsPanels;
861
		0% Uncovered Elements: 52 (52) Complexity: 8 Complexity Density: 0.2
862	0	@Override...
863		public void addFeatureSettingsUI(
864		FeatureSettingsControllerGuiI featureSettings)
865		{
866	0	boolean showInternalFrame = false;
867	0	if (featureSettingsUI == null || featureSettingsPanels == null)
868		{
869	0	showInternalFrame = true;
870	0	featureSettingsPanels = new JTabbedPane();
871	0	featureSettingsPanels.addChangeListener(new ChangeListener()
872		{
873
		0% Uncovered Elements: 10 (10) Complexity: 7 Complexity Density: 1.17
874	0	@Override...
875		public void stateChanged(ChangeEvent e)
876		{
877	0	if (e.getSource() != featureSettingsPanels
878		|| featureSettingsUI == null
879		|| featureSettingsUI.isClosed()
880		|| !featureSettingsUI.isVisible())
881		{
882		// not our tabbed pane
883	0	return;
884		}
885	0	int tab = featureSettingsPanels.getSelectedIndex();
886	0	if (tab < 0 || featureSettingsPanels
887		.getSelectedComponent() instanceof FeatureSettingsControllerGuiI)
888		{
889		// no tab selected or already showing a feature settings GUI
890	0	return;
891		}
892	0	getAlignFrames().get(tab).showFeatureSettingsUI();
893		}
894		});
895	0	featureSettingsUI = new JInternalFrame(MessageManager.getString(
896		"label.sequence_feature_settings_for_CDS_and_Protein"));
897	0	featureSettingsUI.setFrameIcon(null);
898	0	featureSettingsPanels.setOpaque(true);
899
900	0	JPanel dialog = new JPanel();
901	0	dialog.setOpaque(true);
902	0	dialog.setLayout(new BorderLayout());
903	0	dialog.add(featureSettingsPanels, BorderLayout.CENTER);
904	0	JPanel buttons = new JPanel();
905	0	JButton ok = new JButton(MessageManager.getString("action.ok"));
906	0	ok.addActionListener(new ActionListener()
907		{
908
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
909	0	@Override...
910		public void actionPerformed(ActionEvent e)
911		{
912	0	try
913		{
914	0	featureSettingsUI.setClosed(true);
915		} catch (PropertyVetoException pv)
916		{
917	0	pv.printStackTrace();
918		}
919		}
920		});
921	0	JButton cancel = new JButton(
922		MessageManager.getString("action.cancel"));
923	0	cancel.addActionListener(new ActionListener()
924		{
925
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.5
926	0	@Override...
927		public void actionPerformed(ActionEvent e)
928		{
929	0	try
930		{
931	0	for (Component fspanel : featureSettingsPanels.getComponents())
932		{
933	0	if (fspanel instanceof FeatureSettingsControllerGuiI)
934		{
935	0	((FeatureSettingsControllerGuiI) fspanel).revert();
936		}
937		}
938	0	featureSettingsUI.setClosed(true);
939		} catch (Exception pv)
940		{
941	0	pv.printStackTrace();
942		}
943		}
944		});
945	0	buttons.add(ok);
946	0	buttons.add(cancel);
947	0	dialog.add(buttons, BorderLayout.SOUTH);
948	0	featureSettingsUI.setContentPane(dialog);
949	0	createDummyTabs();
950		}
951	0	if (featureSettingsPanels
952		.indexOfTabComponent((Component) featureSettings) > -1)
953		{
954		// just show the feature settings !
955	0	featureSettingsPanels
956		.setSelectedComponent((Component) featureSettings);
957	0	return;
958		}
959		// otherwise replace the dummy tab with the given feature settings
960	0	int pos = getAlignFrames().indexOf(featureSettings.getAlignframe());
961		// if pos==-1 then alignFrame isn't managed by this splitframe
962	0	if (pos == 0)
963		{
964	0	featureSettingsPanels.removeTabAt(0);
965	0	featureSettingsPanels.insertTab(tabName[0], null,
966		(Component) featureSettings,
967		MessageManager.formatMessage(
968		"label.sequence_feature_settings_for", tabName[0]),
969		0);
970		}
971	0	if (pos == 1)
972		{
973	0	featureSettingsPanels.removeTabAt(1);
974	0	featureSettingsPanels.insertTab(tabName[1], null,
975		(Component) featureSettings,
976		MessageManager.formatMessage(
977		"label.sequence_feature_settings_for", tabName[1]),
978		1);
979		}
980	0	featureSettingsPanels.setSelectedComponent((Component) featureSettings);
981
982		// TODO: JAL-3535 - construct a feature settings title including names of
983		// currently selected CDS and Protein names
984
985	0	if (showInternalFrame)
986		{
987	0	if (Platform.isAMacAndNotJS())
988		{
989	0	Desktop.addInternalFrame(featureSettingsUI,
990		MessageManager.getString(
991		"label.sequence_feature_settings_for_CDS_and_Protein"),
992		600, 480);
993		}
994		else
995		{
996	0	Desktop.addInternalFrame(featureSettingsUI,
997		MessageManager.getString(
998		"label.sequence_feature_settings_for_CDS_and_Protein"),
999		600, 450);
1000		}
1001	0	featureSettingsUI
1002		.setMinimumSize(new Dimension(FS_MIN_WIDTH, FS_MIN_HEIGHT));
1003
1004	0	featureSettingsUI.addInternalFrameListener(
1005		new javax.swing.event.InternalFrameAdapter()
1006		{
		0% Uncovered Elements: 12 (12) Complexity: 3 Complexity Density: 0.38
1007	0	@Override...
1008		public void internalFrameClosed(
1009		javax.swing.event.InternalFrameEvent evt)
1010		{
1011	0	for (int tab = 0; tab < featureSettingsPanels
1012		.getTabCount();)
1013		{
1014	0	FeatureSettingsControllerGuiI fsettings = (FeatureSettingsControllerGuiI) featureSettingsPanels
1015		.getTabComponentAt(tab);
1016	0	if (fsettings != null)
1017		{
1018	0	featureSettingsPanels.removeTabAt(tab);
1019	0	fsettings.featureSettings_isClosed();
1020		}
1021		else
1022		{
1023	0	tab++;
1024		}
1025		}
1026	0	featureSettingsPanels = null;
1027	0	featureSettingsUI = null;
1028		};
1029		});
1030	0	featureSettingsUI.setLayer(JLayeredPane.PALETTE_LAYER);
1031		}
1032		}
1033
1034		/**
1035		* tab names for feature settings
1036		*/
1037		private String[] tabName = new String[] {
1038		MessageManager.getString("label.CDS"),
1039		MessageManager.getString("label.protein") };
1040
1041		/**
1042		* create placeholder tabs which materialise the feature settings for a given
1043		* view. Also reinitialises any tabs containing stale feature settings
1044		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
1045	0	private void createDummyTabs()...
1046		{
1047	0	for (int tabIndex = 0; tabIndex < 2; tabIndex++)
1048		{
1049	0	JPanel dummyTab = new JPanel();
1050	0	featureSettingsPanels.addTab(tabName[tabIndex], dummyTab);
1051		}
1052		}
1053
		0% Uncovered Elements: 15 (15) Complexity: 5 Complexity Density: 0.56
1054	0	private void replaceWithDummyTab(FeatureSettingsControllerI toClose)...
1055		{
1056	0	Component dummyTab = null;
1057	0	for (int tabIndex = 0; tabIndex < 2; tabIndex++)
1058		{
1059	0	if (featureSettingsPanels.getTabCount() > tabIndex)
1060		{
1061	0	dummyTab = featureSettingsPanels.getTabComponentAt(tabIndex);
1062	0	if (dummyTab instanceof FeatureSettingsControllerGuiI
1063		&& !dummyTab.isVisible())
1064		{
1065	0	featureSettingsPanels.removeTabAt(tabIndex);
1066		// close the feature Settings tab
1067	0	((FeatureSettingsControllerGuiI) dummyTab)
1068		.featureSettings_isClosed();
1069		// create a dummy tab in its place
1070	0	dummyTab = new JPanel();
1071	0	featureSettingsPanels.insertTab(tabName[tabIndex], null, dummyTab,
1072		MessageManager.formatMessage(
1073		"label.sequence_feature_settings_for",
1074		tabName[tabIndex]),
1075		tabIndex);
1076		}
1077		}
1078		}
1079		}
1080
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
1081	0	@Override...
1082		public void closeFeatureSettings(
1083		FeatureSettingsControllerI featureSettings,
1084		boolean closeContainingFrame)
1085		{
1086	0	if (featureSettingsUI != null)
1087		{
1088	0	if (closeContainingFrame)
1089		{
1090	0	try
1091		{
1092	0	featureSettingsUI.setClosed(true);
1093		} catch (Exception x)
1094		{
1095		}
1096	0	featureSettingsUI = null;
1097		}
1098		else
1099		{
1100	0	replaceWithDummyTab(featureSettings);
1101		}
1102		}
1103		}
1104
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
1105	0	@Override...
1106		public boolean isFeatureSettingsOpen()
1107		{
1108	0	return featureSettingsUI != null && !featureSettingsUI.isClosed();
1109		}
1110		}