Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AnnotationColumnChooser	54	193	50	113	0.5783582357.8%	Show methods
AnnotationColumnChooser.FurtherActionPanel	503	21	7	12	0.586206958.6%	Show methods
AnnotationColumnChooser.StructureFilterPanel	573	50	17	49	0.2898550629%	Show methods
AnnotationColumnChooser.SearchPanel	712	42	14	31	0.4833333248.3%	Show methods

Class AnnotationColumnChooser

Class AnnotationColumnChooser	Line # 54	Total Statements 193	Complexity 50	Uncovered Elements 113	TOTAL Coverage 0.5783582357.8%
AnnotationColumnChooser(AlignViewport,AlignmentPanel)   AnnotationColumnChooser(AlignViewport,AlignmentPanel)	9595	28.028	4.04	9.09	0.71875 0.7187571.9%
jbInit() : void   jbInit() : void	148148	48.048	1.01	0.00	1.0 1.0100%
updateThresholdPanelToolTip() : void   updateThresholdPanelToolTip() : void	218218	7.07	2.02	1.01	0.8888889 0.888888988.9%
reset() : void   reset() : void	234234	7.07	3.03	2.02	0.8181818 0.818181881.8%
valueChanged(boolean) : void   valueChanged(boolean) : void	252252	5.05	2.02	7.07	0.0 0.00%
updateView() : void   updateView() : void	265265	57.057	17.017	59.059	0.33707866 0.3370786633.7%
getOldHiddenColumns() : HiddenColumns   getOldHiddenColumns() : HiddenColumns	398398	1.01	1.01	0.00	1.0 1.0100%
setOldHiddenColumns(HiddenColumns) : void   setOldHiddenColumns(HiddenColumns) : void	403403	2.02	2.02	1.01	0.75 0.7575%
getCurrentFutherActionPanel() : FurtherActionPanel   getCurrentFutherActionPanel() : FurtherActionPanel	411411	1.01	1.01	1.01	0.0 0.00%
setCurrentFutherActionPanel(FurtherActionPanel) : void   setCurrentFutherActionPanel(FurtherActionPanel) : void	416416	1.01	1.01	1.01	0.0 0.00%
getCurrentSearchPanel() : SearchPanel   getCurrentSearchPanel() : SearchPanel	422422	1.01	1.01	0.00	1.0 1.0100%
setCurrentSearchPanel(SearchPanel) : void   setCurrentSearchPanel(SearchPanel) : void	427427	1.01	1.01	1.01	0.0 0.00%
getActionOption() : int   getActionOption() : int	432432	1.01	1.01	0.00	1.0 1.0100%
setActionOption(int) : void   setActionOption(int) : void	437437	1.01	1.01	1.01	0.0 0.00%
getCurrentStructureFilterPanel() : StructureFilterPanel   getCurrentStructureFilterPanel() : StructureFilterPanel	442442	1.01	1.01	0.00	1.0 1.0100%
setCurrentStructureFilterPanel(StructureFilterPanel) : void   setCurrentStructureFilterPanel(StructureFilterPanel) : void	447447	1.01	1.01	1.01	0.0 0.00%
select_action(ActionEvent) : void   select_action(ActionEvent) : void	453453	4.04	2.02	6.06	0.0 0.00%
hide_action(ActionEvent) : void   hide_action(ActionEvent) : void	463463	4.04	2.02	6.06	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	473473	1.01	1.01	1.01	0.0 0.00%
selectedAnnotationChanged() : void   selectedAnnotationChanged() : void	479479	13.013	2.02	1.01	0.93333334 0.9333333493.3%
ok_actionPerformed() : void   ok_actionPerformed() : void	836836	2.02	1.01	2.02	0.0 0.00%
cancel_actionPerformed() : void   cancel_actionPerformed() : void	843843	2.02	1.01	2.02	0.0 0.00%
saveCache() : void   saveCache() : void	850850	4.04	1.01	0.00	1.0 1.0100%

 

Class AnnotationColumnChooser.FurtherActionPanel

Class AnnotationColumnChooser.FurtherActionPanel	Line # 503	Total Statements 21	Complexity 7	Uncovered Elements 12	TOTAL Coverage 0.586206958.6%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	519519	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	529529	1.01	1.01	1.01	0.0 0.00%
FurtherActionPanel(AnnotationColumnChooser)   FurtherActionPanel(AnnotationColumnChooser)	513513	12.012	1.01	0.00	1.0 1.0100%
selectRadioAction(ActionEvent) : void   selectRadioAction(ActionEvent) : void	547547	2.02	1.01	2.02	0.0 0.00%
hideRadioAction(ActionEvent) : void   hideRadioAction(ActionEvent) : void	553553	2.02	1.01	2.02	0.0 0.00%
syncState() : void   syncState() : void	559559	3.03	2.02	2.02	0.6 0.660%

 

Class AnnotationColumnChooser.StructureFilterPanel

Class AnnotationColumnChooser.StructureFilterPanel	Line # 573	Total Statements 50	Complexity 17	Uncovered Elements 49	TOTAL Coverage 0.2898550629%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	592592	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	602602	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	612612	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	622622	1.01	1.01	1.01	0.0 0.00%
StructureFilterPanel(AnnotationColumnChooser)   StructureFilterPanel(AnnotationColumnChooser)	585585	15.015	1.01	0.00	1.0 1.0100%
alphaHelix_actionPerformed() : void   alphaHelix_actionPerformed() : void	639639	3.03	1.01	3.03	0.0 0.00%
betaStrand_actionPerformed() : void   betaStrand_actionPerformed() : void	646646	3.03	1.01	3.03	0.0 0.00%
turn_actionPerformed() : void   turn_actionPerformed() : void	653653	3.03	1.01	3.03	0.0 0.00%
all_actionPerformed() : void   all_actionPerformed() : void	660660	9.09	2.02	11.011	0.0 0.00%
updateSelectAllState() : void   updateSelectAllState() : void	678678	3.03	4.04	5.05	0.0 0.00%
syncState() : void   syncState() : void	691691	10.010	3.03	11.011	0.21428572 0.2142857221.4%

 

Class AnnotationColumnChooser.SearchPanel

Class AnnotationColumnChooser.SearchPanel	Line # 712	Total Statements 42	Complexity 14	Uncovered Elements 31	TOTAL Coverage 0.4833333248.3%
keyPressed(KeyEvent) : void   keyPressed(KeyEvent) : void	738738	3.03	2.02	5.05	0.0 0.00%
focusLost(FocusEvent) : void   focusLost(FocusEvent) : void	750750	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	760760	1.01	1.01	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	770770	1.01	1.01	1.01	0.0 0.00%
SearchPanel(AnnotationColumnChooser)   SearchPanel(AnnotationColumnChooser)	725725	15.015	1.01	0.00	1.0 1.0100%
displayNameCheckboxAction() : void   displayNameCheckboxAction() : void	783783	2.02	1.01	2.02	0.0 0.00%
descriptionCheckboxAction() : void   descriptionCheckboxAction() : void	789789	2.02	1.01	2.02	0.0 0.00%
searchStringAction() : void   searchStringAction() : void	795795	4.04	1.01	4.04	0.0 0.00%
syncState() : void   syncState() : void	803803	8.08	2.02	6.06	0.4 0.440%
updateSearchPanelToolTips() : void   updateSearchPanelToolTips() : void	819819	5.05	3.03	2.02	0.7777778 0.777777877.8%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.51877934	jalview.gui.AnnotationColumnChooserTest.testResetjalview.gui.AnnotationColumnChooserTest.testReset	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
22		package jalview.gui;
23
24		import jalview.datamodel.HiddenColumns;
25		import jalview.io.cache.JvCacheableInputBox;
26		import jalview.schemes.AnnotationColourGradient;
27		import jalview.util.MessageManager;
28		import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
29
30		import java.awt.BorderLayout;
31		import java.awt.CardLayout;
32		import java.awt.Color;
33		import java.awt.Dimension;
34		import java.awt.event.ActionEvent;
35		import java.awt.event.ActionListener;
36		import java.awt.event.FocusAdapter;
37		import java.awt.event.FocusEvent;
38		import java.awt.event.ItemEvent;
39		import java.awt.event.ItemListener;
40		import java.awt.event.KeyEvent;
41
42		import javax.swing.ButtonGroup;
43		import javax.swing.JCheckBox;
44		import javax.swing.JComboBox;
45		import javax.swing.JInternalFrame;
46		import javax.swing.JLayeredPane;
47		import javax.swing.JPanel;
48		import javax.swing.JRadioButton;
49		import javax.swing.border.TitledBorder;
50
51		import net.miginfocom.swing.MigLayout;
52
53		@SuppressWarnings("serial")
		57.8% Uncovered Elements: 113 (268) Complexity: 50 Complexity Density: 0.26
54		public class AnnotationColumnChooser extends AnnotationRowFilter
55		implements ItemListener
56		{
57		private JPanel switchableViewsPanel = new JPanel(new CardLayout());
58
59		private JPanel annotationComboBoxPanel = new JPanel();
60
61		private StructureFilterPanel gStructureFilterPanel;
62
63		private StructureFilterPanel ngStructureFilterPanel;
64
65		private StructureFilterPanel currentStructureFilterPanel;
66
67		private SearchPanel currentSearchPanel;
68
69		private SearchPanel gSearchPanel;
70
71		private SearchPanel ngSearchPanel;
72
73		private FurtherActionPanel currentFurtherActionPanel;
74
75		private FurtherActionPanel gFurtherActionPanel;
76
77		private FurtherActionPanel ngFurtherActionPanel;
78
79		public static final int ACTION_OPTION_SELECT = 1;
80
81		public static int ACTION_OPTION_HIDE = 2;
82
83		public static String NO_GRAPH_VIEW = "0";
84
85		public static String GRAPH_VIEW = "1";
86
87		private int actionOption = ACTION_OPTION_SELECT;
88
89		private HiddenColumns oldHiddenColumns;
90
91		protected int MIN_WIDTH = 420;
92
93		protected int MIN_HEIGHT = 430;
94
		71.9% Uncovered Elements: 9 (32) Complexity: 4 Complexity Density: 0.14
95	1	public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)...
96		{
97	1	super(av, ap);
98	1	frame = new JInternalFrame();
99	1	frame.setContentPane(this);
100	1	frame.setLayer(JLayeredPane.PALETTE_LAYER);
101	1	Desktop.addInternalFrame(frame,
102		MessageManager.getString("label.select_by_annotation"), 520,
103		215);
104	1	frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
105
106	1	addSliderChangeListener();
107	1	addSliderMouseListeners();
108
109	1	if (av.getAlignment().getAlignmentAnnotation() == null)
110		{
111	0	return;
112		}
113	1	setOldHiddenColumns(av.getAlignment().getHiddenColumns());
114	1	adjusting = true;
115
116	1	setAnnotations(new JComboBox<>(getAnnotationItems(false)));
117	1	populateThresholdComboBox(threshold);
118	1	AnnotationColumnChooser lastChooser = av
119		.getAnnotationColumnSelectionState();
120		// restore Object state from the previous session if one exists
121	1	if (lastChooser != null)
122		{
123	0	currentSearchPanel = lastChooser.getCurrentSearchPanel();
124	0	currentStructureFilterPanel = lastChooser
125		.getCurrentStructureFilterPanel();
126	0	annotations.setSelectedIndex(
127		lastChooser.getAnnotations().getSelectedIndex());
128	0	threshold.setSelectedIndex(
129		lastChooser.getThreshold().getSelectedIndex());
130	0	actionOption = lastChooser.getActionOption();
131	0	percentThreshold
132		.setSelected(lastChooser.percentThreshold.isSelected());
133		}
134
135	1	try
136		{
137	1	jbInit();
138		} catch (Exception ex)
139		{
140		}
141	1	adjusting = false;
142
143	1	updateView();
144	1	frame.invalidate();
145	1	frame.pack();
146		}
147
		100% Uncovered Elements: 0 (48) Complexity: 1 Complexity Density: 0.02
148	1	@Override...
149		protected void jbInit()
150		{
151	1	super.jbInit();
152
153	1	JPanel thresholdPanel = new JPanel();
154	1	thresholdPanel.setBorder(new TitledBorder(
155		MessageManager.getString("label.threshold_filter")));
156	1	thresholdPanel.setBackground(Color.white);
157	1	thresholdPanel.setFont(JvSwingUtils.getLabelFont());
158	1	thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
159
160	1	percentThreshold.setBackground(Color.white);
161	1	percentThreshold.setFont(JvSwingUtils.getLabelFont());
162
163	1	JPanel actionPanel = new JPanel();
164	1	actionPanel.setBackground(Color.white);
165	1	actionPanel.setFont(JvSwingUtils.getLabelFont());
166
167	1	JPanel graphFilterView = new JPanel();
168	1	graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
169	1	graphFilterView.setBackground(Color.white);
170
171	1	JPanel noGraphFilterView = new JPanel();
172	1	noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
173	1	noGraphFilterView.setBackground(Color.white);
174
175	1	annotationComboBoxPanel.setBackground(Color.white);
176	1	annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
177
178	1	gSearchPanel = new SearchPanel(this);
179	1	ngSearchPanel = new SearchPanel(this);
180	1	gFurtherActionPanel = new FurtherActionPanel(this);
181	1	ngFurtherActionPanel = new FurtherActionPanel(this);
182	1	gStructureFilterPanel = new StructureFilterPanel(this);
183	1	ngStructureFilterPanel = new StructureFilterPanel(this);
184
185	1	thresholdPanel.add(getThreshold());
186	1	thresholdPanel.add(percentThreshold, "wrap");
187	1	thresholdPanel.add(slider, "grow");
188	1	thresholdPanel.add(thresholdValue, "span, wrap");
189
190	1	actionPanel.add(ok);
191	1	actionPanel.add(cancel);
192
193	1	graphFilterView.add(gSearchPanel, "grow, span, wrap");
194	1	graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
195	1	graphFilterView.add(thresholdPanel, "grow, span, wrap");
196	1	graphFilterView.add(gFurtherActionPanel);
197
198	1	noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
199	1	noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
200	1	noGraphFilterView.add(ngFurtherActionPanel);
201
202	1	annotationComboBoxPanel.add(getAnnotations());
203	1	switchableViewsPanel.add(noGraphFilterView,
204		AnnotationColumnChooser.NO_GRAPH_VIEW);
205	1	switchableViewsPanel.add(graphFilterView,
206		AnnotationColumnChooser.GRAPH_VIEW);
207
208	1	this.setLayout(new BorderLayout());
209	1	this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
210	1	this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
211	1	this.add(actionPanel, java.awt.BorderLayout.SOUTH);
212
213	1	selectedAnnotationChanged();
214	1	updateThresholdPanelToolTip();
215	1	this.validate();
216		}
217
		88.9% Uncovered Elements: 1 (9) Complexity: 2 Complexity Density: 0.29
218	2	protected void updateThresholdPanelToolTip()...
219		{
220	2	thresholdValue.setToolTipText("");
221	2	slider.setToolTipText("");
222
223	2	String defaultTtip = MessageManager
224		.getString("info.change_threshold_mode_to_enable");
225
226	2	String thresh = getThreshold().getSelectedItem().toString();
227	2	if (thresh.equalsIgnoreCase("No Threshold"))
228		{
229	2	thresholdValue.setToolTipText(defaultTtip);
230	2	slider.setToolTipText(defaultTtip);
231		}
232		}
233
		81.8% Uncovered Elements: 2 (11) Complexity: 3 Complexity Density: 0.43
234	3	@Override...
235		protected void reset()
236		{
237	3	if (this.getOldHiddenColumns() != null)
238		{
239	3	av.getColumnSelection().clear();
240
241	3	if (av.getAnnotationColumnSelectionState() != null)
242		{
243	3	HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
244		.getOldHiddenColumns();
245	3	av.getAlignment().setHiddenColumns(oldHidden);
246		}
247	3	av.sendSelection();
248	3	ap.paintAlignment(true, true);
249		}
250		}
251
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
252	0	@Override...
253		public void valueChanged(boolean updateAllAnnotation)
254		{
255	0	if (slider.isEnabled())
256		{
257	0	getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
258	0	updateView();
259	0	propagateSeqAssociatedThreshold(updateAllAnnotation,
260		getCurrentAnnotation());
261	0	ap.paintAlignment(false, false);
262		}
263		}
264
		33.7% Uncovered Elements: 59 (89) Complexity: 17 Complexity Density: 0.3
265	2	@Override...
266		public void updateView()
267		{
268		// Check if combobox is still adjusting
269	2	if (adjusting)
270		{
271	1	return;
272		}
273
274	1	AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
275
276	1	setCurrentAnnotation(av.getAlignment()
277		.getAlignmentAnnotation()[annmap[getAnnotations()
278		.getSelectedIndex()]]);
279
280	1	int selectedThresholdItem = getSelectedThresholdItem(
281		getThreshold().getSelectedIndex());
282
283	1	slider.setEnabled(true);
284	1	thresholdValue.setEnabled(true);
285	1	percentThreshold.setEnabled(true);
286
287	1	if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
288		{
289	1	slider.setEnabled(false);
290	1	thresholdValue.setEnabled(false);
291	1	thresholdValue.setText("");
292	1	percentThreshold.setEnabled(false);
293		// build filter params
294		}
295	0	else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
296		{
297	0	if (getCurrentAnnotation().threshold == null)
298		{
299	0	getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
300		(getCurrentAnnotation().graphMax
301		- getCurrentAnnotation().graphMin) / 2f,
302		"Threshold", Color.black));
303		}
304
305	0	adjusting = true;
306	0	float range = getCurrentAnnotation().graphMax * 1000
307		- getCurrentAnnotation().graphMin * 1000;
308
309	0	slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
310	0	slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
311	0	slider.setValue(
312		(int) (getCurrentAnnotation().threshold.value * 1000));
313
314	0	setThresholdValueText();
315
316	0	slider.setMajorTickSpacing((int) (range / 10f));
317	0	slider.setEnabled(true);
318	0	thresholdValue.setEnabled(true);
319	0	adjusting = false;
320
321		// build filter params
322	0	filterParams.setThresholdType(
323		AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
324	0	if (getCurrentAnnotation().isQuantitative())
325		{
326	0	filterParams
327		.setThresholdValue(getCurrentAnnotation().threshold.value);
328
329	0	if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
330		{
331	0	filterParams.setThresholdType(
332		AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
333		}
334	0	else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
335		{
336	0	filterParams.setThresholdType(
337		AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
338		}
339		}
340		}
341
342	1	updateThresholdPanelToolTip();
343	1	if (currentStructureFilterPanel != null)
344		{
345	0	if (currentStructureFilterPanel.alphaHelix.isSelected())
346		{
347	0	filterParams.setFilterAlphaHelix(true);
348		}
349	0	if (currentStructureFilterPanel.betaStrand.isSelected())
350		{
351	0	filterParams.setFilterBetaSheet(true);
352		}
353	0	if (currentStructureFilterPanel.turn.isSelected())
354		{
355	0	filterParams.setFilterTurn(true);
356		}
357		}
358
359	1	if (currentSearchPanel != null)
360		{
361	0	if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
362		{
363	0	filterParams.setRegexString(
364		currentSearchPanel.searchBox.getUserInput());
365	0	if (currentSearchPanel.displayName.isSelected())
366		{
367	0	filterParams.addRegexSearchField(
368		AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
369		}
370	0	if (currentSearchPanel.description.isSelected())
371		{
372	0	filterParams.addRegexSearchField(
373		AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
374		}
375		}
376		}
377
378		// show hidden columns here, before changing the column selection in
379		// filterAnnotations, because showing hidden columns has the side effect of
380		// adding them to the selection
381	1	av.showAllHiddenColumns();
382	1	av.getColumnSelection().filterAnnotations(
383		getCurrentAnnotation().annotations, filterParams);
384
385	1	boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
386	1	if (hideCols)
387		{
388	0	av.hideSelectedColumns();
389		}
390	1	av.sendSelection();
391
392	1	filterParams = null;
393	1	av.setAnnotationColumnSelectionState(this);
394		// only update overview and structures if columns were hidden
395	1	ap.paintAlignment(hideCols, hideCols);
396		}
397
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
398	6	public HiddenColumns getOldHiddenColumns()...
399		{
400	6	return oldHiddenColumns;
401		}
402
		75% Uncovered Elements: 1 (4) Complexity: 2 Complexity Density: 1
403	4	public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)...
404		{
405	4	if (currentHiddenColumns != null)
406		{
407	4	this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
408		}
409		}
410
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
411	0	public FurtherActionPanel getCurrentFutherActionPanel()...
412		{
413	0	return currentFurtherActionPanel;
414		}
415
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
416	0	public void setCurrentFutherActionPanel(...
417		FurtherActionPanel currentFutherActionPanel)
418		{
419	0	this.currentFurtherActionPanel = currentFutherActionPanel;
420		}
421
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
422	4	public SearchPanel getCurrentSearchPanel()...
423		{
424	4	return currentSearchPanel;
425		}
426
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
427	0	public void setCurrentSearchPanel(SearchPanel currentSearchPanel)...
428		{
429	0	this.currentSearchPanel = currentSearchPanel;
430		}
431
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
432	5	public int getActionOption()...
433		{
434	5	return actionOption;
435		}
436
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
437	0	public void setActionOption(int actionOption)...
438		{
439	0	this.actionOption = actionOption;
440		}
441
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
442	2	public StructureFilterPanel getCurrentStructureFilterPanel()...
443		{
444	2	return currentStructureFilterPanel;
445		}
446
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
447	0	public void setCurrentStructureFilterPanel(...
448		StructureFilterPanel currentStructureFilterPanel)
449		{
450	0	this.currentStructureFilterPanel = currentStructureFilterPanel;
451		}
452
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
453	0	public void select_action(ActionEvent actionEvent)...
454		{
455	0	JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
456	0	if (radioButton.isSelected())
457		{
458	0	setActionOption(ACTION_OPTION_SELECT);
459	0	updateView();
460		}
461		}
462
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
463	0	public void hide_action(ActionEvent actionEvent)...
464		{
465	0	JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
466	0	if (radioButton.isSelected())
467		{
468	0	setActionOption(ACTION_OPTION_HIDE);
469	0	updateView();
470		}
471		}
472
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
473	0	@Override...
474		public void itemStateChanged(ItemEvent e)
475		{
476	0	selectedAnnotationChanged();
477		}
478
		93.3% Uncovered Elements: 1 (15) Complexity: 2 Complexity Density: 0.15
479	1	@Override...
480		public void selectedAnnotationChanged()
481		{
482	1	String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
483	1	if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
484		.getSelectedIndex()]].isQuantitative())
485		{
486	1	currentView = AnnotationColumnChooser.GRAPH_VIEW;
487		}
488	1	saveCache();
489	1	gSearchPanel.syncState();
490	1	gFurtherActionPanel.syncState();
491	1	gStructureFilterPanel.syncState();
492
493	1	ngSearchPanel.syncState();
494	1	ngFurtherActionPanel.syncState();
495	1	ngStructureFilterPanel.syncState();
496
497	1	CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
498		.getLayout();
499	1	switchableViewsLayout.show(switchableViewsPanel, currentView);
500	1	updateView();
501		}
502
		58.6% Uncovered Elements: 12 (29) Complexity: 7 Complexity Density: 0.33
503		public class FurtherActionPanel extends JPanel
504		{
505		private AnnotationColumnChooser aColChooser;
506
507		private JRadioButton hideOption = new JRadioButton();
508
509		private JRadioButton selectOption = new JRadioButton();
510
511		private ButtonGroup optionsGroup = new ButtonGroup();
512
		100% Uncovered Elements: 0 (12) Complexity: 1 Complexity Density: 0.08
513	2	public FurtherActionPanel(AnnotationColumnChooser aColChooser)...
514		{
515	2	this.aColChooser = aColChooser;
516	2	JvSwingUtils.jvInitComponent(selectOption, "action.select");
517	2	selectOption.addActionListener(new ActionListener()
518		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
519	0	@Override...
520		public void actionPerformed(ActionEvent actionEvent)
521		{
522	0	selectRadioAction(actionEvent);
523		}
524		});
525
526	2	JvSwingUtils.jvInitComponent(hideOption, "action.hide");
527	2	hideOption.addActionListener(new ActionListener()
528		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
529	0	@Override...
530		public void actionPerformed(ActionEvent actionEvent)
531		{
532	0	hideRadioAction(actionEvent);
533		}
534		});
535
536	2	optionsGroup.add(selectOption);
537	2	optionsGroup.add(hideOption);
538	2	optionsGroup.setSelected(selectOption.getModel(), true);
539
540	2	JvSwingUtils.jvInitComponent(this);
541	2	syncState();
542
543	2	this.add(selectOption);
544	2	this.add(hideOption);
545		}
546
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
547	0	public void selectRadioAction(ActionEvent actionEvent)...
548		{
549	0	aColChooser.setCurrentFutherActionPanel(this);
550	0	aColChooser.select_action(actionEvent);
551		}
552
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
553	0	public void hideRadioAction(ActionEvent actionEvent)...
554		{
555	0	aColChooser.setCurrentFutherActionPanel(this);
556	0	aColChooser.hide_action(actionEvent);
557		}
558
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
559	4	public void syncState()...
560		{
561	4	if (aColChooser
562		.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
563		{
564	0	this.optionsGroup.setSelected(this.hideOption.getModel(), true);
565		}
566		else
567		{
568	4	this.optionsGroup.setSelected(this.selectOption.getModel(), true);
569		}
570		}
571		}
572
		29% Uncovered Elements: 49 (69) Complexity: 17 Complexity Density: 0.34
573		public class StructureFilterPanel extends JPanel
574		{
575		private AnnotationColumnChooser aColChooser;
576
577		private JCheckBox alphaHelix = new JCheckBox();
578
579		private JCheckBox betaStrand = new JCheckBox();
580
581		private JCheckBox turn = new JCheckBox();
582
583		private JCheckBox all = new JCheckBox();
584
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07
585	2	public StructureFilterPanel(AnnotationColumnChooser aColChooser)...
586		{
587	2	this.aColChooser = aColChooser;
588
589	2	JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
590	2	alphaHelix.addActionListener(new ActionListener()
591		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
592	0	@Override...
593		public void actionPerformed(ActionEvent actionEvent)
594		{
595	0	alphaHelix_actionPerformed();
596		}
597		});
598
599	2	JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
600	2	betaStrand.addActionListener(new ActionListener()
601		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
602	0	@Override...
603		public void actionPerformed(ActionEvent actionEvent)
604		{
605	0	betaStrand_actionPerformed();
606		}
607		});
608
609	2	JvSwingUtils.jvInitComponent(turn, "label.turn");
610	2	turn.addActionListener(new ActionListener()
611		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
612	0	@Override...
613		public void actionPerformed(ActionEvent actionEvent)
614		{
615	0	turn_actionPerformed();
616		}
617		});
618
619	2	JvSwingUtils.jvInitComponent(all, "label.select_all");
620	2	all.addActionListener(new ActionListener()
621		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
622	0	@Override...
623		public void actionPerformed(ActionEvent actionEvent)
624		{
625	0	all_actionPerformed();
626		}
627		});
628
629	2	this.setBorder(new TitledBorder(
630		MessageManager.getString("label.structures_filter")));
631	2	JvSwingUtils.jvInitComponent(this);
632
633	2	this.add(all);
634	2	this.add(alphaHelix);
635	2	this.add(betaStrand);
636	2	this.add(turn);
637		}
638
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
639	0	public void alphaHelix_actionPerformed()...
640		{
641	0	updateSelectAllState();
642	0	aColChooser.setCurrentStructureFilterPanel(this);
643	0	aColChooser.updateView();
644		}
645
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
646	0	public void betaStrand_actionPerformed()...
647		{
648	0	updateSelectAllState();
649	0	aColChooser.setCurrentStructureFilterPanel(this);
650	0	aColChooser.updateView();
651		}
652
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
653	0	public void turn_actionPerformed()...
654		{
655	0	updateSelectAllState();
656	0	aColChooser.setCurrentStructureFilterPanel(this);
657	0	aColChooser.updateView();
658		}
659
		0% Uncovered Elements: 11 (11) Complexity: 2 Complexity Density: 0.22
660	0	public void all_actionPerformed()...
661		{
662	0	if (all.isSelected())
663		{
664	0	alphaHelix.setSelected(true);
665	0	betaStrand.setSelected(true);
666	0	turn.setSelected(true);
667		}
668		else
669		{
670	0	alphaHelix.setSelected(false);
671	0	betaStrand.setSelected(false);
672	0	turn.setSelected(false);
673		}
674	0	aColChooser.setCurrentStructureFilterPanel(this);
675	0	aColChooser.updateView();
676		}
677
		0% Uncovered Elements: 5 (5) Complexity: 4 Complexity Density: 1.33
678	0	public void updateSelectAllState()...
679		{
680	0	if (alphaHelix.isSelected() && betaStrand.isSelected()
681		&& turn.isSelected())
682		{
683	0	all.setSelected(true);
684		}
685		else
686		{
687	0	all.setSelected(false);
688		}
689		}
690
		21.4% Uncovered Elements: 11 (14) Complexity: 3 Complexity Density: 0.3
691	2	public void syncState()...
692		{
693	2	StructureFilterPanel sfp = aColChooser
694		.getCurrentStructureFilterPanel();
695	2	if (sfp != null)
696		{
697	0	alphaHelix.setSelected(sfp.alphaHelix.isSelected());
698	0	betaStrand.setSelected(sfp.betaStrand.isSelected());
699	0	turn.setSelected(sfp.turn.isSelected());
700	0	if (sfp.all.isSelected())
701		{
702	0	all.setSelected(true);
703	0	alphaHelix.setSelected(true);
704	0	betaStrand.setSelected(true);
705	0	turn.setSelected(true);
706		}
707		}
708
709		}
710		}
711
		48.3% Uncovered Elements: 31 (60) Complexity: 14 Complexity Density: 0.33
712		public class SearchPanel extends JPanel
713		{
714		private AnnotationColumnChooser aColChooser;
715
716		private JCheckBox displayName = new JCheckBox();
717
718		private JCheckBox description = new JCheckBox();
719
720		private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
721
722		public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
723		FILTER_BY_ANN_CACHE_KEY);
724
		100% Uncovered Elements: 0 (15) Complexity: 1 Complexity Density: 0.07
725	2	public SearchPanel(AnnotationColumnChooser aColChooser)...
726		{
727
728	2	this.aColChooser = aColChooser;
729	2	JvSwingUtils.jvInitComponent(this);
730	2	this.setBorder(new TitledBorder(
731		MessageManager.getString("label.search_filter")));
732
733	2	searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
734	2	searchBox.getComponent().setToolTipText(
735		MessageManager.getString("info.enter_search_text_here"));
736	2	searchBox.addKeyListener(new java.awt.event.KeyAdapter()
737		{
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
738	0	@Override...
739		public void keyPressed(KeyEvent e)
740		{
741	0	if (e.getKeyCode() == KeyEvent.VK_ENTER)
742		{
743	0	e.consume();
744	0	searchStringAction();
745		}
746		}
747		});
748	2	searchBox.addFocusListener(new FocusAdapter()
749		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
750	0	@Override...
751		public void focusLost(FocusEvent e)
752		{
753	0	searchStringAction();
754		}
755		});
756
757	2	JvSwingUtils.jvInitComponent(displayName, "label.label");
758	2	displayName.addActionListener(new ActionListener()
759		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
760	0	@Override...
761		public void actionPerformed(ActionEvent actionEvent)
762		{
763	0	displayNameCheckboxAction();
764		}
765		});
766
767	2	JvSwingUtils.jvInitComponent(description, "label.description");
768	2	description.addActionListener(new ActionListener()
769		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
770	0	@Override...
771		public void actionPerformed(ActionEvent actionEvent)
772		{
773	0	descriptionCheckboxAction();
774		}
775		});
776
777	2	syncState();
778	2	this.add(searchBox.getComponent());
779	2	this.add(displayName);
780	2	this.add(description);
781		}
782
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
783	0	public void displayNameCheckboxAction()...
784		{
785	0	aColChooser.setCurrentSearchPanel(this);
786	0	aColChooser.updateView();
787		}
788
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
789	0	public void descriptionCheckboxAction()...
790		{
791	0	aColChooser.setCurrentSearchPanel(this);
792	0	aColChooser.updateView();
793		}
794
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
795	0	public void searchStringAction()...
796		{
797	0	aColChooser.setCurrentSearchPanel(this);
798	0	aColChooser.updateView();
799	0	updateSearchPanelToolTips();
800	0	searchBox.updateCache();
801		}
802
		40% Uncovered Elements: 6 (10) Complexity: 2 Complexity Density: 0.25
803	4	public void syncState()...
804		{
805	4	SearchPanel sp = aColChooser.getCurrentSearchPanel();
806	4	if (sp != null)
807		{
808	0	description.setEnabled(sp.description.isEnabled());
809	0	description.setSelected(sp.description.isSelected());
810
811	0	displayName.setEnabled(sp.displayName.isEnabled());
812	0	displayName.setSelected(sp.displayName.isSelected());
813
814	0	searchBox.setSelectedItem(sp.searchBox.getUserInput());
815		}
816	4	updateSearchPanelToolTips();
817		}
818
		77.8% Uncovered Elements: 2 (9) Complexity: 3 Complexity Density: 0.6
819	4	public void updateSearchPanelToolTips()...
820		{
821	4	String defaultTtip = MessageManager
822		.getString("info.enter_search_text_to_enable");
823	4	String labelTtip = MessageManager.formatMessage(
824		"info.search_in_annotation_label",
825		annotations.getSelectedItem().toString());
826	4	String descTtip = MessageManager.formatMessage(
827		"info.search_in_annotation_description",
828		annotations.getSelectedItem().toString());
829	4	displayName.setToolTipText(
830	4	displayName.isEnabled() ? labelTtip : defaultTtip);
831	4	description.setToolTipText(
832	4	description.isEnabled() ? descTtip : defaultTtip);
833		}
834		}
835
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
836	0	@Override...
837		public void ok_actionPerformed()
838		{
839	0	saveCache();
840	0	super.ok_actionPerformed();
841		}
842
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
843	0	@Override...
844		public void cancel_actionPerformed()
845		{
846	0	saveCache();
847	0	super.cancel_actionPerformed();
848		}
849
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
850	1	private void saveCache()...
851		{
852	1	gSearchPanel.searchBox.persistCache();
853	1	ngSearchPanel.searchBox.persistCache();
854	1	gSearchPanel.searchBox.updateCache();
855	1	ngSearchPanel.searchBox.updateCache();
856		}
857		}