Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureEditor	46	224	54	0.00%	Show methods

Class FeatureEditor

Class FeatureEditor	Line # 46	Total Statements 224	Complexity 54	TOTAL Coverage 0.00%
FeatureEditor(AlignmentPanel,List<SequenceI>,List<SequenceFeature>,boolean)   FeatureEditor(AlignmentPanel,List<SequenceI>,List<SequenceFeature>,boolean)	107107	6.06	1.01	0.0 0.00%
insertUpdate(DocumentEvent) : void   insertUpdate(DocumentEvent) : void	131131	1.01	1.01	0.0 0.00%
removeUpdate(DocumentEvent) : void   removeUpdate(DocumentEvent) : void	137137	1.01	1.01	0.0 0.00%
changedUpdate(DocumentEvent) : void   changedUpdate(DocumentEvent) : void	143143	1.01	1.01	0.0 0.00%
insertUpdate(DocumentEvent) : void   insertUpdate(DocumentEvent) : void	153153	1.01	1.01	0.0 0.00%
removeUpdate(DocumentEvent) : void   removeUpdate(DocumentEvent) : void	159159	1.01	1.01	0.0 0.00%
changedUpdate(DocumentEvent) : void   changedUpdate(DocumentEvent) : void	165165	1.01	1.01	0.0 0.00%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	184184	2.02	1.01	0.0 0.00%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	193193	2.02	1.01	0.0 0.00%
colourSelected(Color) : void   colourSelected(Color) : void	218218	2.02	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	241241	3.03	1.01	0.0 0.00%
mousePressed(MouseEvent) : void   mousePressed(MouseEvent) : void	206206	10.010	3.03	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	282282	19.019	3.03	0.0 0.00%
init() : void   init() : void	122122	81.081	7.07	0.0 0.00%
showDialog() : void   showDialog() : void	406406	13.013	4.04	0.0 0.00%
run() : void   run() : void	459459	2.02	1.01	0.0 0.00%
getCancelAction() : Runnable   getCancelAction() : Runnable	455455	2.02	1.01	0.0 0.00%
run() : void   run() : void	485485	18.018	6.06	0.0 0.00%
getCreateAction() : Runnable   getCreateAction() : Runnable	479479	2.02	1.01	0.0 0.00%
run() : void   run() : void	541541	5.05	1.01	0.0 0.00%
getDeleteAction() : Runnable   getDeleteAction() : Runnable	537537	2.02	1.01	0.0 0.00%
updateColourButton(JPanel,JLabel,FeatureColourI) : void   updateColourButton(JPanel,JLabel,FeatureColourI) : void	560560	10.010	2.02	0.0 0.00%
warnIfGroupHidden(JPanel,String) : void   warnIfGroupHidden(JPanel,String) : void	587587	3.03	2.02	0.0 0.00%
warnIfTypeHidden(JPanel,String) : void   warnIfTypeHidden(JPanel,String) : void	604604	4.04	3.03	0.0 0.00%
repaintPanel() : void   repaintPanel() : void	623623	4.04	1.01	0.0 0.00%
run() : void   run() : void	649649	26.026	6.06	0.0 0.00%
getAmendAction() : Runnable   getAmendAction() : Runnable	639639	2.02	1.01	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.gui;
2
3		import jalview.api.FeatureColourI;
4		import jalview.datamodel.SearchResults;
5		import jalview.datamodel.SearchResultsI;
6		import jalview.datamodel.SequenceFeature;
7		import jalview.datamodel.SequenceI;
8		import jalview.gui.JalviewColourChooser.ColourChooserListener;
9		import jalview.io.FeaturesFile;
10		import jalview.schemes.FeatureColour;
11		import jalview.util.ColorUtils;
12		import jalview.util.MessageManager;
13
14		import java.awt.BorderLayout;
15		import java.awt.Color;
16		import java.awt.Dimension;
17		import java.awt.Font;
18		import java.awt.GridLayout;
19		import java.awt.event.ActionEvent;
20		import java.awt.event.ActionListener;
21		import java.awt.event.ItemEvent;
22		import java.awt.event.ItemListener;
23		import java.awt.event.MouseAdapter;
24		import java.awt.event.MouseEvent;
25		import java.util.ArrayList;
26		import java.util.List;
27
28		import javax.swing.JComboBox;
29		import javax.swing.JLabel;
30		import javax.swing.JPanel;
31		import javax.swing.JScrollPane;
32		import javax.swing.JSpinner;
33		import javax.swing.JTextArea;
34		import javax.swing.JTextField;
35		import javax.swing.SpinnerNumberModel;
36		import javax.swing.SwingConstants;
37		import javax.swing.event.ChangeEvent;
38		import javax.swing.event.ChangeListener;
39		import javax.swing.event.DocumentEvent;
40		import javax.swing.event.DocumentListener;
41
42		/**
43		* Provides a dialog allowing the user to add new features, or amend or delete
44		* existing features
45		*/
		0% Uncovered Elements: 301 (301) Complexity: 54 Complexity Density: 0.24
46		public class FeatureEditor
47		{
48		/*
49		* defaults for creating a new feature are the last created
50		* feature type and group
51		*/
52		static String lastFeatureAdded = "feature_1";
53
54		static String lastFeatureGroupAdded = "Jalview";
55
56		/*
57		* the sequence(s) with features to be created / amended
58		*/
59		final List<SequenceI> sequences;
60
61		/*
62		* the features (or template features) to be created / amended
63		*/
64		final List<SequenceFeature> features;
65
66		/*
67		* true if the dialog is to create a new feature, false if
68		* for amend or delete of existing feature(s)
69		*/
70		final boolean forCreate;
71
72		/*
73		* index into the list of features
74		*/
75		int featureIndex;
76
77		FeatureColourI oldColour;
78
79		FeatureColourI featureColour;
80
81		FeatureRenderer fr;
82
83		AlignmentPanel ap;
84
85		JTextField name;
86
87		JTextField group;
88
89		JTextArea description;
90
91		JSpinner start;
92
93		JSpinner end;
94
95		JPanel mainPanel;
96
97		/**
98		* Constructor
99		*
100		* @param alignPanel
101		* @param seqs
102		* @param feats
103		* @param create
104		* if true create a new feature, else amend or delete an existing
105		* feature
106		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
107	0	public FeatureEditor(AlignmentPanel alignPanel, List<SequenceI> seqs,...
108		List<SequenceFeature> feats, boolean create)
109		{
110	0	ap = alignPanel;
111	0	fr = alignPanel.getSeqPanel().seqCanvas.fr;
112	0	sequences = seqs;
113	0	features = feats;
114	0	this.forCreate = create;
115
116	0	init();
117		}
118
119		/**
120		* Initialise the layout and controls
121		*/
		0% Uncovered Elements: 91 (91) Complexity: 7 Complexity Density: 0.09
122	0	protected void init()...
123		{
124	0	featureIndex = 0;
125
126	0	mainPanel = new JPanel(new BorderLayout());
127
128	0	name = new JTextField(25);
129	0	name.getDocument().addDocumentListener(new DocumentListener()
130		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
131	0	@Override...
132		public void insertUpdate(DocumentEvent e)
133		{
134	0	warnIfTypeHidden(mainPanel, name.getText());
135		}
136
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
137	0	@Override...
138		public void removeUpdate(DocumentEvent e)
139		{
140	0	warnIfTypeHidden(mainPanel, name.getText());
141		}
142
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
143	0	@Override...
144		public void changedUpdate(DocumentEvent e)
145		{
146	0	warnIfTypeHidden(mainPanel, name.getText());
147		}
148		});
149
150	0	group = new JTextField(25);
151	0	group.getDocument().addDocumentListener(new DocumentListener()
152		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
153	0	@Override...
154		public void insertUpdate(DocumentEvent e)
155		{
156	0	warnIfGroupHidden(mainPanel, group.getText());
157		}
158
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
159	0	@Override...
160		public void removeUpdate(DocumentEvent e)
161		{
162	0	warnIfGroupHidden(mainPanel, group.getText());
163		}
164
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
165	0	@Override...
166		public void changedUpdate(DocumentEvent e)
167		{
168	0	warnIfGroupHidden(mainPanel, group.getText());
169		}
170		});
171
172	0	description = new JTextArea(3, 25);
173
174	0	start = new JSpinner();
175	0	end = new JSpinner();
176	0	start.setPreferredSize(new Dimension(80, 20));
177	0	end.setPreferredSize(new Dimension(80, 20));
178
179		/*
180		* ensure that start can never be more than end
181		*/
182	0	start.addChangeListener(new ChangeListener()
183		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
184	0	@Override...
185		public void stateChanged(ChangeEvent e)
186		{
187	0	Integer startVal = (Integer) start.getValue();
188	0	((SpinnerNumberModel) end.getModel()).setMinimum(startVal);
189		}
190		});
191	0	end.addChangeListener(new ChangeListener()
192		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
193	0	@Override...
194		public void stateChanged(ChangeEvent e)
195		{
196	0	Integer endVal = (Integer) end.getValue();
197	0	((SpinnerNumberModel) start.getModel()).setMaximum(endVal);
198		}
199		});
200
201	0	final JLabel colour = new JLabel();
202	0	colour.setOpaque(true);
203	0	colour.setMaximumSize(new Dimension(30, 16));
204	0	colour.addMouseListener(new MouseAdapter()
205		{
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
206	0	@Override...
207		public void mousePressed(MouseEvent evt)
208		{
209	0	if (featureColour.isSimpleColour())
210		{
211		/*
212		* open colour chooser on click in colour panel
213		*/
214	0	String title = MessageManager
215		.getString("label.select_feature_colour");
216	0	ColourChooserListener listener = new ColourChooserListener()
217		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
218	0	@Override...
219		public void colourSelected(Color c)
220		{
221	0	featureColour = new FeatureColour(c);
222	0	updateColourButton(mainPanel, colour, featureColour);
223		};
224		};
225	0	JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
226		title, featureColour.getColour(), listener);
227		}
228		else
229		{
230		/*
231		* variable colour dialog - on OK, refetch the updated
232		* feature colour and update this display
233		*/
234	0	final String ft = features.get(featureIndex).getType();
235	0	final String type = ft == null ? lastFeatureAdded : ft;
236	0	FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type);
237	0	fcc.setRequestFocusEnabled(true);
238	0	fcc.requestFocus();
239	0	fcc.addActionListener(new ActionListener()
240		{
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
241	0	@Override...
242		public void actionPerformed(ActionEvent e)
243		{
244	0	featureColour = fr.getFeatureStyle(ft);
245	0	fr.setColour(type, featureColour);
246	0	updateColourButton(mainPanel, colour, featureColour);
247		}
248		});
249		}
250		}
251		});
252	0	JPanel gridPanel = new JPanel(new GridLayout(3, 1));
253
254	0	if (!forCreate && features.size() > 1)
255		{
256		/*
257		* more than one feature at selected position -
258		* add a drop-down to choose the feature to amend
259		* space pad text if necessary to make entries distinct
260		*/
261	0	gridPanel = new JPanel(new GridLayout(4, 1));
262	0	JPanel choosePanel = new JPanel();
263	0	choosePanel.add(new JLabel(
264		MessageManager.getString("label.select_feature") + ":"));
265	0	final JComboBox<String> overlaps = new JComboBox<>();
266	0	List<String> added = new ArrayList<>();
267	0	for (SequenceFeature sf : features)
268		{
269	0	String text = String.format("%s/%d-%d (%s)", sf.getType(),
270		sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
271	0	while (added.contains(text))
272		{
273	0	text += " ";
274		}
275	0	overlaps.addItem(text);
276	0	added.add(text);
277		}
278	0	choosePanel.add(overlaps);
279
280	0	overlaps.addItemListener(new ItemListener()
281		{
		0% Uncovered Elements: 23 (23) Complexity: 3 Complexity Density: 0.16
282	0	@Override...
283		public void itemStateChanged(ItemEvent e)
284		{
285	0	int index = overlaps.getSelectedIndex();
286	0	if (index != -1)
287		{
288	0	featureIndex = index;
289	0	SequenceFeature sf = features.get(index);
290	0	name.setText(sf.getType());
291	0	description.setText(sf.getDescription());
292	0	group.setText(sf.getFeatureGroup());
293	0	start.setValue(new Integer(sf.getBegin()));
294	0	end.setValue(new Integer(sf.getEnd()));
295	0	((SpinnerNumberModel) start.getModel()).setMaximum(sf.getEnd());
296	0	((SpinnerNumberModel) end.getModel()).setMinimum(sf.getBegin());
297
298	0	SearchResultsI highlight = new SearchResults();
299	0	highlight.addResult(sequences.get(0), sf.getBegin(),
300		sf.getEnd());
301
302	0	ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
303		}
304	0	FeatureColourI col = fr.getFeatureStyle(name.getText());
305	0	if (col == null)
306		{
307	0	col = new FeatureColour(
308		ColorUtils.createColourFromName(name.getText()));
309		}
310	0	oldColour = featureColour = col;
311	0	updateColourButton(mainPanel, colour, col);
312		}
313		});
314
315	0	gridPanel.add(choosePanel);
316		}
317
318	0	JPanel namePanel = new JPanel();
319	0	gridPanel.add(namePanel);
320	0	namePanel.add(new JLabel(MessageManager.getString("label.name:"),
321		JLabel.RIGHT));
322	0	namePanel.add(name);
323
324	0	JPanel groupPanel = new JPanel();
325	0	gridPanel.add(groupPanel);
326	0	groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
327		JLabel.RIGHT));
328	0	groupPanel.add(group);
329
330	0	JPanel colourPanel = new JPanel();
331	0	gridPanel.add(colourPanel);
332	0	colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
333		JLabel.RIGHT));
334	0	colourPanel.add(colour);
335	0	colour.setPreferredSize(new Dimension(150, 15));
336	0	colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
337	0	colour.setForeground(Color.black);
338	0	colour.setHorizontalAlignment(SwingConstants.CENTER);
339	0	colour.setVerticalAlignment(SwingConstants.CENTER);
340	0	colour.setHorizontalTextPosition(SwingConstants.CENTER);
341	0	colour.setVerticalTextPosition(SwingConstants.CENTER);
342	0	mainPanel.add(gridPanel, BorderLayout.NORTH);
343
344	0	JPanel descriptionPanel = new JPanel();
345	0	descriptionPanel.add(new JLabel(
346		MessageManager.getString("label.description:"), JLabel.RIGHT));
347	0	description.setFont(JvSwingUtils.getTextAreaFont());
348	0	description.setLineWrap(true);
349	0	descriptionPanel.add(new JScrollPane(description));
350
351	0	if (!forCreate)
352		{
353	0	mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
354
355	0	JPanel startEndPanel = new JPanel();
356	0	startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
357		JLabel.RIGHT));
358	0	startEndPanel.add(start);
359	0	startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
360		JLabel.RIGHT));
361	0	startEndPanel.add(end);
362	0	mainPanel.add(startEndPanel, BorderLayout.CENTER);
363		}
364		else
365		{
366	0	mainPanel.add(descriptionPanel, BorderLayout.CENTER);
367		}
368
369		/*
370		* default feature type and group to that of the first feature supplied,
371		* or to the last feature created if not supplied (null value)
372		*/
373	0	SequenceFeature firstFeature = features.get(0);
374	0	boolean useLastDefaults = firstFeature.getType() == null;
375	0	final String featureType = useLastDefaults ? lastFeatureAdded
376		: firstFeature.getType();
377	0	final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
378		: firstFeature.getFeatureGroup();
379	0	name.setText(featureType);
380	0	group.setText(featureGroup);
381
382	0	start.setValue(new Integer(firstFeature.getBegin()));
383	0	end.setValue(new Integer(firstFeature.getEnd()));
384	0	((SpinnerNumberModel) start.getModel()).setMaximum(firstFeature.getEnd());
385	0	((SpinnerNumberModel) end.getModel()).setMinimum(firstFeature.getBegin());
386
387	0	description.setText(firstFeature.getDescription());
388	0	featureColour = fr.getFeatureStyle(featureType);
389	0	oldColour = featureColour;
390	0	updateColourButton(mainPanel, colour, oldColour);
391		}
392
393		/**
394		* Presents a dialog allowing the user to add new features, or amend or delete
395		* an existing feature. Currently this can be on
396		* <ul>
397		* <li>double-click on a sequence - Amend/Delete a selected feature at the
398		* position</li>
399		* <li>Create sequence feature(s) from pop-up menu on selected region</li>
400		* <li>Create features for pattern matches from Find</li>
401		* </ul>
402		* If the supplied feature type is null, show (and update on confirm) the type
403		* and group of the last new feature created (with initial defaults of
404		* "feature_1" and "Jalview").
405		*/
		0% Uncovered Elements: 19 (19) Complexity: 4 Complexity Density: 0.31
406	0	public void showDialog()...
407		{
408	0	Runnable okAction = forCreate ? getCreateAction() : getAmendAction();
409	0	Runnable cancelAction = getCancelAction();
410
411		/*
412		* set dialog action handlers for OK (create/Amend) and Cancel options
413		* also for Delete if applicable (when amending features)
414		*/
415	0	JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
416		.setResponseHandler(0, okAction).setResponseHandler(2, cancelAction);
417	0	if (!forCreate)
418		{
419	0	dialog.setResponseHandler(1, getDeleteAction());
420		}
421
422	0	String title = null;
423	0	Object[] options = null;
424	0	if (forCreate)
425		{
426	0	title = MessageManager
427		.getString("label.create_new_sequence_features");
428	0	options = new Object[] { MessageManager.getString("action.ok"),
429		MessageManager.getString("action.cancel") };
430		}
431		else
432		{
433	0	title = MessageManager.formatMessage("label.amend_delete_features",
434		new String[]
435		{ sequences.get(0).getName() });
436	0	options = new Object[] { MessageManager.getString("label.amend"),
437		MessageManager.getString("action.delete"),
438		MessageManager.getString("action.cancel") };
439		}
440
441	0	dialog.showInternalDialog(mainPanel, title,
442		JvOptionPane.YES_NO_CANCEL_OPTION,
443		JvOptionPane.PLAIN_MESSAGE, null, options,
444		MessageManager.getString("action.ok"));
445		}
446
447		/**
448		* Answers an action to run on Cancel in the dialog. This is just to remove
449		* any feature highlighting from the display. Changes in the dialog are not
450		* applied until it is dismissed with OK, Amend or Delete, so there are no
451		* updates to reset on Cancel.
452		*
453		* @return
454		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
455	0	protected Runnable getCancelAction()...
456		{
457	0	Runnable okAction = new Runnable()
458		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
459	0	@Override...
460		public void run()
461		{
462	0	ap.highlightSearchResults(null);
463	0	ap.paintAlignment(false, false);
464		}
465		};
466	0	return okAction;
467		}
468
469		/**
470		* Returns the action to be run on OK in the dialog when creating one or more
471		* sequence features. Note these may have a pre-supplied feature type (such as
472		* a Find pattern), or none, in which case the feature type and group default
473		* to those last added through this dialog. The action includes refreshing the
474		* Feature Settings panel (if it is open), to show any new feature type, or
475		* amended colour for an existing type.
476		*
477		* @return
478		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
479	0	protected Runnable getCreateAction()...
480		{
481	0	Runnable okAction = new Runnable()
482		{
483		boolean useLastDefaults = features.get(0).getType() == null;
484
		0% Uncovered Elements: 28 (28) Complexity: 6 Complexity Density: 0.33
485	0	public void run()...
486		{
487	0	final String enteredType = name.getText().trim();
488	0	final String enteredGroup = group.getText().trim();
489	0	final String enteredDescription = description.getText()
490		.replaceAll("\n", " ");
491	0	if (enteredType.length() > 0)
492		{
493		/*
494		* update default values only if creating using default values
495		*/
496	0	if (useLastDefaults)
497		{
498	0	lastFeatureAdded = enteredType;
499	0	lastFeatureGroupAdded = enteredGroup;
500		// TODO: determine if the null feature group is valid
501	0	if (lastFeatureGroupAdded.length() < 1)
502		{
503	0	lastFeatureGroupAdded = null;
504		}
505		}
506		}
507
508	0	if (enteredType.length() > 0)
509		{
510	0	for (int i = 0; i < sequences.size(); i++)
511		{
512	0	SequenceFeature sf = features.get(i);
513	0	SequenceFeature sf2 = new SequenceFeature(enteredType,
514		enteredDescription, sf.getBegin(), sf.getEnd(),
515		enteredGroup);
516	0	new FeaturesFile().parseDescriptionHTML(sf2, false);
517	0	sequences.get(i).addSequenceFeature(sf2);
518		}
519
520	0	fr.setColour(enteredType, featureColour);
521	0	fr.featuresAdded();
522
523	0	repaintPanel();
524		}
525		}
526		};
527	0	return okAction;
528		}
529
530		/**
531		* Answers the action to run on Delete in the dialog. Note this includes
532		* refreshing the Feature Settings (if open) in case the only instance of a
533		* feature type or group has been deleted.
534		*
535		* @return
536		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
537	0	protected Runnable getDeleteAction()...
538		{
539	0	Runnable deleteAction = new Runnable()
540		{
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
541	0	public void run()...
542		{
543	0	SequenceFeature sf = features.get(featureIndex);
544	0	sequences.get(0).getDatasetSequence().deleteFeature(sf);
545	0	fr.featuresAdded();
546	0	ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
547	0	ap.paintAlignment(true, true);
548		}
549		};
550	0	return deleteAction;
551		}
552
553		/**
554		* update the amend feature button dependent on the given style
555		*
556		* @param bigPanel
557		* @param col
558		* @param col
559		*/
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
560	0	protected void updateColourButton(JPanel bigPanel, JLabel colour,...
561		FeatureColourI col)
562		{
563	0	colour.removeAll();
564	0	colour.setIcon(null);
565	0	colour.setText("");
566
567	0	if (col.isSimpleColour())
568		{
569	0	colour.setToolTipText(null);
570	0	colour.setBackground(col.getColour());
571		}
572		else
573		{
574	0	colour.setBackground(bigPanel.getBackground());
575	0	colour.setForeground(Color.black);
576	0	colour.setToolTipText(FeatureSettings.getColorTooltip(col, false));
577	0	FeatureSettings.renderGraduatedColor(colour, col);
578		}
579		}
580
581		/**
582		* Show a warning message if the entered group is one that is currently hidden
583		*
584		* @param panel
585		* @param group
586		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
587	0	protected void warnIfGroupHidden(JPanel panel, String group)...
588		{
589	0	if (!fr.isGroupVisible(group))
590		{
591	0	String msg = MessageManager.formatMessage("label.warning_hidden",
592		MessageManager.getString("label.group"), group);
593	0	JvOptionPane.showMessageDialog(panel, msg, "",
594		JvOptionPane.OK_OPTION);
595		}
596		}
597
598		/**
599		* Show a warning message if the entered type is one that is currently hidden
600		*
601		* @param panel
602		* @param type
603		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
604	0	protected void warnIfTypeHidden(JPanel panel, String type)...
605		{
606	0	if (fr.getRenderOrder().contains(type))
607		{
608	0	if (!fr.showFeatureOfType(type))
609		{
610	0	String msg = MessageManager.formatMessage("label.warning_hidden",
611		MessageManager.getString("label.feature_type"), type);
612	0	JvOptionPane.showMessageDialog(panel, msg, "",
613		JvOptionPane.OK_OPTION);
614		}
615		}
616		}
617
618		/**
619		* On closing the dialog - ensure feature display is turned on, to show any
620		* new features - remove highlighting of the last selected feature - repaint
621		* the panel to show any changes
622		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
623	0	protected void repaintPanel()...
624		{
625	0	ap.alignFrame.showSeqFeatures.setSelected(true);
626	0	ap.av.setShowSequenceFeatures(true);
627	0	ap.av.setSearchResults(null);
628	0	ap.paintAlignment(true, true);
629		}
630
631		/**
632		* Returns the action to be run on OK in the dialog when amending a feature.
633		* Note this may include refreshing the Feature Settings panel (if it is
634		* open), if feature type, group or colour has changed (but not for
635		* description or extent).
636		*
637		* @return
638		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
639	0	protected Runnable getAmendAction()...
640		{
641	0	Runnable okAction = new Runnable()
642		{
643		boolean useLastDefaults = features.get(0).getType() == null;
644
645		String featureType = name.getText();
646
647		String featureGroup = group.getText();
648
		0% Uncovered Elements: 34 (34) Complexity: 6 Complexity Density: 0.23
649	0	public void run()...
650		{
651	0	final String enteredType = name.getText().trim();
652	0	final String enteredGroup = group.getText().trim();
653	0	final String enteredDescription = description.getText()
654		.replaceAll("\n", " ");
655	0	if (enteredType.length() > 0)
656
657		{
658		/*
659		* update default values only if creating using default values
660		*/
661	0	if (useLastDefaults)
662		{
663	0	lastFeatureAdded = enteredType;
664	0	lastFeatureGroupAdded = enteredGroup;
665		// TODO: determine if the null feature group is valid
666	0	if (lastFeatureGroupAdded.length() < 1)
667		{
668	0	lastFeatureGroupAdded = null;
669		}
670		}
671		}
672
673	0	SequenceFeature sf = features.get(featureIndex);
674
675		/*
676		* Need to refresh Feature Settings if type, group or colour changed;
677		* note we don't force the feature to be visible - the user has been
678		* warned if a hidden feature type or group was entered
679		*/
680	0	boolean refreshSettings = (!featureType.equals(enteredType)
681		|| !featureGroup.equals(enteredGroup));
682	0	refreshSettings |= (featureColour != oldColour);
683	0	fr.setColour(enteredType, featureColour);
684	0	int newBegin = sf.begin;
685	0	int newEnd = sf.end;
686	0	try
687		{
688	0	newBegin = ((Integer) start.getValue()).intValue();
689	0	newEnd = ((Integer) end.getValue()).intValue();
690		} catch (NumberFormatException ex)
691		{
692		// JSpinner doesn't accept invalid format data :-)
693		}
694
695		/*
696		* 'amend' the feature by deleting it and adding a new one
697		* (to ensure integrity of SequenceFeatures data store)
698		* note this dialog only updates one sequence at a time
699		*/
700	0	sequences.get(0).deleteFeature(sf);
701	0	SequenceFeature newSf = new SequenceFeature(sf, enteredType,
702		newBegin, newEnd, enteredGroup, sf.getScore());
703	0	newSf.setDescription(enteredDescription);
704	0	new FeaturesFile().parseDescriptionHTML(newSf, false);
705	0	sequences.get(0).addSequenceFeature(newSf);
706
707	0	if (refreshSettings)
708		{
709	0	fr.featuresAdded();
710		}
711	0	repaintPanel();
712		}
713		};
714	0	return okAction;
715		}
716
717		}