Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
FeatureEditor	44	214	52	289	0.00%	Show methods

Class FeatureEditor

Class FeatureEditor	Line # 44	Total Statements 214	Complexity 52	Uncovered Elements 289	TOTAL Coverage 0.00%
FeatureEditor(AlignmentPanel,List<SequenceI>,List<SequenceFeature>,boolean)   FeatureEditor(AlignmentPanel,List<SequenceI>,List<SequenceFeature>,boolean)	105105	6.06	1.01	6.06	0.0 0.00%
insertUpdate(DocumentEvent) : void   insertUpdate(DocumentEvent) : void	129129	1.01	1.01	1.01	0.0 0.00%
removeUpdate(DocumentEvent) : void   removeUpdate(DocumentEvent) : void	135135	1.01	1.01	1.01	0.0 0.00%
changedUpdate(DocumentEvent) : void   changedUpdate(DocumentEvent) : void	141141	1.01	1.01	1.01	0.0 0.00%
insertUpdate(DocumentEvent) : void   insertUpdate(DocumentEvent) : void	151151	1.01	1.01	1.01	0.0 0.00%
removeUpdate(DocumentEvent) : void   removeUpdate(DocumentEvent) : void	157157	1.01	1.01	1.01	0.0 0.00%
changedUpdate(DocumentEvent) : void   changedUpdate(DocumentEvent) : void	163163	1.01	1.01	1.01	0.0 0.00%
colourSelected(Color) : void   colourSelected(Color) : void	192192	2.02	1.01	2.02	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	215215	3.03	1.01	3.03	0.0 0.00%
mousePressed(MouseEvent) : void   mousePressed(MouseEvent) : void	180180	10.010	3.03	14.014	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	256256	17.017	3.03	21.021	0.0 0.00%
init() : void   init() : void	120120	77.077	7.07	87.087	0.0 0.00%
showDialog() : void   showDialog() : void	375375	13.013	4.04	19.019	0.0 0.00%
run() : void   run() : void	428428	2.02	1.01	2.02	0.0 0.00%
getCancelAction() : RunResponse   getCancelAction() : RunResponse	424424	2.02	1.01	2.02	0.0 0.00%
run() : void   run() : void	454454	18.018	6.06	28.028	0.0 0.00%
getCreateAction() : RunResponse   getCreateAction() : RunResponse	448448	2.02	1.01	2.02	0.0 0.00%
run() : void   run() : void	510510	5.05	1.01	5.05	0.0 0.00%
getDeleteAction() : RunResponse   getDeleteAction() : RunResponse	506506	2.02	1.01	2.02	0.0 0.00%
updateColourButton(JPanel,JLabel,FeatureColourI) : void   updateColourButton(JPanel,JLabel,FeatureColourI) : void	529529	10.010	2.02	12.012	0.0 0.00%
warnIfGroupHidden(JPanel,String) : void   warnIfGroupHidden(JPanel,String) : void	556556	3.03	2.02	5.05	0.0 0.00%
warnIfTypeHidden(JPanel,String) : void   warnIfTypeHidden(JPanel,String) : void	573573	4.04	3.03	8.08	0.0 0.00%
repaintPanel() : void   repaintPanel() : void	592592	4.04	1.01	4.04	0.0 0.00%
run() : void   run() : void	618618	26.026	6.06	34.034	0.0 0.00%
getAmendAction() : RunResponse   getAmendAction() : RunResponse	608608	2.02	1.01	2.02	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		import jalview.util.dialogrunner.RunResponse;
14
15		import java.awt.BorderLayout;
16		import java.awt.Color;
17		import java.awt.Dimension;
18		import java.awt.Font;
19		import java.awt.GridLayout;
20		import java.awt.event.ActionEvent;
21		import java.awt.event.ActionListener;
22		import java.awt.event.ItemEvent;
23		import java.awt.event.ItemListener;
24		import java.awt.event.MouseAdapter;
25		import java.awt.event.MouseEvent;
26		import java.util.ArrayList;
27		import java.util.List;
28
29		import javax.swing.JComboBox;
30		import javax.swing.JLabel;
31		import javax.swing.JPanel;
32		import javax.swing.JScrollPane;
33		import javax.swing.JSpinner;
34		import javax.swing.JTextArea;
35		import javax.swing.JTextField;
36		import javax.swing.SwingConstants;
37		import javax.swing.event.DocumentEvent;
38		import javax.swing.event.DocumentListener;
39
40		/**
41		* Provides a dialog allowing the user to add new features, or amend or delete
42		* existing features
43		*/
		0% Uncovered Elements: 289 (289) Complexity: 52 Complexity Density: 0.24
44		public class FeatureEditor
45		{
46		/*
47		* defaults for creating a new feature are the last created
48		* feature type and group
49		*/
50		static String lastFeatureAdded = "feature_1";
51
52		static String lastFeatureGroupAdded = "Jalview";
53
54		/*
55		* the sequence(s) with features to be created / amended
56		*/
57		final List<SequenceI> sequences;
58
59		/*
60		* the features (or template features) to be created / amended
61		*/
62		final List<SequenceFeature> features;
63
64		/*
65		* true if the dialog is to create a new feature, false if
66		* for amend or delete of existing feature(s)
67		*/
68		final boolean forCreate;
69
70		/*
71		* index into the list of features
72		*/
73		int featureIndex;
74
75		FeatureColourI oldColour;
76
77		FeatureColourI featureColour;
78
79		FeatureRenderer fr;
80
81		AlignmentPanel ap;
82
83		JTextField name;
84
85		JTextField group;
86
87		JTextArea description;
88
89		JSpinner start;
90
91		JSpinner end;
92
93		JPanel mainPanel;
94
95		/**
96		* Constructor
97		*
98		* @param alignPanel
99		* @param seqs
100		* @param feats
101		* @param create
102		* if true create a new feature, else amend or delete an existing
103		* feature
104		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
105	0	public FeatureEditor(AlignmentPanel alignPanel, List<SequenceI> seqs,...
106		List<SequenceFeature> feats, boolean create)
107		{
108	0	ap = alignPanel;
109	0	fr = alignPanel.getSeqPanel().seqCanvas.fr;
110	0	sequences = seqs;
111	0	features = feats;
112	0	this.forCreate = create;
113
114	0	init();
115		}
116
117		/**
118		* Initialise the layout and controls
119		*/
		0% Uncovered Elements: 87 (87) Complexity: 7 Complexity Density: 0.09
120	0	protected void init()...
121		{
122	0	featureIndex = 0;
123
124	0	mainPanel = new JPanel(new BorderLayout());
125
126	0	name = new JTextField(25);
127	0	name.getDocument().addDocumentListener(new DocumentListener()
128		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
129	0	@Override...
130		public void insertUpdate(DocumentEvent e)
131		{
132	0	warnIfTypeHidden(mainPanel, name.getText());
133		}
134
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
135	0	@Override...
136		public void removeUpdate(DocumentEvent e)
137		{
138	0	warnIfTypeHidden(mainPanel, name.getText());
139		}
140
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
141	0	@Override...
142		public void changedUpdate(DocumentEvent e)
143		{
144	0	warnIfTypeHidden(mainPanel, name.getText());
145		}
146		});
147
148	0	group = new JTextField(25);
149	0	group.getDocument().addDocumentListener(new DocumentListener()
150		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
151	0	@Override...
152		public void insertUpdate(DocumentEvent e)
153		{
154	0	warnIfGroupHidden(mainPanel, group.getText());
155		}
156
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
157	0	@Override...
158		public void removeUpdate(DocumentEvent e)
159		{
160	0	warnIfGroupHidden(mainPanel, group.getText());
161		}
162
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
163	0	@Override...
164		public void changedUpdate(DocumentEvent e)
165		{
166	0	warnIfGroupHidden(mainPanel, group.getText());
167		}
168		});
169
170	0	description = new JTextArea(3, 25);
171	0	start = new JSpinner();
172	0	end = new JSpinner();
173	0	start.setPreferredSize(new Dimension(80, 20));
174	0	end.setPreferredSize(new Dimension(80, 20));
175	0	final JLabel colour = new JLabel();
176	0	colour.setOpaque(true);
177	0	colour.setMaximumSize(new Dimension(30, 16));
178	0	colour.addMouseListener(new MouseAdapter()
179		{
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
180	0	@Override...
181		public void mousePressed(MouseEvent evt)
182		{
183	0	if (featureColour.isSimpleColour())
184		{
185		/*
186		* open colour chooser on click in colour panel
187		*/
188	0	String title = MessageManager
189		.getString("label.select_feature_colour");
190	0	ColourChooserListener listener = new ColourChooserListener()
191		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
192	0	@Override...
193		public void colourSelected(Color c)
194		{
195	0	featureColour = new FeatureColour(c);
196	0	updateColourButton(mainPanel, colour, featureColour);
197		};
198		};
199	0	JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
200		title, featureColour.getColour(), listener);
201		}
202		else
203		{
204		/*
205		* variable colour dialog - on OK, refetch the updated
206		* feature colour and update this display
207		*/
208	0	final String ft = features.get(featureIndex).getType();
209	0	final String type = ft == null ? lastFeatureAdded : ft;
210	0	FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type);
211	0	fcc.setRequestFocusEnabled(true);
212	0	fcc.requestFocus();
213	0	fcc.addActionListener(new ActionListener()
214		{
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
215	0	@Override...
216		public void actionPerformed(ActionEvent e)
217		{
218	0	featureColour = fr.getFeatureStyle(ft);
219	0	fr.setColour(type, featureColour);
220	0	updateColourButton(mainPanel, colour, featureColour);
221		}
222		});
223		}
224		}
225		});
226	0	JPanel gridPanel = new JPanel(new GridLayout(3, 1));
227
228	0	if (!forCreate && features.size() > 1)
229		{
230		/*
231		* more than one feature at selected position -
232		* add a drop-down to choose the feature to amend
233		* space pad text if necessary to make entries distinct
234		*/
235	0	gridPanel = new JPanel(new GridLayout(4, 1));
236	0	JPanel choosePanel = new JPanel();
237	0	choosePanel.add(new JLabel(
238		MessageManager.getString("label.select_feature") + ":"));
239	0	final JComboBox<String> overlaps = new JComboBox<>();
240	0	List<String> added = new ArrayList<>();
241	0	for (SequenceFeature sf : features)
242		{
243	0	String text = String.format("%s/%d-%d (%s)", sf.getType(),
244		sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
245	0	while (added.contains(text))
246		{
247	0	text += " ";
248		}
249	0	overlaps.addItem(text);
250	0	added.add(text);
251		}
252	0	choosePanel.add(overlaps);
253
254	0	overlaps.addItemListener(new ItemListener()
255		{
		0% Uncovered Elements: 21 (21) Complexity: 3 Complexity Density: 0.18
256	0	@Override...
257		public void itemStateChanged(ItemEvent e)
258		{
259	0	int index = overlaps.getSelectedIndex();
260	0	if (index != -1)
261		{
262	0	featureIndex = index;
263	0	SequenceFeature sf = features.get(index);
264	0	name.setText(sf.getType());
265	0	description.setText(sf.getDescription());
266	0	group.setText(sf.getFeatureGroup());
267	0	start.setValue(new Integer(sf.getBegin()));
268	0	end.setValue(new Integer(sf.getEnd()));
269
270	0	SearchResultsI highlight = new SearchResults();
271	0	highlight.addResult(sequences.get(0), sf.getBegin(),
272		sf.getEnd());
273
274	0	ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
275		}
276	0	FeatureColourI col = fr.getFeatureStyle(name.getText());
277	0	if (col == null)
278		{
279	0	col = new FeatureColour(
280		ColorUtils.createColourFromName(name.getText()));
281		}
282	0	oldColour = featureColour = col;
283	0	updateColourButton(mainPanel, colour, col);
284		}
285		});
286
287	0	gridPanel.add(choosePanel);
288		}
289
290	0	JPanel namePanel = new JPanel();
291	0	gridPanel.add(namePanel);
292	0	namePanel.add(new JLabel(MessageManager.getString("label.name:"),
293		JLabel.RIGHT));
294	0	namePanel.add(name);
295
296	0	JPanel groupPanel = new JPanel();
297	0	gridPanel.add(groupPanel);
298	0	groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
299		JLabel.RIGHT));
300	0	groupPanel.add(group);
301
302	0	JPanel colourPanel = new JPanel();
303	0	gridPanel.add(colourPanel);
304	0	colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
305		JLabel.RIGHT));
306	0	colourPanel.add(colour);
307	0	colour.setPreferredSize(new Dimension(150, 15));
308	0	colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
309	0	colour.setForeground(Color.black);
310	0	colour.setHorizontalAlignment(SwingConstants.CENTER);
311	0	colour.setVerticalAlignment(SwingConstants.CENTER);
312	0	colour.setHorizontalTextPosition(SwingConstants.CENTER);
313	0	colour.setVerticalTextPosition(SwingConstants.CENTER);
314	0	mainPanel.add(gridPanel, BorderLayout.NORTH);
315
316	0	JPanel descriptionPanel = new JPanel();
317	0	descriptionPanel.add(new JLabel(
318		MessageManager.getString("label.description:"), JLabel.RIGHT));
319	0	description.setFont(JvSwingUtils.getTextAreaFont());
320	0	description.setLineWrap(true);
321	0	descriptionPanel.add(new JScrollPane(description));
322
323	0	if (!forCreate)
324		{
325	0	mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
326
327	0	JPanel startEndPanel = new JPanel();
328	0	startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
329		JLabel.RIGHT));
330	0	startEndPanel.add(start);
331	0	startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
332		JLabel.RIGHT));
333	0	startEndPanel.add(end);
334	0	mainPanel.add(startEndPanel, BorderLayout.CENTER);
335		}
336		else
337		{
338	0	mainPanel.add(descriptionPanel, BorderLayout.CENTER);
339		}
340
341		/*
342		* default feature type and group to that of the first feature supplied,
343		* or to the last feature created if not supplied (null value)
344		*/
345	0	SequenceFeature firstFeature = features.get(0);
346	0	boolean useLastDefaults = firstFeature.getType() == null;
347	0	final String featureType = useLastDefaults ? lastFeatureAdded
348		: firstFeature.getType();
349	0	final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
350		: firstFeature.getFeatureGroup();
351	0	name.setText(featureType);
352	0	group.setText(featureGroup);
353
354	0	start.setValue(new Integer(firstFeature.getBegin()));
355	0	end.setValue(new Integer(firstFeature.getEnd()));
356	0	description.setText(firstFeature.getDescription());
357	0	featureColour = fr.getFeatureStyle(featureType);
358	0	oldColour = featureColour;
359	0	updateColourButton(mainPanel, colour, oldColour);
360		}
361
362		/**
363		* Presents a dialog allowing the user to add new features, or amend or delete
364		* an existing feature. Currently this can be on
365		* <ul>
366		* <li>double-click on a sequence - Amend/Delete a selected feature at the
367		* position</li>
368		* <li>Create sequence feature(s) from pop-up menu on selected region</li>
369		* <li>Create features for pattern matches from Find</li>
370		* </ul>
371		* If the supplied feature type is null, show (and update on confirm) the type
372		* and group of the last new feature created (with initial defaults of
373		* "feature_1" and "Jalview").
374		*/
		0% Uncovered Elements: 19 (19) Complexity: 4 Complexity Density: 0.31
375	0	public void showDialog()...
376		{
377	0	RunResponse okAction = forCreate ? getCreateAction() : getAmendAction();
378	0	RunResponse cancelAction = getCancelAction();
379
380		/*
381		* set dialog action handlers for OK (create/Amend) and Cancel options
382		* also for Delete if applicable (when amending features)
383		*/
384	0	JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
385		.response(okAction).response(cancelAction);
386	0	if (!forCreate)
387		{
388	0	dialog.response(getDeleteAction());
389		}
390
391	0	String title = null;
392	0	Object[] options = null;
393	0	if (forCreate)
394		{
395	0	title = MessageManager
396		.getString("label.create_new_sequence_features");
397	0	options = new Object[] { MessageManager.getString("action.ok"),
398		MessageManager.getString("action.cancel") };
399		}
400		else
401		{
402	0	title = MessageManager.formatMessage("label.amend_delete_features",
403		new String[]
404		{ sequences.get(0).getName() });
405	0	options = new Object[] { MessageManager.getString("label.amend"),
406		MessageManager.getString("action.delete"),
407		MessageManager.getString("action.cancel") };
408		}
409
410	0	dialog.showInternalDialog(mainPanel, title,
411		JvOptionPane.YES_NO_CANCEL_OPTION,
412		JvOptionPane.PLAIN_MESSAGE, null, options,
413		MessageManager.getString("action.ok"));
414		}
415
416		/**
417		* Answers an action to run on Cancel in the dialog. This is just to remove
418		* any feature highlighting from the display. Changes in the dialog are not
419		* applied until it is dismissed with OK, Amend or Delete, so there are no
420		* updates to reset on Cancel.
421		*
422		* @return
423		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
424	0	protected RunResponse getCancelAction()...
425		{
426	0	RunResponse okAction = new RunResponse(JvOptionPane.CANCEL_OPTION)
427		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
428	0	@Override...
429		public void run()
430		{
431	0	ap.highlightSearchResults(null);
432	0	ap.paintAlignment(false, false);
433		}
434		};
435	0	return okAction;
436		}
437
438		/**
439		* Returns the action to be run on OK in the dialog when creating one or more
440		* sequence features. Note these may have a pre-supplied feature type (such as
441		* a Find pattern), or none, in which case the feature type and group default
442		* to those last added through this dialog. The action includes refreshing the
443		* Feature Settings panel (if it is open), to show any new feature type, or
444		* amended colour for an existing type.
445		*
446		* @return
447		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
448	0	protected RunResponse getCreateAction()...
449		{
450	0	RunResponse okAction = new RunResponse(JvOptionPane.OK_OPTION)
451		{
452		boolean useLastDefaults = features.get(0).getType() == null;
453
		0% Uncovered Elements: 28 (28) Complexity: 6 Complexity Density: 0.33
454	0	public void run()...
455		{
456	0	final String enteredType = name.getText().trim();
457	0	final String enteredGroup = group.getText().trim();
458	0	final String enteredDescription = description.getText()
459		.replaceAll("\n", " ");
460	0	if (enteredType.length() > 0)
461		{
462		/*
463		* update default values only if creating using default values
464		*/
465	0	if (useLastDefaults)
466		{
467	0	lastFeatureAdded = enteredType;
468	0	lastFeatureGroupAdded = enteredGroup;
469		// TODO: determine if the null feature group is valid
470	0	if (lastFeatureGroupAdded.length() < 1)
471		{
472	0	lastFeatureGroupAdded = null;
473		}
474		}
475		}
476
477	0	if (enteredType.length() > 0)
478		{
479	0	for (int i = 0; i < sequences.size(); i++)
480		{
481	0	SequenceFeature sf = features.get(i);
482	0	SequenceFeature sf2 = new SequenceFeature(enteredType,
483		enteredDescription, sf.getBegin(), sf.getEnd(),
484		enteredGroup);
485	0	new FeaturesFile().parseDescriptionHTML(sf2, false);
486	0	sequences.get(i).addSequenceFeature(sf2);
487		}
488
489	0	fr.setColour(enteredType, featureColour);
490	0	fr.featuresAdded();
491
492	0	repaintPanel();
493		}
494		}
495		};
496	0	return okAction;
497		}
498
499		/**
500		* Answers the action to run on Delete in the dialog. Note this includes
501		* refreshing the Feature Settings (if open) in case the only instance of a
502		* feature type or group has been deleted.
503		*
504		* @return
505		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
506	0	protected RunResponse getDeleteAction()...
507		{
508	0	RunResponse deleteAction = new RunResponse(JvOptionPane.NO_OPTION)
509		{
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
510	0	public void run()...
511		{
512	0	SequenceFeature sf = features.get(featureIndex);
513	0	sequences.get(0).getDatasetSequence().deleteFeature(sf);
514	0	fr.featuresAdded();
515	0	ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
516	0	ap.paintAlignment(true, true);
517		}
518		};
519	0	return deleteAction;
520		}
521
522		/**
523		* update the amend feature button dependent on the given style
524		*
525		* @param bigPanel
526		* @param col
527		* @param col
528		*/
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
529	0	protected void updateColourButton(JPanel bigPanel, JLabel colour,...
530		FeatureColourI col)
531		{
532	0	colour.removeAll();
533	0	colour.setIcon(null);
534	0	colour.setText("");
535
536	0	if (col.isSimpleColour())
537		{
538	0	colour.setToolTipText(null);
539	0	colour.setBackground(col.getColour());
540		}
541		else
542		{
543	0	colour.setBackground(bigPanel.getBackground());
544	0	colour.setForeground(Color.black);
545	0	colour.setToolTipText(FeatureSettings.getColorTooltip(col, false));
546	0	FeatureSettings.renderGraduatedColor(colour, col);
547		}
548		}
549
550		/**
551		* Show a warning message if the entered group is one that is currently hidden
552		*
553		* @param panel
554		* @param group
555		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
556	0	protected void warnIfGroupHidden(JPanel panel, String group)...
557		{
558	0	if (!fr.isGroupVisible(group))
559		{
560	0	String msg = MessageManager.formatMessage("label.warning_hidden",
561		MessageManager.getString("label.group"), group);
562	0	JvOptionPane.showMessageDialog(panel, msg, "",
563		JvOptionPane.OK_OPTION);
564		}
565		}
566
567		/**
568		* Show a warning message if the entered type is one that is currently hidden
569		*
570		* @param panel
571		* @param type
572		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
573	0	protected void warnIfTypeHidden(JPanel panel, String type)...
574		{
575	0	if (fr.getRenderOrder().contains(type))
576		{
577	0	if (!fr.showFeatureOfType(type))
578		{
579	0	String msg = MessageManager.formatMessage("label.warning_hidden",
580		MessageManager.getString("label.feature_type"), type);
581	0	JvOptionPane.showMessageDialog(panel, msg, "",
582		JvOptionPane.OK_OPTION);
583		}
584		}
585		}
586
587		/**
588		* On closing the dialog - ensure feature display is turned on, to show any
589		* new features - remove highlighting of the last selected feature - repaint
590		* the panel to show any changes
591		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
592	0	protected void repaintPanel()...
593		{
594	0	ap.alignFrame.showSeqFeatures.setSelected(true);
595	0	ap.av.setShowSequenceFeatures(true);
596	0	ap.av.setSearchResults(null);
597	0	ap.paintAlignment(true, true);
598		}
599
600		/**
601		* Returns the action to be run on OK in the dialog when amending a feature.
602		* Note this may include refreshing the Feature Settings panel (if it is
603		* open), if feature type, group or colour has changed (but not for
604		* description or extent).
605		*
606		* @return
607		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
608	0	protected RunResponse getAmendAction()...
609		{
610	0	RunResponse okAction = new RunResponse(JvOptionPane.OK_OPTION)
611		{
612		boolean useLastDefaults = features.get(0).getType() == null;
613
614		String featureType = name.getText();
615
616		String featureGroup = group.getText();
617
		0% Uncovered Elements: 34 (34) Complexity: 6 Complexity Density: 0.23
618	0	public void run()...
619		{
620	0	final String enteredType = name.getText().trim();
621	0	final String enteredGroup = group.getText().trim();
622	0	final String enteredDescription = description.getText()
623		.replaceAll("\n", " ");
624	0	if (enteredType.length() > 0)
625
626		{
627		/*
628		* update default values only if creating using default values
629		*/
630	0	if (useLastDefaults)
631		{
632	0	lastFeatureAdded = enteredType;
633	0	lastFeatureGroupAdded = enteredGroup;
634		// TODO: determine if the null feature group is valid
635	0	if (lastFeatureGroupAdded.length() < 1)
636		{
637	0	lastFeatureGroupAdded = null;
638		}
639		}
640		}
641
642	0	SequenceFeature sf = features.get(featureIndex);
643
644		/*
645		* Need to refresh Feature Settings if type, group or colour changed;
646		* note we don't force the feature to be visible - the user has been
647		* warned if a hidden feature type or group was entered
648		*/
649	0	boolean refreshSettings = (!featureType.equals(enteredType)
650		|| !featureGroup.equals(enteredGroup));
651	0	refreshSettings |= (featureColour != oldColour);
652	0	fr.setColour(enteredType, featureColour);
653	0	int newBegin = sf.begin;
654	0	int newEnd = sf.end;
655	0	try
656		{
657	0	newBegin = ((Integer) start.getValue()).intValue();
658	0	newEnd = ((Integer) end.getValue()).intValue();
659		} catch (NumberFormatException ex)
660		{
661		// JSpinner doesn't accept invalid format data :-)
662		}
663
664		/*
665		* 'amend' the feature by deleting it and adding a new one
666		* (to ensure integrity of SequenceFeatures data store)
667		* note this dialog only updates one sequence at a time
668		*/
669	0	sequences.get(0).deleteFeature(sf);
670	0	SequenceFeature newSf = new SequenceFeature(sf, enteredType,
671		newBegin, newEnd, enteredGroup, sf.getScore());
672	0	newSf.setDescription(enteredDescription);
673	0	new FeaturesFile().parseDescriptionHTML(newSf, false);
674	0	sequences.get(0).addSequenceFeature(newSf);
675
676	0	if (refreshSettings)
677		{
678	0	fr.featuresAdded();
679		}
680	0	repaintPanel();
681		}
682		};
683	0	return okAction;
684		}
685
686		}