Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureEditor	66	224	52	0.00%	Show methods

Class FeatureEditor

Class FeatureEditor	Line # 66	Total Statements 224	Complexity 52	TOTAL Coverage 0.00%
FeatureEditor(AlignmentPanel,List<SequenceI>,List<SequenceFeature>,boolean)   FeatureEditor(AlignmentPanel,List<SequenceI>,List<SequenceFeature>,boolean)	127127	6.06	1.01	0.0 0.00%
insertUpdate(DocumentEvent) : void   insertUpdate(DocumentEvent) : void	151151	1.01	1.01	0.0 0.00%
removeUpdate(DocumentEvent) : void   removeUpdate(DocumentEvent) : void	157157	1.01	1.01	0.0 0.00%
changedUpdate(DocumentEvent) : void   changedUpdate(DocumentEvent) : void	163163	1.01	1.01	0.0 0.00%
insertUpdate(DocumentEvent) : void   insertUpdate(DocumentEvent) : void	173173	1.01	1.01	0.0 0.00%
removeUpdate(DocumentEvent) : void   removeUpdate(DocumentEvent) : void	179179	1.01	1.01	0.0 0.00%
changedUpdate(DocumentEvent) : void   changedUpdate(DocumentEvent) : void	185185	1.01	1.01	0.0 0.00%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	204204	2.02	1.01	0.0 0.00%
stateChanged(ChangeEvent) : void   stateChanged(ChangeEvent) : void	213213	2.02	1.01	0.0 0.00%
colourSelected(Color) : void   colourSelected(Color) : void	238238	2.02	1.01	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	261261	3.03	1.01	0.0 0.00%
mousePressed(MouseEvent) : void   mousePressed(MouseEvent) : void	226226	10.010	3.03	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	302302	19.019	3.03	0.0 0.00%
init() : void   init() : void	142142	81.081	7.07	0.0 0.00%
showDialog() : void   showDialog() : void	426426	13.013	4.04	0.0 0.00%
getCancelAction() : Runnable   getCancelAction() : Runnable	476476	4.04	1.01	0.0 0.00%
run() : void   run() : void	501501	18.018	6.06	0.0 0.00%
getCreateAction() : Runnable   getCreateAction() : Runnable	495495	2.02	1.01	0.0 0.00%
getDeleteAction() : Runnable   getDeleteAction() : Runnable	554554	7.07	1.01	0.0 0.00%
updateColourButton(JPanel,JLabel,FeatureColourI) : void   updateColourButton(JPanel,JLabel,FeatureColourI) : void	573573	10.010	2.02	0.0 0.00%
warnIfGroupHidden(JPanel,String) : void   warnIfGroupHidden(JPanel,String) : void	600600	3.03	2.02	0.0 0.00%
warnIfTypeHidden(JPanel,String) : void   warnIfTypeHidden(JPanel,String) : void	617617	4.04	3.03	0.0 0.00%
repaintPanel() : void   repaintPanel() : void	636636	4.04	1.01	0.0 0.00%
run() : void   run() : void	661661	26.026	6.06	0.0 0.00%
getAmendAction() : Runnable   getAmendAction() : Runnable	652652	2.02	1.01	0.0 0.00%

 

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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.FeatureColourI;
24		import jalview.datamodel.SearchResults;
25		import jalview.datamodel.SearchResultsI;
26		import jalview.datamodel.SequenceFeature;
27		import jalview.datamodel.SequenceI;
28		import jalview.gui.JalviewColourChooser.ColourChooserListener;
29		import jalview.io.FeaturesFile;
30		import jalview.schemes.FeatureColour;
31		import jalview.util.ColorUtils;
32		import jalview.util.MessageManager;
33
34		import java.awt.BorderLayout;
35		import java.awt.Color;
36		import java.awt.Dimension;
37		import java.awt.Font;
38		import java.awt.GridLayout;
39		import java.awt.event.ActionEvent;
40		import java.awt.event.ActionListener;
41		import java.awt.event.ItemEvent;
42		import java.awt.event.ItemListener;
43		import java.awt.event.MouseAdapter;
44		import java.awt.event.MouseEvent;
45		import java.util.ArrayList;
46		import java.util.List;
47
48		import javax.swing.JComboBox;
49		import javax.swing.JLabel;
50		import javax.swing.JPanel;
51		import javax.swing.JScrollPane;
52		import javax.swing.JSpinner;
53		import javax.swing.JTextArea;
54		import javax.swing.JTextField;
55		import javax.swing.SpinnerNumberModel;
56		import javax.swing.SwingConstants;
57		import javax.swing.event.ChangeEvent;
58		import javax.swing.event.ChangeListener;
59		import javax.swing.event.DocumentEvent;
60		import javax.swing.event.DocumentListener;
61
62		/**
63		* Provides a dialog allowing the user to add new features, or amend or delete
64		* existing features
65		*/
		0% Uncovered Elements: 299 (299) Complexity: 52 Complexity Density: 0.23
66		public class FeatureEditor
67		{
68		/*
69		* defaults for creating a new feature are the last created
70		* feature type and group
71		*/
72		static String lastFeatureAdded = "feature_1";
73
74		static String lastFeatureGroupAdded = "Jalview";
75
76		/*
77		* the sequence(s) with features to be created / amended
78		*/
79		final List<SequenceI> sequences;
80
81		/*
82		* the features (or template features) to be created / amended
83		*/
84		final List<SequenceFeature> features;
85
86		/*
87		* true if the dialog is to create a new feature, false if
88		* for amend or delete of existing feature(s)
89		*/
90		final boolean forCreate;
91
92		/*
93		* index into the list of features
94		*/
95		int featureIndex;
96
97		FeatureColourI oldColour;
98
99		FeatureColourI featureColour;
100
101		FeatureRenderer fr;
102
103		AlignmentPanel ap;
104
105		JTextField name;
106
107		JTextField group;
108
109		JTextArea description;
110
111		JSpinner start;
112
113		JSpinner end;
114
115		JPanel mainPanel;
116
117		/**
118		* Constructor
119		*
120		* @param alignPanel
121		* @param seqs
122		* @param feats
123		* @param create
124		* if true create a new feature, else amend or delete an existing
125		* feature
126		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
127	0	public FeatureEditor(AlignmentPanel alignPanel, List<SequenceI> seqs,...
128		List<SequenceFeature> feats, boolean create)
129		{
130	0	ap = alignPanel;
131	0	fr = alignPanel.getSeqPanel().seqCanvas.fr;
132	0	sequences = seqs;
133	0	features = feats;
134	0	this.forCreate = create;
135
136	0	init();
137		}
138
139		/**
140		* Initialise the layout and controls
141		*/
		0% Uncovered Elements: 91 (91) Complexity: 7 Complexity Density: 0.09
142	0	protected void init()...
143		{
144	0	featureIndex = 0;
145
146	0	mainPanel = new JPanel(new BorderLayout());
147
148	0	name = new JTextField(25);
149	0	name.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	warnIfTypeHidden(mainPanel, name.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	warnIfTypeHidden(mainPanel, name.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	warnIfTypeHidden(mainPanel, name.getText());
167		}
168		});
169
170	0	group = new JTextField(25);
171	0	group.getDocument().addDocumentListener(new DocumentListener()
172		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
173	0	@Override...
174		public void insertUpdate(DocumentEvent e)
175		{
176	0	warnIfGroupHidden(mainPanel, group.getText());
177		}
178
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
179	0	@Override...
180		public void removeUpdate(DocumentEvent e)
181		{
182	0	warnIfGroupHidden(mainPanel, group.getText());
183		}
184
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
185	0	@Override...
186		public void changedUpdate(DocumentEvent e)
187		{
188	0	warnIfGroupHidden(mainPanel, group.getText());
189		}
190		});
191
192	0	description = new JTextArea(3, 25);
193
194	0	start = new JSpinner();
195	0	end = new JSpinner();
196	0	start.setPreferredSize(new Dimension(80, 20));
197	0	end.setPreferredSize(new Dimension(80, 20));
198
199		/*
200		* ensure that start can never be more than end
201		*/
202	0	start.addChangeListener(new ChangeListener()
203		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
204	0	@Override...
205		public void stateChanged(ChangeEvent e)
206		{
207	0	Integer startVal = (Integer) start.getValue();
208	0	((SpinnerNumberModel) end.getModel()).setMinimum(startVal);
209		}
210		});
211	0	end.addChangeListener(new ChangeListener()
212		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
213	0	@Override...
214		public void stateChanged(ChangeEvent e)
215		{
216	0	Integer endVal = (Integer) end.getValue();
217	0	((SpinnerNumberModel) start.getModel()).setMaximum(endVal);
218		}
219		});
220
221	0	final JLabel colour = new JLabel();
222	0	colour.setOpaque(true);
223	0	colour.setMaximumSize(new Dimension(30, 16));
224	0	colour.addMouseListener(new MouseAdapter()
225		{
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
226	0	@Override...
227		public void mousePressed(MouseEvent evt)
228		{
229	0	if (featureColour.isSimpleColour())
230		{
231		/*
232		* open colour chooser on click in colour panel
233		*/
234	0	String title = MessageManager
235		.getString("label.select_feature_colour");
236	0	ColourChooserListener listener = new ColourChooserListener()
237		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
238	0	@Override...
239		public void colourSelected(Color c)
240		{
241	0	featureColour = new FeatureColour(c);
242	0	updateColourButton(mainPanel, colour, featureColour);
243		};
244		};
245	0	JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
246		title, featureColour.getColour(), listener);
247		}
248		else
249		{
250		/*
251		* variable colour dialog - on OK, refetch the updated
252		* feature colour and update this display
253		*/
254	0	final String ft = features.get(featureIndex).getType();
255	0	final String type = ft == null ? lastFeatureAdded : ft;
256	0	FeatureTypeSettings fcc = new FeatureTypeSettings(fr, type, true);
257	0	fcc.setRequestFocusEnabled(true);
258	0	fcc.requestFocus();
259	0	fcc.addActionListener(new ActionListener()
260		{
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
261	0	@Override...
262		public void actionPerformed(ActionEvent e)
263		{
264	0	featureColour = fr.getFeatureStyle(ft);
265	0	fr.setColour(type, featureColour);
266	0	updateColourButton(mainPanel, colour, featureColour);
267		}
268		});
269		}
270		}
271		});
272	0	JPanel gridPanel = new JPanel(new GridLayout(3, 1));
273
274	0	if (!forCreate && features.size() > 1)
275		{
276		/*
277		* more than one feature at selected position -
278		* add a drop-down to choose the feature to amend
279		* space pad text if necessary to make entries distinct
280		*/
281	0	gridPanel = new JPanel(new GridLayout(4, 1));
282	0	JPanel choosePanel = new JPanel();
283	0	choosePanel.add(new JLabel(
284		MessageManager.getString("label.select_feature") + ":"));
285	0	final JComboBox<String> overlaps = new JComboBox<>();
286	0	List<String> added = new ArrayList<>();
287	0	for (SequenceFeature sf : features)
288		{
289	0	String text = String.format("%s/%d-%d (%s)", sf.getType(),
290		sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
291	0	while (added.contains(text))
292		{
293	0	text += " ";
294		}
295	0	overlaps.addItem(text);
296	0	added.add(text);
297		}
298	0	choosePanel.add(overlaps);
299
300	0	overlaps.addItemListener(new ItemListener()
301		{
		0% Uncovered Elements: 23 (23) Complexity: 3 Complexity Density: 0.16
302	0	@Override...
303		public void itemStateChanged(ItemEvent e)
304		{
305	0	int index = overlaps.getSelectedIndex();
306	0	if (index != -1)
307		{
308	0	featureIndex = index;
309	0	SequenceFeature sf = features.get(index);
310	0	name.setText(sf.getType());
311	0	description.setText(sf.getDescription());
312	0	group.setText(sf.getFeatureGroup());
313	0	start.setValue(new Integer(sf.getBegin()));
314	0	end.setValue(new Integer(sf.getEnd()));
315	0	((SpinnerNumberModel) start.getModel()).setMaximum(sf.getEnd());
316	0	((SpinnerNumberModel) end.getModel()).setMinimum(sf.getBegin());
317
318	0	SearchResultsI highlight = new SearchResults();
319	0	highlight.addResult(sequences.get(0), sf.getBegin(),
320		sf.getEnd());
321
322	0	ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
323		}
324	0	FeatureColourI col = fr.getFeatureStyle(name.getText());
325	0	if (col == null)
326		{
327	0	col = new FeatureColour(
328		ColorUtils.createColourFromName(name.getText()));
329		}
330	0	oldColour = featureColour = col;
331	0	updateColourButton(mainPanel, colour, col);
332		}
333		});
334
335	0	gridPanel.add(choosePanel);
336		}
337
338	0	JPanel namePanel = new JPanel();
339	0	gridPanel.add(namePanel);
340	0	namePanel.add(new JLabel(MessageManager.getString("label.name:"),
341		JLabel.RIGHT));
342	0	namePanel.add(name);
343
344	0	JPanel groupPanel = new JPanel();
345	0	gridPanel.add(groupPanel);
346	0	groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
347		JLabel.RIGHT));
348	0	groupPanel.add(group);
349
350	0	JPanel colourPanel = new JPanel();
351	0	gridPanel.add(colourPanel);
352	0	colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
353		JLabel.RIGHT));
354	0	colourPanel.add(colour);
355	0	colour.setPreferredSize(new Dimension(150, 15));
356	0	colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
357	0	colour.setForeground(Color.black);
358	0	colour.setHorizontalAlignment(SwingConstants.CENTER);
359	0	colour.setVerticalAlignment(SwingConstants.CENTER);
360	0	colour.setHorizontalTextPosition(SwingConstants.CENTER);
361	0	colour.setVerticalTextPosition(SwingConstants.CENTER);
362	0	mainPanel.add(gridPanel, BorderLayout.NORTH);
363
364	0	JPanel descriptionPanel = new JPanel();
365	0	descriptionPanel.add(new JLabel(
366		MessageManager.getString("label.description:"), JLabel.RIGHT));
367	0	description.setFont(JvSwingUtils.getTextAreaFont());
368	0	description.setLineWrap(true);
369	0	descriptionPanel.add(new JScrollPane(description));
370
371	0	if (!forCreate)
372		{
373	0	mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
374
375	0	JPanel startEndPanel = new JPanel();
376	0	startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
377		JLabel.RIGHT));
378	0	startEndPanel.add(start);
379	0	startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
380		JLabel.RIGHT));
381	0	startEndPanel.add(end);
382	0	mainPanel.add(startEndPanel, BorderLayout.CENTER);
383		}
384		else
385		{
386	0	mainPanel.add(descriptionPanel, BorderLayout.CENTER);
387		}
388
389		/*
390		* default feature type and group to that of the first feature supplied,
391		* or to the last feature created if not supplied (null value)
392		*/
393	0	SequenceFeature firstFeature = features.get(0);
394	0	boolean useLastDefaults = firstFeature.getType() == null;
395	0	final String featureType = useLastDefaults ? lastFeatureAdded
396		: firstFeature.getType();
397	0	final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
398		: firstFeature.getFeatureGroup();
399	0	name.setText(featureType);
400	0	group.setText(featureGroup);
401
402	0	start.setValue(new Integer(firstFeature.getBegin()));
403	0	end.setValue(new Integer(firstFeature.getEnd()));
404	0	((SpinnerNumberModel) start.getModel()).setMaximum(firstFeature.getEnd());
405	0	((SpinnerNumberModel) end.getModel()).setMinimum(firstFeature.getBegin());
406
407	0	description.setText(firstFeature.getDescription());
408	0	featureColour = fr.getFeatureStyle(featureType);
409	0	oldColour = featureColour;
410	0	updateColourButton(mainPanel, colour, oldColour);
411		}
412
413		/**
414		* Presents a dialog allowing the user to add new features, or amend or delete
415		* an existing feature. Currently this can be on
416		* <ul>
417		* <li>double-click on a sequence - Amend/Delete a selected feature at the
418		* position</li>
419		* <li>Create sequence feature(s) from pop-up menu on selected region</li>
420		* <li>Create features for pattern matches from Find</li>
421		* </ul>
422		* If the supplied feature type is null, show (and update on confirm) the type
423		* and group of the last new feature created (with initial defaults of
424		* "feature_1" and "Jalview").
425		*/
		0% Uncovered Elements: 19 (19) Complexity: 4 Complexity Density: 0.31
426	0	public void showDialog()...
427		{
428	0	Runnable okAction = forCreate ? getCreateAction() : getAmendAction();
429	0	Runnable cancelAction = getCancelAction();
430
431		/*
432		* set dialog action handlers for OK (create/Amend) and Cancel options
433		* also for Delete if applicable (when amending features)
434		*/
435	0	JvOptionPane dialog = JvOptionPane.newOptionDialog(ap.alignFrame)
436		.setResponseHandler(0, okAction)
437		.setResponseHandler(2, cancelAction);
438	0	if (!forCreate)
439		{
440	0	dialog.setResponseHandler(1, getDeleteAction());
441		}
442
443	0	String title = null;
444	0	Object[] options = null;
445	0	if (forCreate)
446		{
447	0	title = MessageManager
448		.getString("label.create_new_sequence_features");
449	0	options = new Object[] { MessageManager.getString("action.ok"),
450		MessageManager.getString("action.cancel") };
451		}
452		else
453		{
454	0	title = MessageManager.formatMessage("label.amend_delete_features",
455		new String[]
456		{ sequences.get(0).getName() });
457	0	options = new Object[] { MessageManager.getString("label.amend"),
458		MessageManager.getString("action.delete"),
459		MessageManager.getString("action.cancel") };
460		}
461
462	0	dialog.showInternalDialog(mainPanel, title,
463		JvOptionPane.YES_NO_CANCEL_OPTION,
464		JvOptionPane.PLAIN_MESSAGE, null, options,
465		MessageManager.getString("action.ok"));
466		}
467
468		/**
469		* Answers an action to run on Cancel in the dialog. This is just to remove
470		* any feature highlighting from the display. Changes in the dialog are not
471		* applied until it is dismissed with OK, Amend or Delete, so there are no
472		* updates to reset on Cancel.
473		*
474		* @return
475		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
476	0	protected Runnable getCancelAction()...
477		{
478	0	Runnable okAction = () -> {
479	0	ap.highlightSearchResults(null);
480	0	ap.paintAlignment(false, false);
481		};
482	0	return okAction;
483		}
484
485		/**
486		* Returns the action to be run on OK in the dialog when creating one or more
487		* sequence features. Note these may have a pre-supplied feature type (such as
488		* a Find pattern), or none, in which case the feature type and group default
489		* to those last added through this dialog. The action includes refreshing the
490		* Feature Settings panel (if it is open), to show any new feature type, or
491		* amended colour for an existing type.
492		*
493		* @return
494		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
495	0	protected Runnable getCreateAction()...
496		{
497	0	Runnable okAction = new Runnable()
498		{
499		boolean useLastDefaults = features.get(0).getType() == null;
500
		0% Uncovered Elements: 28 (28) Complexity: 6 Complexity Density: 0.33
501	0	@Override...
502		public void run()
503		{
504	0	final String enteredType = name.getText().trim();
505	0	final String enteredGroup = group.getText().trim();
506	0	final String enteredDescription = description.getText()
507		.replaceAll("\n", " ");
508	0	if (enteredType.length() > 0)
509		{
510		/*
511		* update default values only if creating using default values
512		*/
513	0	if (useLastDefaults)
514		{
515	0	lastFeatureAdded = enteredType;
516	0	lastFeatureGroupAdded = enteredGroup;
517		// TODO: determine if the null feature group is valid
518	0	if (lastFeatureGroupAdded.length() < 1)
519		{
520	0	lastFeatureGroupAdded = null;
521		}
522		}
523		}
524
525	0	if (enteredType.length() > 0)
526		{
527	0	for (int i = 0; i < sequences.size(); i++)
528		{
529	0	SequenceFeature sf = features.get(i);
530	0	SequenceFeature sf2 = new SequenceFeature(enteredType,
531		enteredDescription, sf.getBegin(), sf.getEnd(),
532		enteredGroup);
533	0	new FeaturesFile().parseDescriptionHTML(sf2, false);
534	0	sequences.get(i).addSequenceFeature(sf2);
535		}
536
537	0	fr.setColour(enteredType, featureColour);
538	0	fr.featuresAdded();
539
540	0	repaintPanel();
541		}
542		}
543		};
544	0	return okAction;
545		}
546
547		/**
548		* Answers the action to run on Delete in the dialog. Note this includes
549		* refreshing the Feature Settings (if open) in case the only instance of a
550		* feature type or group has been deleted.
551		*
552		* @return
553		*/
		0% Uncovered Elements: 7 (7) Complexity: 1 Complexity Density: 0.14
554	0	protected Runnable getDeleteAction()...
555		{
556	0	Runnable deleteAction = () -> {
557	0	SequenceFeature sf = features.get(featureIndex);
558	0	sequences.get(0).getDatasetSequence().deleteFeature(sf);
559	0	fr.featuresAdded();
560	0	ap.getSeqPanel().seqCanvas.highlightSearchResults(null);
561	0	ap.paintAlignment(true, true);
562		};
563	0	return deleteAction;
564		}
565
566		/**
567		* update the amend feature button dependent on the given style
568		*
569		* @param bigPanel
570		* @param col
571		* @param col
572		*/
		0% Uncovered Elements: 12 (12) Complexity: 2 Complexity Density: 0.2
573	0	protected void updateColourButton(JPanel bigPanel, JLabel colour,...
574		FeatureColourI col)
575		{
576	0	colour.removeAll();
577	0	colour.setIcon(null);
578	0	colour.setText("");
579
580	0	if (col.isSimpleColour())
581		{
582	0	colour.setToolTipText(null);
583	0	colour.setBackground(col.getColour());
584		}
585		else
586		{
587	0	colour.setBackground(bigPanel.getBackground());
588	0	colour.setForeground(Color.black);
589	0	colour.setToolTipText(FeatureSettings.getColorTooltip(col, false));
590	0	FeatureSettings.renderGraduatedColor(colour, col);
591		}
592		}
593
594		/**
595		* Show a warning message if the entered group is one that is currently hidden
596		*
597		* @param panel
598		* @param group
599		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
600	0	protected void warnIfGroupHidden(JPanel panel, String group)...
601		{
602	0	if (!fr.isGroupVisible(group))
603		{
604	0	String msg = MessageManager.formatMessage("label.warning_hidden",
605		MessageManager.getString("label.group"), group);
606	0	JvOptionPane.showMessageDialog(panel, msg, "",
607		JvOptionPane.OK_OPTION);
608		}
609		}
610
611		/**
612		* Show a warning message if the entered type is one that is currently hidden
613		*
614		* @param panel
615		* @param type
616		*/
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
617	0	protected void warnIfTypeHidden(JPanel panel, String type)...
618		{
619	0	if (fr.getRenderOrder().contains(type))
620		{
621	0	if (!fr.showFeatureOfType(type))
622		{
623	0	String msg = MessageManager.formatMessage("label.warning_hidden",
624		MessageManager.getString("label.feature_type"), type);
625	0	JvOptionPane.showMessageDialog(panel, msg, "",
626		JvOptionPane.OK_OPTION);
627		}
628		}
629		}
630
631		/**
632		* On closing the dialog - ensure feature display is turned on, to show any
633		* new features - remove highlighting of the last selected feature - repaint
634		* the panel to show any changes
635		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
636	0	protected void repaintPanel()...
637		{
638	0	ap.alignFrame.showSeqFeatures.setSelected(true);
639	0	ap.av.setShowSequenceFeatures(true);
640	0	ap.av.setSearchResults(null);
641	0	ap.paintAlignment(true, true);
642		}
643
644		/**
645		* Returns the action to be run on OK in the dialog when amending a feature.
646		* Note this may include refreshing the Feature Settings panel (if it is
647		* open), if feature type, group or colour has changed (but not for
648		* description or extent).
649		*
650		* @return
651		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
652	0	protected Runnable getAmendAction()...
653		{
654	0	Runnable okAction = new Runnable()
655		{
656		boolean useLastDefaults = features.get(0).getType() == null;
657
658		String featureType = name.getText();
659
660		String featureGroup = group.getText();
		0% Uncovered Elements: 34 (34) Complexity: 6 Complexity Density: 0.23
661	0	@Override...
662		public void run()
663		{
664	0	final String enteredType = name.getText().trim();
665	0	final String enteredGroup = group.getText().trim();
666	0	final String enteredDescription = description.getText()
667		.replaceAll("\n", " ");
668	0	if (enteredType.length() > 0)
669
670		{
671		/*
672		* update default values only if creating using default values
673		*/
674	0	if (useLastDefaults)
675		{
676	0	lastFeatureAdded = enteredType;
677	0	lastFeatureGroupAdded = enteredGroup;
678		// TODO: determine if the null feature group is valid
679	0	if (lastFeatureGroupAdded.length() < 1)
680		{
681	0	lastFeatureGroupAdded = null;
682		}
683		}
684		}
685
686	0	SequenceFeature sf = features.get(featureIndex);
687
688		/*
689		* Need to refresh Feature Settings if type, group or colour changed;
690		* note we don't force the feature to be visible - the user has been
691		* warned if a hidden feature type or group was entered
692		*/
693	0	boolean refreshSettings = (!featureType.equals(enteredType)
694		|| !featureGroup.equals(enteredGroup));
695	0	refreshSettings |= (featureColour != oldColour);
696	0	fr.setColour(enteredType, featureColour);
697	0	int newBegin = sf.begin;
698	0	int newEnd = sf.end;
699	0	try
700		{
701	0	newBegin = ((Integer) start.getValue()).intValue();
702	0	newEnd = ((Integer) end.getValue()).intValue();
703		} catch (NumberFormatException ex)
704		{
705		// JSpinner doesn't accept invalid format data :-)
706		}
707
708		/*
709		* 'amend' the feature by deleting it and adding a new one
710		* (to ensure integrity of SequenceFeatures data store)
711		* note this dialog only updates one sequence at a time
712		*/
713	0	sequences.get(0).deleteFeature(sf);
714	0	SequenceFeature newSf = new SequenceFeature(sf, enteredType,
715		newBegin, newEnd, enteredGroup, sf.getScore());
716	0	newSf.setDescription(enteredDescription);
717	0	new FeaturesFile().parseDescriptionHTML(newSf, false);
718	0	sequences.get(0).addSequenceFeature(newSf);
719
720	0	if (refreshSettings)
721		{
722	0	fr.featuresAdded();
723		}
724	0	repaintPanel();
725		}
726		};
727	0	return okAction;
728		}
729
730		}