Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationLabels	56	307	111	0.00%	Show methods

Class AnnotationLabels

Class AnnotationLabels	Line # 56	Total Statements 307	Complexity 111	TOTAL Coverage 0.00%
AnnotationLabels(AlignmentPanel)   AnnotationLabels(AlignmentPanel)	101101	5.05	1.01	0.0 0.00%
AnnotationLabels(AlignViewport)   AnnotationLabels(AlignViewport)	110110	1.01	1.01	0.0 0.00%
setScrollOffset(int,boolean) : void   setScrollOffset(int,boolean) : void	115115	3.03	2.02	0.0 0.00%
getSelectedRow(int) : int   getSelectedRow(int) : int	130130	14.014	5.05	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	159159	26.026	12.012	0.0 0.00%
refresh() : void   refresh() : void	220220	4.04	1.01	0.0 0.00%
editLabelDescription(AlignmentAnnotation) : boolean   editLabelDescription(AlignmentAnnotation) : boolean	229229	14.014	2.02	0.0 0.00%
mouseMoved(MouseEvent) : void   mouseMoved(MouseEvent) : void	264264	10.010	5.05	0.0 0.00%
cancelDrag() : void   cancelDrag() : void	307307	2.02	1.01	0.0 0.00%
mouseDragged(MouseEvent) : void   mouseDragged(MouseEvent) : void	313313	28.028	7.07	0.0 0.00%
mouseClicked(MouseEvent) : void   mouseClicked(MouseEvent) : void	375375	0.00	1.01	-1.0 -1.0 -
mouseReleased(MouseEvent) : void   mouseReleased(MouseEvent) : void	380380	16.016	6.06	0.0 0.00%
mouseEntered(MouseEvent) : void   mouseEntered(MouseEvent) : void	413413	4.04	4.04	0.0 0.00%
mouseExited(MouseEvent) : void   mouseExited(MouseEvent) : void	425425	6.06	3.03	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	503503	2.02	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	542542	4.04	2.02	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	566566	2.02	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	586586	2.02	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	608608	3.03	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	632632	3.03	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	656656	3.03	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	681681	4.04	1.01	0.0 0.00%
mousePressed(MouseEvent) : void   mousePressed(MouseEvent) : void	444444	111.0111	31.031	0.0 0.00%
copy_annotseqtoclipboard(SequenceI) : void   copy_annotseqtoclipboard(SequenceI) : void	836836	6.06	4.04	0.0 0.00%
update(Graphics) : void   update(Graphics) : void	853853	1.01	1.01	0.0 0.00%
paint(Graphics) : void   paint(Graphics) : void	859859	6.06	4.04	0.0 0.00%
drawComponent(Graphics,int) : void   drawComponent(Graphics,int) : void	874874	27.027	11.011	0.0 0.00%

 

Contributing tests

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.appletgui;
22
23		import jalview.analysis.AlignmentUtils;
24		import jalview.datamodel.AlignmentAnnotation;
25		import jalview.datamodel.Annotation;
26		import jalview.datamodel.HiddenColumns;
27		import jalview.datamodel.SequenceGroup;
28		import jalview.datamodel.SequenceI;
29		import jalview.util.MessageManager;
30		import jalview.util.ParseHtmlBodyAndLinks;
31
32		import java.awt.Checkbox;
33		import java.awt.CheckboxMenuItem;
34		import java.awt.Color;
35		import java.awt.Cursor;
36		import java.awt.Dimension;
37		import java.awt.FlowLayout;
38		import java.awt.FontMetrics;
39		import java.awt.Frame;
40		import java.awt.Graphics;
41		import java.awt.Image;
42		import java.awt.MenuItem;
43		import java.awt.Panel;
44		import java.awt.PopupMenu;
45		import java.awt.event.ActionEvent;
46		import java.awt.event.ActionListener;
47		import java.awt.event.InputEvent;
48		import java.awt.event.ItemEvent;
49		import java.awt.event.ItemListener;
50		import java.awt.event.MouseEvent;
51		import java.awt.event.MouseListener;
52		import java.awt.event.MouseMotionListener;
53		import java.util.Arrays;
54		import java.util.Collections;
55
		0% Uncovered Elements: 466 (466) Complexity: 111 Complexity Density: 0.36
56		public class AnnotationLabels extends Panel
57		implements ActionListener, MouseListener, MouseMotionListener
58		{
59		Image image;
60
61		/**
62		* width in pixels within which height adjuster arrows are shown and active
63		*/
64		private static final int HEIGHT_ADJUSTER_WIDTH = 50;
65
66		/**
67		* height in pixels for allowing height adjuster to be active
68		*/
69		private static int HEIGHT_ADJUSTER_HEIGHT = 10;
70
71		boolean active = false;
72
73		AlignmentPanel ap;
74
75		AlignViewport av;
76
77		boolean resizing = false;
78
79		int oldY, mouseX;
80
81		static String ADDNEW = "Add New Row";
82
83		static String EDITNAME = "Edit Label/Description";
84
85		static String HIDE = "Hide This Row";
86
87		static String SHOWALL = "Show All Hidden Rows";
88
89		static String OUTPUT_TEXT = "Show Values In Textbox";
90
91		static String COPYCONS_SEQ = "Copy Consensus Sequence";
92
93		int scrollOffset = 0;
94
95		int selectedRow = -1;
96
97		Tooltip tooltip;
98
99		private boolean hasHiddenRows;
100
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
101	0	public AnnotationLabels(AlignmentPanel ap)...
102		{
103	0	this.ap = ap;
104	0	this.av = ap.av;
105	0	setLayout(null);
106	0	addMouseListener(this);
107	0	addMouseMotionListener(this);
108		}
109
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	public AnnotationLabels(AlignViewport av)...
111		{
112	0	this.av = av;
113		}
114
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
115	0	public void setScrollOffset(int y, boolean repaint)...
116		{
117	0	scrollOffset = y;
118	0	if (repaint)
119		{
120	0	repaint();
121		}
122		}
123
124		/**
125		*
126		* @param y
127		* @return -2 if no rows are visible at all, -1 if no visible rows were
128		* selected
129		*/
		0% Uncovered Elements: 22 (22) Complexity: 5 Complexity Density: 0.36
130	0	int getSelectedRow(int y)...
131		{
132	0	int row = -2;
133	0	AlignmentAnnotation[] aa = ap.av.getAlignment()
134		.getAlignmentAnnotation();
135
136	0	if (aa == null)
137		{
138	0	return row;
139		}
140	0	int height = 0;
141	0	for (int i = 0; i < aa.length; i++)
142		{
143	0	row = -1;
144	0	if (!aa[i].visible)
145		{
146	0	continue;
147		}
148	0	height += aa[i].height;
149	0	if (y < height)
150		{
151	0	row = i;
152	0	break;
153		}
154		}
155
156	0	return row;
157		}
158
		0% Uncovered Elements: 48 (48) Complexity: 12 Complexity Density: 0.46
159	0	@Override...
160		public void actionPerformed(ActionEvent evt)
161		{
162	0	AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
163
164	0	if (evt.getActionCommand().equals(ADDNEW))
165		{
166	0	AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
167		new Annotation[ap.av.getAlignment().getWidth()]);
168
169	0	if (!editLabelDescription(newAnnotation))
170		{
171	0	return;
172		}
173
174	0	ap.av.getAlignment().addAnnotation(newAnnotation);
175	0	ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
176		}
177	0	else if (evt.getActionCommand().equals(EDITNAME))
178		{
179	0	editLabelDescription(aa[selectedRow]);
180		}
181	0	else if (evt.getActionCommand().equals(HIDE))
182		{
183	0	aa[selectedRow].visible = false;
184		}
185	0	else if (evt.getActionCommand().equals(SHOWALL))
186		{
187	0	for (int i = 0; i < aa.length; i++)
188		{
189	0	aa[i].visible = (aa[i].annotations == null) ? false : true;
190		}
191		}
192	0	else if (evt.getActionCommand().equals(OUTPUT_TEXT))
193		{
194	0	CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
195		ap.alignFrame);
196	0	Frame frame = new Frame();
197	0	frame.add(cap);
198	0	jalview.bin.JalviewLite.addFrame(frame,
199		ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
200		100);
201	0	cap.setText(aa[selectedRow].toString());
202		}
203	0	else if (evt.getActionCommand().equals(COPYCONS_SEQ))
204		{
205	0	SequenceGroup group = aa[selectedRow].groupRef;
206	0	SequenceI cons = group == null ? av.getConsensusSeq()
207		: group.getConsensusSeq();
208	0	if (cons != null)
209		{
210	0	copy_annotseqtoclipboard(cons);
211		}
212
213		}
214	0	refresh();
215		}
216
217		/**
218		* Adjust size and repaint
219		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
220	0	protected void refresh()...
221		{
222	0	ap.annotationPanel.adjustPanelHeight();
223	0	setSize(getSize().width, ap.annotationPanel.getSize().height);
224	0	ap.validate();
225		// TODO: only paint if we needed to
226	0	ap.paintAlignment(true, true);
227		}
228
		0% Uncovered Elements: 16 (16) Complexity: 2 Complexity Density: 0.14
229	0	boolean editLabelDescription(AlignmentAnnotation annotation)...
230		{
231	0	Checkbox padGaps = new Checkbox(
232		"Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
233		annotation.padGaps);
234
235	0	EditNameDialog dialog = new EditNameDialog(annotation.label,
236		annotation.description, " Annotation Label",
237		"Annotation Description", ap.alignFrame,
238		"Edit Annotation Name / Description", 500, 180, false);
239
240	0	Panel empty = new Panel(new FlowLayout());
241	0	empty.add(padGaps);
242	0	dialog.add(empty);
243	0	dialog.pack();
244
245	0	dialog.setVisible(true);
246
247	0	if (dialog.accept)
248		{
249	0	annotation.label = dialog.getName();
250	0	annotation.description = dialog.getDescription();
251	0	annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
252	0	repaint();
253	0	return true;
254		}
255		else
256		{
257	0	return false;
258		}
259
260		}
261
262		boolean resizePanel = false;
263
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.5
264	0	@Override...
265		public void mouseMoved(MouseEvent evt)
266		{
267	0	resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
268		&& evt.getX() < HEIGHT_ADJUSTER_WIDTH;
269	0	setCursor(Cursor.getPredefinedCursor(
270	0	resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
271	0	int row = getSelectedRow(evt.getY() + scrollOffset);
272
273	0	if (row > -1)
274		{
275	0	ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
276		av.getAlignment().getAlignmentAnnotation()[row]
277		.getDescription(true),
278		true, "\n");
279	0	if (tooltip == null)
280		{
281	0	tooltip = new Tooltip(phb.getNonHtmlContent(), this);
282		}
283		else
284		{
285	0	tooltip.setTip(phb.getNonHtmlContent());
286		}
287		}
288	0	else if (tooltip != null)
289		{
290	0	tooltip.setTip("");
291		}
292		}
293
294		/**
295		* curent drag position
296		*/
297		MouseEvent dragEvent = null;
298
299		/**
300		* flag to indicate drag events should be ignored
301		*/
302		private boolean dragCancelled = false;
303
304		/**
305		* clear any drag events in progress
306		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
307	0	public void cancelDrag()...
308		{
309	0	dragEvent = null;
310	0	dragCancelled = true;
311		}
312
		0% Uncovered Elements: 38 (38) Complexity: 7 Complexity Density: 0.25
313	0	@Override...
314		public void mouseDragged(MouseEvent evt)
315		{
316	0	if (dragCancelled)
317		{
318	0	return;
319		}
320	0	;
321	0	dragEvent = evt;
322
323	0	if (resizePanel)
324		{
325	0	Dimension d = ap.annotationPanelHolder.getSize(),
326		e = ap.annotationSpaceFillerHolder.getSize(),
327		f = ap.seqPanelHolder.getSize();
328	0	int dif = evt.getY() - oldY;
329
330	0	dif /= ap.av.getCharHeight();
331	0	dif *= ap.av.getCharHeight();
332
333	0	if ((d.height - dif) > 20 && (f.height + dif) > 20)
334		{
335	0	ap.annotationPanel.setSize(d.width, d.height - dif);
336	0	setSize(new Dimension(e.width, d.height - dif));
337	0	ap.annotationSpaceFillerHolder
338		.setSize(new Dimension(e.width, d.height - dif));
339	0	ap.annotationPanelHolder
340		.setSize(new Dimension(d.width, d.height - dif));
341	0	ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
342		av.calcPanelHeight());
343	0	f.height += dif;
344	0	ap.seqPanelHolder.setPreferredSize(f);
345	0	ap.setScrollValues(av.getRanges().getStartRes(),
346		av.getRanges().getStartSeq());
347	0	ap.validate();
348		// ap.paintAlignment(true);
349	0	ap.addNotify();
350		}
351
352		}
353		else
354		{
355	0	int diff;
356	0	if ((diff = 6 - evt.getY()) > 0)
357		{
358		// nudge scroll up
359	0	ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
360	0	ap.adjustmentValueChanged(null);
361
362		}
363	0	else if ((0 < (diff = 6
364		- ap.annotationSpaceFillerHolder.getSize().height
365		+ evt.getY())))
366		{
367		// nudge scroll down
368	0	ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
369	0	ap.adjustmentValueChanged(null);
370		}
371	0	repaint();
372		}
373		}
374
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
375	0	@Override...
376		public void mouseClicked(MouseEvent evt)
377		{
378		}
379
		0% Uncovered Elements: 22 (22) Complexity: 6 Complexity Density: 0.38
380	0	@Override...
381		public void mouseReleased(MouseEvent evt)
382		{
383	0	if (!resizePanel && !dragCancelled)
384		{
385	0	int start = selectedRow;
386
387	0	int end = getSelectedRow(evt.getY() + scrollOffset);
388
389	0	if (start > -1 && start != end)
390		{
391		// Swap these annotations
392	0	AlignmentAnnotation startAA = ap.av.getAlignment()
393		.getAlignmentAnnotation()[start];
394	0	if (end == -1)
395		{
396	0	end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
397		}
398	0	AlignmentAnnotation endAA = ap.av.getAlignment()
399		.getAlignmentAnnotation()[end];
400
401	0	ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
402	0	ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
403		}
404		}
405	0	resizePanel = false;
406	0	dragEvent = null;
407	0	dragCancelled = false;
408	0	setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
409	0	repaint();
410	0	ap.annotationPanel.repaint();
411		}
412
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 1
413	0	@Override...
414		public void mouseEntered(MouseEvent evt)
415		{
416	0	if (evt.getY() < 10 && evt.getX() < 14)
417		{
418	0	resizePanel = true;
419	0	repaint();
420		}
421	0	setCursor(Cursor.getPredefinedCursor(
422	0	resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
423		}
424
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
425	0	@Override...
426		public void mouseExited(MouseEvent evt)
427		{
428	0	dragCancelled = false;
429
430	0	if (dragEvent == null)
431		{
432	0	resizePanel = false;
433		}
434		else
435		{
436	0	if (!resizePanel)
437		{
438	0	dragEvent = null;
439		}
440		}
441	0	repaint();
442		}
443
		0% Uncovered Elements: 159 (159) Complexity: 31 Complexity Density: 0.28
444	0	@Override...
445		public void mousePressed(MouseEvent evt)
446		{
447	0	oldY = evt.getY();
448	0	if (resizePanel)
449		{
450	0	return;
451		}
452	0	dragCancelled = false;
453		// todo: move below to mouseClicked ?
454	0	selectedRow = getSelectedRow(evt.getY() + scrollOffset);
455
456	0	AlignmentAnnotation[] aa = ap.av.getAlignment()
457		.getAlignmentAnnotation();
458
459		// DETECT RIGHT MOUSE BUTTON IN AWT
460	0	if ((evt.getModifiersEx()
461		& InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
462		{
463
464	0	PopupMenu popup = new PopupMenu(
465		MessageManager.getString("label.annotations"));
466
467	0	MenuItem item = new MenuItem(ADDNEW);
468	0	item.addActionListener(this);
469	0	popup.add(item);
470	0	if (selectedRow < 0)
471		{
472		// this never happens at moment: - see comment on JAL-563
473	0	if (hasHiddenRows)
474		{
475	0	item = new MenuItem(SHOWALL);
476	0	item.addActionListener(this);
477	0	popup.add(item);
478		}
479	0	this.add(popup);
480	0	popup.show(this, evt.getX(), evt.getY());
481	0	return;
482		}
483		// add the rest if there are actually rows to show
484	0	item = new MenuItem(EDITNAME);
485	0	item.addActionListener(this);
486	0	popup.add(item);
487	0	item = new MenuItem(HIDE);
488	0	item.addActionListener(this);
489	0	popup.add(item);
490
491		/*
492		* Hide all <label>:
493		*/
494	0	if (selectedRow < aa.length)
495		{
496	0	if (aa[selectedRow].sequenceRef != null)
497		{
498	0	final String label = aa[selectedRow].label;
499	0	MenuItem hideType = new MenuItem(
500		MessageManager.getString("label.hide_all") + " " + label);
501	0	hideType.addActionListener(new ActionListener()
502		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
503	0	@Override...
504		public void actionPerformed(ActionEvent e)
505		{
506	0	AlignmentUtils.showOrHideSequenceAnnotations(
507		ap.av.getAlignment(), Collections.singleton(label),
508		null, false, false);
509	0	refresh();
510		}
511		});
512	0	popup.add(hideType);
513		}
514		}
515
516	0	if (hasHiddenRows)
517		{
518	0	item = new MenuItem(SHOWALL);
519	0	item.addActionListener(this);
520	0	popup.add(item);
521		}
522	0	this.add(popup);
523	0	item = new MenuItem(OUTPUT_TEXT);
524	0	item.addActionListener(this);
525	0	popup.add(item);
526	0	if (selectedRow < aa.length)
527		{
528	0	if (aa[selectedRow].autoCalculated)
529		{
530	0	if (aa[selectedRow].label.indexOf("Consensus") > -1)
531		{
532	0	popup.addSeparator();
533	0	final CheckboxMenuItem cbmi = new CheckboxMenuItem(
534		MessageManager.getString("label.ignore_gaps_consensus"),
535	0	(aa[selectedRow].groupRef != null)
536		? aa[selectedRow].groupRef
537		.getIgnoreGapsConsensus()
538		: ap.av.isIgnoreGapsConsensus());
539	0	final AlignmentAnnotation aaa = aa[selectedRow];
540	0	cbmi.addItemListener(new ItemListener()
541		{
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
542	0	@Override...
543		public void itemStateChanged(ItemEvent e)
544		{
545	0	if (aaa.groupRef != null)
546		{
547		// TODO: pass on reference to ap so the view can be updated.
548	0	aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
549		}
550		else
551		{
552	0	ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
553		}
554	0	ap.paintAlignment(true, true);
555		}
556		});
557	0	popup.add(cbmi);
558	0	if (aaa.groupRef != null)
559		{
560	0	final CheckboxMenuItem chist = new CheckboxMenuItem(
561		MessageManager
562		.getString("label.show_group_histogram"),
563		aa[selectedRow].groupRef.isShowConsensusHistogram());
564	0	chist.addItemListener(new ItemListener()
565		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
566	0	@Override...
567		public void itemStateChanged(ItemEvent e)
568		{
569		// TODO: pass on reference
570		// to ap
571		// so the
572		// view
573		// can be
574		// updated.
575	0	aaa.groupRef.setShowConsensusHistogram(chist.getState());
576	0	ap.repaint();
577		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
578		}
579		});
580	0	popup.add(chist);
581	0	final CheckboxMenuItem cprofl = new CheckboxMenuItem(
582		MessageManager.getString("label.show_group_logo"),
583		aa[selectedRow].groupRef.isShowSequenceLogo());
584	0	cprofl.addItemListener(new ItemListener()
585		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
586	0	@Override...
587		public void itemStateChanged(ItemEvent e)
588		{
589		// TODO: pass on reference
590		// to ap
591		// so the
592		// view
593		// can be
594		// updated.
595	0	aaa.groupRef.setshowSequenceLogo(cprofl.getState());
596	0	ap.repaint();
597		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
598		}
599		});
600
601	0	popup.add(cprofl);
602	0	final CheckboxMenuItem cprofn = new CheckboxMenuItem(
603		MessageManager
604		.getString("label.normalise_group_logo"),
605		aa[selectedRow].groupRef.isNormaliseSequenceLogo());
606	0	cprofn.addItemListener(new ItemListener()
607		{
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
608	0	@Override...
609		public void itemStateChanged(ItemEvent e)
610		{
611		// TODO: pass on reference
612		// to ap
613		// so the
614		// view
615		// can be
616		// updated.
617	0	aaa.groupRef.setshowSequenceLogo(true);
618	0	aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
619	0	ap.repaint();
620		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
621		}
622		});
623	0	popup.add(cprofn);
624		}
625		else
626		{
627	0	final CheckboxMenuItem chist = new CheckboxMenuItem(
628		MessageManager.getString("label.show_histogram"),
629		av.isShowConsensusHistogram());
630	0	chist.addItemListener(new ItemListener()
631		{
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
632	0	@Override...
633		public void itemStateChanged(ItemEvent e)
634		{
635		// TODO: pass on reference
636		// to ap
637		// so the
638		// view
639		// can be
640		// updated.
641	0	av.setShowConsensusHistogram(chist.getState());
642	0	ap.alignFrame.showConsensusHistogram
643		.setState(chist.getState()); // TODO: implement
644		// ap.updateGUI()/alignFrame.updateGUI
645		// for applet
646	0	ap.repaint();
647		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
648		}
649		});
650	0	popup.add(chist);
651	0	final CheckboxMenuItem cprof = new CheckboxMenuItem(
652		MessageManager.getString("label.show_logo"),
653		av.isShowSequenceLogo());
654	0	cprof.addItemListener(new ItemListener()
655		{
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
656	0	@Override...
657		public void itemStateChanged(ItemEvent e)
658		{
659		// TODO: pass on reference
660		// to ap
661		// so the
662		// view
663		// can be
664		// updated.
665	0	av.setShowSequenceLogo(cprof.getState());
666	0	ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
667		// implement
668		// ap.updateGUI()/alignFrame.updateGUI
669		// for
670		// applet
671	0	ap.repaint();
672		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
673		}
674		});
675	0	popup.add(cprof);
676	0	final CheckboxMenuItem cprofn = new CheckboxMenuItem(
677		MessageManager.getString("label.normalise_logo"),
678		av.isNormaliseSequenceLogo());
679	0	cprofn.addItemListener(new ItemListener()
680		{
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
681	0	@Override...
682		public void itemStateChanged(ItemEvent e)
683		{
684		// TODO: pass on reference
685		// to ap
686		// so the
687		// view
688		// can be
689		// updated.
690	0	av.setShowSequenceLogo(true);
691	0	ap.alignFrame.normSequenceLogo
692		.setState(cprofn.getState()); // TODO:
693		// implement
694		// ap.updateGUI()/alignFrame.updateGUI
695		// for
696		// applet
697	0	av.setNormaliseSequenceLogo(cprofn.getState());
698	0	ap.repaint();
699		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
700		}
701		});
702	0	popup.add(cprofn);
703		}
704
705	0	item = new MenuItem(COPYCONS_SEQ);
706	0	item.addActionListener(this);
707	0	popup.add(item);
708		}
709		}
710		}
711	0	popup.show(this, evt.getX(), evt.getY());
712		}
713		else
714		{
715		// selection action.
716	0	if (selectedRow > -1 && selectedRow < aa.length)
717		{
718	0	if (aa[selectedRow].groupRef != null)
719		{
720	0	if (evt.getClickCount() >= 2)
721		{
722		// todo: make the ap scroll to the selection - not necessary, first
723		// click highlights/scrolls, second selects
724	0	ap.seqPanel.ap.idPanel.highlightSearchResults(null);
725		// process modifiers
726	0	SequenceGroup sg = ap.av.getSelectionGroup();
727	0	if (sg == null || sg == aa[selectedRow].groupRef
728		|| !(jalview.util.Platform.isControlDown(evt)
729		|| evt.isShiftDown()))
730		{
731	0	if (jalview.util.Platform.isControlDown(evt)
732		|| evt.isShiftDown())
733		{
734		// clone a new selection group from the associated group
735	0	ap.av.setSelectionGroup(
736		new SequenceGroup(aa[selectedRow].groupRef));
737		}
738		else
739		{
740		// set selection to the associated group so it can be edited
741	0	ap.av.setSelectionGroup(aa[selectedRow].groupRef);
742		}
743		}
744		else
745		{
746		// modify current selection with associated group
747	0	int remainToAdd = aa[selectedRow].groupRef.getSize();
748	0	for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
749		{
750	0	if (jalview.util.Platform.isControlDown(evt))
751		{
752	0	sg.addOrRemove(sgs, --remainToAdd == 0);
753		}
754		else
755		{
756		// notionally, we should also add intermediate sequences from
757		// last added sequence ?
758	0	sg.addSequence(sgs, --remainToAdd == 0);
759		}
760		}
761		}
762	0	ap.paintAlignment(false, false);
763	0	PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
764	0	ap.av.sendSelection();
765		}
766		else
767		{
768	0	ap.seqPanel.ap.idPanel.highlightSearchResults(
769		aa[selectedRow].groupRef.getSequences(null));
770		}
771	0	return;
772		}
773	0	else if (aa[selectedRow].sequenceRef != null)
774		{
775	0	if (evt.getClickCount() == 1)
776		{
777	0	ap.seqPanel.ap.idPanel
778		.highlightSearchResults(Arrays.asList(new SequenceI[]
779		{ aa[selectedRow].sequenceRef }));
780		}
781	0	else if (evt.getClickCount() >= 2)
782		{
783	0	ap.seqPanel.ap.idPanel.highlightSearchResults(null);
784	0	SequenceGroup sg = ap.av.getSelectionGroup();
785	0	if (sg != null)
786		{
787		// we make a copy rather than edit the current selection if no
788		// modifiers pressed
789		// see Enhancement JAL-1557
790	0	if (!(jalview.util.Platform.isControlDown(evt)
791		|| evt.isShiftDown()))
792		{
793	0	sg = new SequenceGroup(sg);
794	0	sg.clear();
795	0	sg.addSequence(aa[selectedRow].sequenceRef, false);
796		}
797		else
798		{
799	0	if (jalview.util.Platform.isControlDown(evt))
800		{
801	0	sg.addOrRemove(aa[selectedRow].sequenceRef, true);
802		}
803		else
804		{
805		// notionally, we should also add intermediate sequences from
806		// last added sequence ?
807	0	sg.addSequence(aa[selectedRow].sequenceRef, true);
808		}
809		}
810		}
811		else
812		{
813	0	sg = new SequenceGroup();
814	0	sg.setStartRes(0);
815	0	sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
816	0	sg.addSequence(aa[selectedRow].sequenceRef, false);
817		}
818	0	ap.av.setSelectionGroup(sg);
819	0	ap.paintAlignment(false, false);
820	0	PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
821	0	ap.av.sendSelection();
822		}
823
824		}
825		}
826
827		}
828		}
829
830		/**
831		* DOCUMENT ME!
832		*
833		* @param e
834		* DOCUMENT ME!
835		*/
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
836	0	protected void copy_annotseqtoclipboard(SequenceI sq)...
837		{
838	0	if (sq == null || sq.getLength() < 1)
839		{
840	0	return;
841		}
842	0	jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
843	0	jalview.appletgui.AlignFrame.copiedSequences
844		.append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd()
845		+ "\t" + sq.getSequenceAsString() + "\n");
846	0	if (av.hasHiddenColumns())
847		{
848	0	jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns(
849		av.getAlignment().getHiddenColumns());
850		}
851		}
852
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
853	0	@Override...
854		public void update(Graphics g)
855		{
856	0	paint(g);
857		}
858
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 0.67
859	0	@Override...
860		public void paint(Graphics g)
861		{
862	0	int w = getSize().width;
863	0	int h = getSize().height;
864	0	if (image == null || w != image.getWidth(this)
865		|| h != image.getHeight(this))
866		{
867	0	image = createImage(w, ap.annotationPanel.getSize().height);
868		}
869
870	0	drawComponent(image.getGraphics(), w);
871	0	g.drawImage(image, 0, 0, this);
872		}
873
		0% Uncovered Elements: 37 (37) Complexity: 11 Complexity Density: 0.41
874	0	public void drawComponent(Graphics g, int width)...
875		{
876	0	g.setFont(av.getFont());
877	0	FontMetrics fm = g.getFontMetrics(av.getFont());
878	0	g.setColor(Color.white);
879	0	g.fillRect(0, 0, getSize().width, getSize().height);
880
881	0	g.translate(0, -scrollOffset);
882	0	g.setColor(Color.black);
883
884	0	AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
885	0	int y = 0, fy = g.getFont().getSize();
886	0	int x = 0, offset;
887
888	0	if (aa != null)
889		{
890	0	hasHiddenRows = false;
891	0	for (int i = 0; i < aa.length; i++)
892		{
893	0	if (!aa[i].visible)
894		{
895	0	hasHiddenRows = true;
896	0	continue;
897		}
898
899	0	x = width - fm.stringWidth(aa[i].label) - 3;
900
901	0	y += aa[i].height;
902	0	offset = -(aa[i].height - fy) / 2;
903
904	0	g.drawString(aa[i].label, x, y + offset);
905		}
906		}
907	0	g.translate(0, +scrollOffset);
908
909	0	if (!resizePanel && !dragCancelled && dragEvent != null && aa != null)
910		{
911	0	g.setColor(Color.lightGray);
912	0	g.drawString(aa[selectedRow].label, dragEvent.getX(),
913		dragEvent.getY());
914		}
915
916	0	if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
917		{
918	0	g.setColor(Color.black);
919	0	g.drawString(MessageManager.getString("label.right_click"), 2, 8);
920	0	g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
921		18);
922		}
923		}
924		}