Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AnnotationLabels	56	308	111	0.00%	Show methods

Class AnnotationLabels

Class AnnotationLabels	Line # 56	Total Statements 308	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	5.05	1.01	0.0 0.00%
editLabelDescription(AlignmentAnnotation) : boolean   editLabelDescription(AlignmentAnnotation) : boolean	230230	14.014	2.02	0.0 0.00%
mouseMoved(MouseEvent) : void   mouseMoved(MouseEvent) : void	265265	10.010	5.05	0.0 0.00%
cancelDrag() : void   cancelDrag() : void	308308	2.02	1.01	0.0 0.00%
mouseDragged(MouseEvent) : void   mouseDragged(MouseEvent) : void	314314	28.028	7.07	0.0 0.00%
mouseClicked(MouseEvent) : void   mouseClicked(MouseEvent) : void	376376	0.00	1.01	-1.0 -1.0 -
mouseReleased(MouseEvent) : void   mouseReleased(MouseEvent) : void	381381	16.016	6.06	0.0 0.00%
mouseEntered(MouseEvent) : void   mouseEntered(MouseEvent) : void	414414	4.04	4.04	0.0 0.00%
mouseExited(MouseEvent) : void   mouseExited(MouseEvent) : void	426426	6.06	3.03	0.0 0.00%
actionPerformed(ActionEvent) : void   actionPerformed(ActionEvent) : void	504504	2.02	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	543543	4.04	2.02	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	567567	2.02	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	587587	2.02	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	609609	3.03	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	633633	3.03	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	657657	3.03	1.01	0.0 0.00%
itemStateChanged(ItemEvent) : void   itemStateChanged(ItemEvent) : void	682682	4.04	1.01	0.0 0.00%
mousePressed(MouseEvent) : void   mousePressed(MouseEvent) : void	445445	111.0111	31.031	0.0 0.00%
copy_annotseqtoclipboard(SequenceI) : void   copy_annotseqtoclipboard(SequenceI) : void	837837	6.06	4.04	0.0 0.00%
update(Graphics) : void   update(Graphics) : void	854854	1.01	1.01	0.0 0.00%
paint(Graphics) : void   paint(Graphics) : void	860860	6.06	4.04	0.0 0.00%
drawComponent(Graphics,int) : void   drawComponent(Graphics,int) : void	875875	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: 467 (467) 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: 5 (5) Complexity: 1 Complexity Density: 0.2
220	0	protected void refresh()...
221		{
222	0	ap.updateAnnotation();
223	0	ap.annotationPanel.adjustPanelHeight();
224	0	setSize(getSize().width, ap.annotationPanel.getSize().height);
225	0	ap.validate();
226		// TODO: only paint if we needed to
227	0	ap.paintAlignment(true, true);
228		}
229
		0% Uncovered Elements: 16 (16) Complexity: 2 Complexity Density: 0.14
230	0	boolean editLabelDescription(AlignmentAnnotation annotation)...
231		{
232	0	Checkbox padGaps = new Checkbox(
233		"Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
234		annotation.padGaps);
235
236	0	EditNameDialog dialog = new EditNameDialog(annotation.label,
237		annotation.description, " Annotation Label",
238		"Annotation Description", ap.alignFrame,
239		"Edit Annotation Name / Description", 500, 180, false);
240
241	0	Panel empty = new Panel(new FlowLayout());
242	0	empty.add(padGaps);
243	0	dialog.add(empty);
244	0	dialog.pack();
245
246	0	dialog.setVisible(true);
247
248	0	if (dialog.accept)
249		{
250	0	annotation.label = dialog.getName();
251	0	annotation.description = dialog.getDescription();
252	0	annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
253	0	repaint();
254	0	return true;
255		}
256		else
257		{
258	0	return false;
259		}
260
261		}
262
263		boolean resizePanel = false;
264
		0% Uncovered Elements: 18 (18) Complexity: 5 Complexity Density: 0.5
265	0	@Override...
266		public void mouseMoved(MouseEvent evt)
267		{
268	0	resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
269		&& evt.getX() < HEIGHT_ADJUSTER_WIDTH;
270	0	setCursor(Cursor.getPredefinedCursor(
271	0	resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
272	0	int row = getSelectedRow(evt.getY() + scrollOffset);
273
274	0	if (row > -1)
275		{
276	0	ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
277		av.getAlignment().getAlignmentAnnotation()[row]
278		.getDescription(true),
279		true, "\n");
280	0	if (tooltip == null)
281		{
282	0	tooltip = new Tooltip(phb.getNonHtmlContent(), this);
283		}
284		else
285		{
286	0	tooltip.setTip(phb.getNonHtmlContent());
287		}
288		}
289	0	else if (tooltip != null)
290		{
291	0	tooltip.setTip("");
292		}
293		}
294
295		/**
296		* curent drag position
297		*/
298		MouseEvent dragEvent = null;
299
300		/**
301		* flag to indicate drag events should be ignored
302		*/
303		private boolean dragCancelled = false;
304
305		/**
306		* clear any drag events in progress
307		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
308	0	public void cancelDrag()...
309		{
310	0	dragEvent = null;
311	0	dragCancelled = true;
312		}
313
		0% Uncovered Elements: 38 (38) Complexity: 7 Complexity Density: 0.25
314	0	@Override...
315		public void mouseDragged(MouseEvent evt)
316		{
317	0	if (dragCancelled)
318		{
319	0	return;
320		}
321	0	;
322	0	dragEvent = evt;
323
324	0	if (resizePanel)
325		{
326	0	Dimension d = ap.annotationPanelHolder.getSize(),
327		e = ap.annotationSpaceFillerHolder.getSize(),
328		f = ap.seqPanelHolder.getSize();
329	0	int dif = evt.getY() - oldY;
330
331	0	dif /= ap.av.getCharHeight();
332	0	dif *= ap.av.getCharHeight();
333
334	0	if ((d.height - dif) > 20 && (f.height + dif) > 20)
335		{
336	0	ap.annotationPanel.setSize(d.width, d.height - dif);
337	0	setSize(new Dimension(e.width, d.height - dif));
338	0	ap.annotationSpaceFillerHolder
339		.setSize(new Dimension(e.width, d.height - dif));
340	0	ap.annotationPanelHolder
341		.setSize(new Dimension(d.width, d.height - dif));
342	0	ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
343		av.calcPanelHeight());
344	0	f.height += dif;
345	0	ap.seqPanelHolder.setPreferredSize(f);
346	0	ap.setScrollValues(av.getRanges().getStartRes(),
347		av.getRanges().getStartSeq());
348	0	ap.validate();
349		// ap.paintAlignment(true);
350	0	ap.addNotify();
351		}
352
353		}
354		else
355		{
356	0	int diff;
357	0	if ((diff = 6 - evt.getY()) > 0)
358		{
359		// nudge scroll up
360	0	ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
361	0	ap.adjustmentValueChanged(null);
362
363		}
364	0	else if ((0 < (diff = 6
365		- ap.annotationSpaceFillerHolder.getSize().height
366		+ evt.getY())))
367		{
368		// nudge scroll down
369	0	ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
370	0	ap.adjustmentValueChanged(null);
371		}
372	0	repaint();
373		}
374		}
375
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
376	0	@Override...
377		public void mouseClicked(MouseEvent evt)
378		{
379		}
380
		0% Uncovered Elements: 22 (22) Complexity: 6 Complexity Density: 0.38
381	0	@Override...
382		public void mouseReleased(MouseEvent evt)
383		{
384	0	if (!resizePanel && !dragCancelled)
385		{
386	0	int start = selectedRow;
387
388	0	int end = getSelectedRow(evt.getY() + scrollOffset);
389
390	0	if (start > -1 && start != end)
391		{
392		// Swap these annotations
393	0	AlignmentAnnotation startAA = ap.av.getAlignment()
394		.getAlignmentAnnotation()[start];
395	0	if (end == -1)
396		{
397	0	end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
398		}
399	0	AlignmentAnnotation endAA = ap.av.getAlignment()
400		.getAlignmentAnnotation()[end];
401
402	0	ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
403	0	ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
404		}
405		}
406	0	resizePanel = false;
407	0	dragEvent = null;
408	0	dragCancelled = false;
409	0	setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
410	0	repaint();
411	0	ap.annotationPanel.repaint();
412		}
413
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 1
414	0	@Override...
415		public void mouseEntered(MouseEvent evt)
416		{
417	0	if (evt.getY() < 10 && evt.getX() < 14)
418		{
419	0	resizePanel = true;
420	0	repaint();
421		}
422	0	setCursor(Cursor.getPredefinedCursor(
423	0	resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
424		}
425
		0% Uncovered Elements: 10 (10) Complexity: 3 Complexity Density: 0.5
426	0	@Override...
427		public void mouseExited(MouseEvent evt)
428		{
429	0	dragCancelled = false;
430
431	0	if (dragEvent == null)
432		{
433	0	resizePanel = false;
434		}
435		else
436		{
437	0	if (!resizePanel)
438		{
439	0	dragEvent = null;
440		}
441		}
442	0	repaint();
443		}
444
		0% Uncovered Elements: 159 (159) Complexity: 31 Complexity Density: 0.28
445	0	@Override...
446		public void mousePressed(MouseEvent evt)
447		{
448	0	oldY = evt.getY();
449	0	if (resizePanel)
450		{
451	0	return;
452		}
453	0	dragCancelled = false;
454		// todo: move below to mouseClicked ?
455	0	selectedRow = getSelectedRow(evt.getY() + scrollOffset);
456
457	0	AlignmentAnnotation[] aa = ap.av.getAlignment()
458		.getAlignmentAnnotation();
459
460		// DETECT RIGHT MOUSE BUTTON IN AWT
461	0	if ((evt.getModifiersEx()
462		& InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
463		{
464
465	0	PopupMenu popup = new PopupMenu(
466		MessageManager.getString("label.annotations"));
467
468	0	MenuItem item = new MenuItem(ADDNEW);
469	0	item.addActionListener(this);
470	0	popup.add(item);
471	0	if (selectedRow < 0)
472		{
473		// this never happens at moment: - see comment on JAL-563
474	0	if (hasHiddenRows)
475		{
476	0	item = new MenuItem(SHOWALL);
477	0	item.addActionListener(this);
478	0	popup.add(item);
479		}
480	0	this.add(popup);
481	0	popup.show(this, evt.getX(), evt.getY());
482	0	return;
483		}
484		// add the rest if there are actually rows to show
485	0	item = new MenuItem(EDITNAME);
486	0	item.addActionListener(this);
487	0	popup.add(item);
488	0	item = new MenuItem(HIDE);
489	0	item.addActionListener(this);
490	0	popup.add(item);
491
492		/*
493		* Hide all <label>:
494		*/
495	0	if (selectedRow < aa.length)
496		{
497	0	if (aa[selectedRow].sequenceRef != null)
498		{
499	0	final String label = aa[selectedRow].label;
500	0	MenuItem hideType = new MenuItem(
501		MessageManager.getString("label.hide_all") + " " + label);
502	0	hideType.addActionListener(new ActionListener()
503		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
504	0	@Override...
505		public void actionPerformed(ActionEvent e)
506		{
507	0	AlignmentUtils.showOrHideSequenceAnnotations(
508		ap.av.getAlignment(), Collections.singleton(label),
509		null, false, false);
510	0	refresh();
511		}
512		});
513	0	popup.add(hideType);
514		}
515		}
516
517	0	if (hasHiddenRows)
518		{
519	0	item = new MenuItem(SHOWALL);
520	0	item.addActionListener(this);
521	0	popup.add(item);
522		}
523	0	this.add(popup);
524	0	item = new MenuItem(OUTPUT_TEXT);
525	0	item.addActionListener(this);
526	0	popup.add(item);
527	0	if (selectedRow < aa.length)
528		{
529	0	if (aa[selectedRow].autoCalculated)
530		{
531	0	if (aa[selectedRow].label.indexOf("Consensus") > -1)
532		{
533	0	popup.addSeparator();
534	0	final CheckboxMenuItem cbmi = new CheckboxMenuItem(
535		MessageManager.getString("label.ignore_gaps_consensus"),
536	0	(aa[selectedRow].groupRef != null)
537		? aa[selectedRow].groupRef
538		.getIgnoreGapsConsensus()
539		: ap.av.isIgnoreGapsConsensus());
540	0	final AlignmentAnnotation aaa = aa[selectedRow];
541	0	cbmi.addItemListener(new ItemListener()
542		{
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
543	0	@Override...
544		public void itemStateChanged(ItemEvent e)
545		{
546	0	if (aaa.groupRef != null)
547		{
548		// TODO: pass on reference to ap so the view can be updated.
549	0	aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
550		}
551		else
552		{
553	0	ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
554		}
555	0	ap.paintAlignment(true, true);
556		}
557		});
558	0	popup.add(cbmi);
559	0	if (aaa.groupRef != null)
560		{
561	0	final CheckboxMenuItem chist = new CheckboxMenuItem(
562		MessageManager
563		.getString("label.show_group_histogram"),
564		aa[selectedRow].groupRef.isShowConsensusHistogram());
565	0	chist.addItemListener(new ItemListener()
566		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
567	0	@Override...
568		public void itemStateChanged(ItemEvent e)
569		{
570		// TODO: pass on reference
571		// to ap
572		// so the
573		// view
574		// can be
575		// updated.
576	0	aaa.groupRef.setShowConsensusHistogram(chist.getState());
577	0	ap.repaint();
578		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
579		}
580		});
581	0	popup.add(chist);
582	0	final CheckboxMenuItem cprofl = new CheckboxMenuItem(
583		MessageManager.getString("label.show_group_logo"),
584		aa[selectedRow].groupRef.isShowSequenceLogo());
585	0	cprofl.addItemListener(new ItemListener()
586		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
587	0	@Override...
588		public void itemStateChanged(ItemEvent e)
589		{
590		// TODO: pass on reference
591		// to ap
592		// so the
593		// view
594		// can be
595		// updated.
596	0	aaa.groupRef.setshowSequenceLogo(cprofl.getState());
597	0	ap.repaint();
598		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
599		}
600		});
601
602	0	popup.add(cprofl);
603	0	final CheckboxMenuItem cprofn = new CheckboxMenuItem(
604		MessageManager
605		.getString("label.normalise_group_logo"),
606		aa[selectedRow].groupRef.isNormaliseSequenceLogo());
607	0	cprofn.addItemListener(new ItemListener()
608		{
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
609	0	@Override...
610		public void itemStateChanged(ItemEvent e)
611		{
612		// TODO: pass on reference
613		// to ap
614		// so the
615		// view
616		// can be
617		// updated.
618	0	aaa.groupRef.setshowSequenceLogo(true);
619	0	aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
620	0	ap.repaint();
621		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
622		}
623		});
624	0	popup.add(cprofn);
625		}
626		else
627		{
628	0	final CheckboxMenuItem chist = new CheckboxMenuItem(
629		MessageManager.getString("label.show_histogram"),
630		av.isShowConsensusHistogram());
631	0	chist.addItemListener(new ItemListener()
632		{
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
633	0	@Override...
634		public void itemStateChanged(ItemEvent e)
635		{
636		// TODO: pass on reference
637		// to ap
638		// so the
639		// view
640		// can be
641		// updated.
642	0	av.setShowConsensusHistogram(chist.getState());
643	0	ap.alignFrame.showConsensusHistogram
644		.setState(chist.getState()); // TODO: implement
645		// ap.updateGUI()/alignFrame.updateGUI
646		// for applet
647	0	ap.repaint();
648		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
649		}
650		});
651	0	popup.add(chist);
652	0	final CheckboxMenuItem cprof = new CheckboxMenuItem(
653		MessageManager.getString("label.show_logo"),
654		av.isShowSequenceLogo());
655	0	cprof.addItemListener(new ItemListener()
656		{
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
657	0	@Override...
658		public void itemStateChanged(ItemEvent e)
659		{
660		// TODO: pass on reference
661		// to ap
662		// so the
663		// view
664		// can be
665		// updated.
666	0	av.setShowSequenceLogo(cprof.getState());
667	0	ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
668		// implement
669		// ap.updateGUI()/alignFrame.updateGUI
670		// for
671		// applet
672	0	ap.repaint();
673		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
674		}
675		});
676	0	popup.add(cprof);
677	0	final CheckboxMenuItem cprofn = new CheckboxMenuItem(
678		MessageManager.getString("label.normalise_logo"),
679		av.isNormaliseSequenceLogo());
680	0	cprofn.addItemListener(new ItemListener()
681		{
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
682	0	@Override...
683		public void itemStateChanged(ItemEvent e)
684		{
685		// TODO: pass on reference
686		// to ap
687		// so the
688		// view
689		// can be
690		// updated.
691	0	av.setShowSequenceLogo(true);
692	0	ap.alignFrame.normSequenceLogo
693		.setState(cprofn.getState()); // TODO:
694		// implement
695		// ap.updateGUI()/alignFrame.updateGUI
696		// for
697		// applet
698	0	av.setNormaliseSequenceLogo(cprofn.getState());
699	0	ap.repaint();
700		// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
701		}
702		});
703	0	popup.add(cprofn);
704		}
705
706	0	item = new MenuItem(COPYCONS_SEQ);
707	0	item.addActionListener(this);
708	0	popup.add(item);
709		}
710		}
711		}
712	0	popup.show(this, evt.getX(), evt.getY());
713		}
714		else
715		{
716		// selection action.
717	0	if (selectedRow > -1 && selectedRow < aa.length)
718		{
719	0	if (aa[selectedRow].groupRef != null)
720		{
721	0	if (evt.getClickCount() >= 2)
722		{
723		// todo: make the ap scroll to the selection - not necessary, first
724		// click highlights/scrolls, second selects
725	0	ap.seqPanel.ap.idPanel.highlightSearchResults(null);
726		// process modifiers
727	0	SequenceGroup sg = ap.av.getSelectionGroup();
728	0	if (sg == null || sg == aa[selectedRow].groupRef
729		|| !(jalview.util.Platform.isControlDown(evt)
730		|| evt.isShiftDown()))
731		{
732	0	if (jalview.util.Platform.isControlDown(evt)
733		|| evt.isShiftDown())
734		{
735		// clone a new selection group from the associated group
736	0	ap.av.setSelectionGroup(
737		new SequenceGroup(aa[selectedRow].groupRef));
738		}
739		else
740		{
741		// set selection to the associated group so it can be edited
742	0	ap.av.setSelectionGroup(aa[selectedRow].groupRef);
743		}
744		}
745		else
746		{
747		// modify current selection with associated group
748	0	int remainToAdd = aa[selectedRow].groupRef.getSize();
749	0	for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
750		{
751	0	if (jalview.util.Platform.isControlDown(evt))
752		{
753	0	sg.addOrRemove(sgs, --remainToAdd == 0);
754		}
755		else
756		{
757		// notionally, we should also add intermediate sequences from
758		// last added sequence ?
759	0	sg.addSequence(sgs, --remainToAdd == 0);
760		}
761		}
762		}
763	0	ap.paintAlignment(false, false);
764	0	PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
765	0	ap.av.sendSelection();
766		}
767		else
768		{
769	0	ap.seqPanel.ap.idPanel.highlightSearchResults(
770		aa[selectedRow].groupRef.getSequences(null));
771		}
772	0	return;
773		}
774	0	else if (aa[selectedRow].sequenceRef != null)
775		{
776	0	if (evt.getClickCount() == 1)
777		{
778	0	ap.seqPanel.ap.idPanel
779		.highlightSearchResults(Arrays.asList(new SequenceI[]
780		{ aa[selectedRow].sequenceRef }));
781		}
782	0	else if (evt.getClickCount() >= 2)
783		{
784	0	ap.seqPanel.ap.idPanel.highlightSearchResults(null);
785	0	SequenceGroup sg = ap.av.getSelectionGroup();
786	0	if (sg != null)
787		{
788		// we make a copy rather than edit the current selection if no
789		// modifiers pressed
790		// see Enhancement JAL-1557
791	0	if (!(jalview.util.Platform.isControlDown(evt)
792		|| evt.isShiftDown()))
793		{
794	0	sg = new SequenceGroup(sg);
795	0	sg.clear();
796	0	sg.addSequence(aa[selectedRow].sequenceRef, false);
797		}
798		else
799		{
800	0	if (jalview.util.Platform.isControlDown(evt))
801		{
802	0	sg.addOrRemove(aa[selectedRow].sequenceRef, true);
803		}
804		else
805		{
806		// notionally, we should also add intermediate sequences from
807		// last added sequence ?
808	0	sg.addSequence(aa[selectedRow].sequenceRef, true);
809		}
810		}
811		}
812		else
813		{
814	0	sg = new SequenceGroup();
815	0	sg.setStartRes(0);
816	0	sg.setEndRes(ap.av.getAlignment().getWidth() - 1);
817	0	sg.addSequence(aa[selectedRow].sequenceRef, false);
818		}
819	0	ap.av.setSelectionGroup(sg);
820	0	ap.paintAlignment(false, false);
821	0	PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
822	0	ap.av.sendSelection();
823		}
824
825		}
826		}
827
828		}
829		}
830
831		/**
832		* DOCUMENT ME!
833		*
834		* @param e
835		* DOCUMENT ME!
836		*/
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
837	0	protected void copy_annotseqtoclipboard(SequenceI sq)...
838		{
839	0	if (sq == null || sq.getLength() < 1)
840		{
841	0	return;
842		}
843	0	jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
844	0	jalview.appletgui.AlignFrame.copiedSequences
845		.append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd()
846		+ "\t" + sq.getSequenceAsString() + "\n");
847	0	if (av.hasHiddenColumns())
848		{
849	0	jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns(
850		av.getAlignment().getHiddenColumns());
851		}
852		}
853
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
854	0	@Override...
855		public void update(Graphics g)
856		{
857	0	paint(g);
858		}
859
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 0.67
860	0	@Override...
861		public void paint(Graphics g)
862		{
863	0	int w = getSize().width;
864	0	int h = getSize().height;
865	0	if (image == null || w != image.getWidth(this)
866		|| h != image.getHeight(this))
867		{
868	0	image = createImage(w, ap.annotationPanel.getSize().height);
869		}
870
871	0	drawComponent(image.getGraphics(), w);
872	0	g.drawImage(image, 0, 0, this);
873		}
874
		0% Uncovered Elements: 37 (37) Complexity: 11 Complexity Density: 0.41
875	0	public void drawComponent(Graphics g, int width)...
876		{
877	0	g.setFont(av.getFont());
878	0	FontMetrics fm = g.getFontMetrics(av.getFont());
879	0	g.setColor(Color.white);
880	0	g.fillRect(0, 0, getSize().width, getSize().height);
881
882	0	g.translate(0, -scrollOffset);
883	0	g.setColor(Color.black);
884
885	0	AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
886	0	int y = 0, fy = g.getFont().getSize();
887	0	int x = 0, offset;
888
889	0	if (aa != null)
890		{
891	0	hasHiddenRows = false;
892	0	for (int i = 0; i < aa.length; i++)
893		{
894	0	if (!aa[i].visible)
895		{
896	0	hasHiddenRows = true;
897	0	continue;
898		}
899
900	0	x = width - fm.stringWidth(aa[i].label) - 3;
901
902	0	y += aa[i].height;
903	0	offset = -(aa[i].height - fy) / 2;
904
905	0	g.drawString(aa[i].label, x, y + offset);
906		}
907		}
908	0	g.translate(0, +scrollOffset);
909
910	0	if (!resizePanel && !dragCancelled && dragEvent != null && aa != null)
911		{
912	0	g.setColor(Color.lightGray);
913	0	g.drawString(aa[selectedRow].label, dragEvent.getX(),
914		dragEvent.getY());
915		}
916
917	0	if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
918		{
919	0	g.setColor(Color.black);
920	0	g.drawString(MessageManager.getString("label.right_click"), 2, 8);
921	0	g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
922		18);
923		}
924		}
925		}