Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
OverviewDimensionsShowHiddenTest	45	538	29	0	1.0100%	Show methods

Class OverviewDimensionsShowHiddenTest

Class OverviewDimensionsShowHiddenTest	Line # 45	Total Statements 538	Complexity 29	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpAlignment() : void   setUpAlignment() : void	6464	2.02	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	7272	18.018	2.02	0.00	1.0 1.0100%
cleanUp() : void   cleanUp() : void	110110	1.01	1.01	0.00	1.0 1.0100%
testConstructor() : void   testConstructor() : void	120120	51.051	1.01	0.00	1.0 1.0100%
testSetBoxFromMouseClick() : void   testSetBoxFromMouseClick() : void	199199	55.055	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenColsAtStart() : void   testFromMouseWithHiddenColsAtStart() : void	301301	35.035	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenColsInMiddle() : void   testFromMouseWithHiddenColsInMiddle() : void	371371	47.047	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenColsAtEnd() : void   testFromMouseWithHiddenColsAtEnd() : void	461461	42.042	1.01	0.00	1.0 1.0100%
testSetBoxFromViewport() : void   testSetBoxFromViewport() : void	540540	20.020	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenColsAtStart() : void   testSetBoxFromViewportHiddenColsAtStart() : void	581581	13.013	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenColsInMiddle() : void   testSetBoxFromViewportHiddenColsInMiddle() : void	610610	23.023	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenColsAtEnd() : void   testSetBoxFromViewportHiddenColsAtEnd() : void	664664	13.013	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenRowsAtStart() : void   testSetBoxFromViewportHiddenRowsAtStart() : void	695695	13.013	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenRowsInMiddle() : void   testSetBoxFromViewportHiddenRowsInMiddle() : void	727727	13.013	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenRowsAtEnd() : void   testSetBoxFromViewportHiddenRowsAtEnd() : void	758758	13.013	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenRowsAtStart() : void   testFromMouseWithHiddenRowsAtStart() : void	790790	24.024	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenRowsInMiddle() : void   testFromMouseWithHiddenRowsInMiddle() : void	836836	22.022	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenRowsAtEnd() : void   testFromMouseWithHiddenRowsAtEnd() : void	883883	33.033	1.01	0.00	1.0 1.0100%
testPositionInBox() : void   testPositionInBox() : void	945945	34.034	1.01	0.00	1.0 1.0100%
testDragging() : void   testDragging() : void	997997	20.020	1.01	0.00	1.0 1.0100%
moveViewportH(int) : void   moveViewportH(int) : void	10441044	2.02	1.01	0.00	1.0 1.0100%
moveViewportV(int) : void   moveViewportV(int) : void	10531053	2.02	1.01	0.00	1.0 1.0100%
moveViewport(int,int) : void   moveViewport(int,int) : void	10621062	3.03	1.01	0.00	1.0 1.0100%
mouseClick(OverviewDimensions,int,int) : void   mouseClick(OverviewDimensions,int,int) : void	10721072	2.02	1.01	0.00	1.0 1.0100%
testBoxIsAtClickPoint(int,int) : void   testBoxIsAtClickPoint(int,int) : void	10861086	5.05	1.01	0.00	1.0 1.0100%
hideSequences(int,int) : void   hideSequences(int,int) : void	10991099	6.06	2.02	0.00	1.0 1.0100%
testFromMouseWithHiddenRowsAtStartWrapped() : void   testFromMouseWithHiddenRowsAtStartWrapped() : void	11171117	26.026	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.108963095	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromMouseClickjalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromMouseClick	1PASS
	0.091388404	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenColsAtEndjalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenColsAtEnd	1PASS
	0.091388404	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testConstructorjalview.viewmodel.OverviewDimensionsShowHiddenTest.testConstructor	1PASS
	0.08963093	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenColsInMiddlejalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenColsInMiddle	1PASS
	0.08084358	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenRowsAtEndjalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenRowsAtEnd	1PASS
	0.077328645	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testPositionInBoxjalview.viewmodel.OverviewDimensionsShowHiddenTest.testPositionInBox	1PASS
	0.0685413	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenRowsAtStartWrappedjalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenRowsAtStartWrapped	1PASS
	0.0685413	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenColsAtStartjalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenColsAtStart	1PASS
	0.065026365	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenRowsAtStartjalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenRowsAtStart	1PASS
	0.061511423	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenRowsInMiddlejalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenRowsInMiddle	1PASS
	0.054481547	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportjalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewport	1PASS
	0.05272408	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testDraggingjalview.viewmodel.OverviewDimensionsShowHiddenTest.testDragging	1PASS
	0.04920914	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenColsInMiddlejalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenColsInMiddle	1PASS
	0.04745167	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsInMiddlejalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsInMiddle	1PASS
	0.04745167	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsAtStartjalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsAtStart	1PASS
	0.04745167	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsAtEndjalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsAtEnd	1PASS
	0.031634446	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenColsAtStartjalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenColsAtStart	1PASS
	0.031634446	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenColsAtEndjalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenColsAtEnd	1PASS

 

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.viewmodel;
22
23		import static org.testng.Assert.assertEquals;
24		import static org.testng.Assert.assertFalse;
25		import static org.testng.Assert.assertTrue;
26
27		import jalview.analysis.AlignmentGenerator;
28		import jalview.datamodel.Alignment;
29		import jalview.datamodel.AlignmentI;
30		import jalview.datamodel.ColumnSelection;
31		import jalview.datamodel.HiddenColumns;
32		import jalview.datamodel.Sequence;
33		import jalview.datamodel.SequenceCollectionI;
34		import jalview.datamodel.SequenceGroup;
35		import jalview.datamodel.SequenceI;
36
37		import java.util.Hashtable;
38
39		import org.testng.annotations.AfterClass;
40		import org.testng.annotations.BeforeClass;
41		import org.testng.annotations.BeforeMethod;
42		import org.testng.annotations.Test;
43
44		@Test(singleThreaded = true)
		100% Uncovered Elements: 0 (569) Complexity: 29 Complexity Density: 0.05
45		public class OverviewDimensionsShowHiddenTest
46		{
47		AlignmentI al;
48		OverviewDimensionsShowHidden od;
49
50		// cached widths and heights
51		int boxWidth;
52		int boxHeight;
53		int viewHeight;
54		int viewWidth;
55		int alheight;
56		int alwidth;
57
58		ViewportRanges vpranges;
59
60		Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<>();
61
62		HiddenColumns hiddenCols = new HiddenColumns();
63
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
64	1	@BeforeClass(alwaysRun = true)...
65		public void setUpAlignment()
66		{
67		// create random alignment
68	1	AlignmentGenerator gen = new AlignmentGenerator(false);
69	1	al = gen.generate(157, 525, 123, 5, 5);
70		}
71
		100% Uncovered Elements: 0 (20) Complexity: 2 Complexity Density: 0.11
72	18	@BeforeMethod(alwaysRun = true)...
73		public void setUp()
74		{
75	18	if (!hiddenRepSequences.isEmpty())
76		{
77	16	al.getHiddenSequences().showAll(hiddenRepSequences);
78		}
79	18	ColumnSelection colsel = new ColumnSelection();
80	18	hiddenCols.revealAllHiddenColumns(colsel);
81
82	18	vpranges = new ViewportRanges(al);
83	18	vpranges.setViewportStartAndHeight(0, 18);
84	18	vpranges.setViewportStartAndWidth(0, 63);
85
86	18	viewHeight = vpranges.getEndSeq() - vpranges.getStartSeq() + 1;
87	18	viewWidth = vpranges.getEndRes() - vpranges.getStartRes() + 1;
88
89	18	HiddenColumns hiddenCols = new HiddenColumns();
90
91	18	od = new OverviewDimensionsShowHidden(vpranges, true);
92		// Initial box sizing - default path through code
93	18	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
94
95	18	mouseClick(od, 0, 0);
96	18	moveViewport(0, 0);
97
98		// calculate before hidden columns so we get absolute values
99	18	alheight = vpranges.getAbsoluteAlignmentHeight();
100	18	alwidth = vpranges.getAbsoluteAlignmentWidth();
101
102	18	boxWidth = Math.round((float) (vpranges.getEndRes()
103		- vpranges.getStartRes() + 1)
104		* od.getWidth() / alwidth);
105	18	boxHeight = Math.round((float) (vpranges.getEndSeq()
106		- vpranges.getStartSeq() + 1)
107		* od.getSequencesHeight() / alheight);
108		}
109
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
110	1	@AfterClass(alwaysRun = true)...
111		public void cleanUp()
112		{
113	1	al = null;
114		}
115
116		/**
117		* Test that the OverviewDimensions constructor sets width and height
118		* correctly
119		*/
		100% Uncovered Elements: 0 (51) Complexity: 1 Complexity Density: 0.02 1PASS
120	1	@Test(groups = { "Functional" })...
121		public void testConstructor()
122		{
123	1	SequenceI seqa = new Sequence("Seq1", "ABC");
124	1	SequenceI seqb = new Sequence("Seq2", "ABC");
125	1	SequenceI seqc = new Sequence("Seq3", "ABC");
126	1	SequenceI seqd = new Sequence("Seq4", "ABC");
127	1	SequenceI seqe = new Sequence("Seq5",
128		"ABCABCABCABCABCABCABCABCBACBACBACBAC");
129
130	1	int defaultGraphHeight = 20;
131	1	int maxWidth = 400;
132	1	int minWidth = 120;
133	1	int maxSeqHeight = 300;
134	1	int minSeqHeight = 40;
135
136		// test for alignment with width > height
137	1	SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
138	1	Alignment al1 = new Alignment(seqs1);
139	1	ViewportRanges props = new ViewportRanges(al1);
140
141	1	OverviewDimensions od = new OverviewDimensionsShowHidden(props, true);
142	1	int scaledHeight = 267;
143	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
144	1	assertEquals(od.getSequencesHeight(), scaledHeight);
145	1	assertEquals(od.getWidth(), maxWidth);
146	1	assertEquals(od.getHeight(), scaledHeight + defaultGraphHeight);
147
148		// test for alignment with width < height
149	1	SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
150	1	Alignment al2 = new Alignment(seqs2);
151	1	props = new ViewportRanges(al2);
152
153	1	od = new OverviewDimensionsShowHidden(props, true);
154	1	int scaledWidth = 300;
155	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
156	1	assertEquals(od.getSequencesHeight(), maxSeqHeight);
157	1	assertEquals(od.getWidth(), scaledWidth);
158	1	assertEquals(od.getHeight(), scaledWidth + defaultGraphHeight);
159
160		// test for alignment with width > height and sequence height scaled below
161		// min value
162	1	SequenceI[] seqs3 = new SequenceI[] { seqe };
163	1	Alignment al3 = new Alignment(seqs3);
164	1	props = new ViewportRanges(al3);
165
166	1	od = new OverviewDimensionsShowHidden(props, true);
167	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
168	1	assertEquals(od.getSequencesHeight(), minSeqHeight);
169	1	assertEquals(od.getWidth(), maxWidth);
170	1	assertEquals(od.getHeight(), minSeqHeight + defaultGraphHeight);
171
172		// test for alignment with width < height and width scaled below min value
173	1	SequenceI[] seqs4 = new SequenceI[] { seqa, seqb, seqc, seqd, seqa,
174		seqb, seqc, seqd, seqa, seqb, seqc, seqd, seqa, seqb, seqc, seqd };
175	1	Alignment al4 = new Alignment(seqs4);
176	1	props = new ViewportRanges(al4);
177
178	1	od = new OverviewDimensionsShowHidden(props, true);
179	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
180	1	assertEquals(od.getSequencesHeight(), maxSeqHeight);
181	1	assertEquals(od.getWidth(), minWidth);
182	1	assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);
183
184	1	Alignment al5 = new Alignment(seqs4);
185	1	props = new ViewportRanges(al5);
186
187	1	od = new OverviewDimensionsShowHidden(props, false);
188	1	assertEquals(od.getGraphHeight(), 0);
189	1	assertEquals(od.getSequencesHeight(), maxSeqHeight);
190	1	assertEquals(od.getWidth(), minWidth);
191	1	assertEquals(od.getHeight(), maxSeqHeight);
192		}
193
194		/**
195		* Test that validation after mouse adjustments to boxX and boxY sets box
196		* dimensions and scroll values correctly, when there are no hidden rows or
197		* columns.
198		*/
		100% Uncovered Elements: 0 (55) Complexity: 1 Complexity Density: 0.02 1PASS
199	1	@Test(groups = { "Functional" })...
200		public void testSetBoxFromMouseClick()
201		{
202	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
203	1	assertEquals(od.getBoxX(), 0);
204	1	assertEquals(od.getBoxY(), 0);
205	1	assertEquals(od.getBoxWidth(), boxWidth);
206	1	assertEquals(vpranges.getStartRes(), 0);
207	1	assertEquals(vpranges.getStartSeq(), 0);
208
209		// negative boxX value reset to 0
210	1	mouseClick(od, -5, 10);
211	1	assertEquals(od.getBoxX(), 0);
212	1	assertEquals(od.getBoxWidth(), boxWidth);
213	1	assertEquals(od.getBoxHeight(), boxHeight);
214	1	assertEquals(vpranges.getStartSeq() + vpranges.getViewportHeight() / 2,
215		Math.round((float) 10 * alheight / od.getSequencesHeight()));
216	1	assertEquals(vpranges.getStartRes(), 0);
217
218		// negative boxY value reset to 0
219	1	mouseClick(od, 6, -2);
220	1	assertEquals(od.getBoxY(), 0);
221	1	assertEquals(od.getBoxWidth(), boxWidth);
222	1	assertEquals(od.getBoxHeight(), boxHeight);
223	1	assertEquals(vpranges.getStartRes(), 0);
224	1	assertEquals(vpranges.getStartSeq(), 0);
225
226		// overly large boxX value reset to width-boxWidth
227	1	mouseClick(od, 101, 6);
228	1	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
229	1	assertEquals(od.getBoxY(), 1);
230	1	assertEquals(od.getBoxWidth(), boxWidth);
231	1	assertEquals(od.getBoxHeight(), boxHeight);
232	1	assertEquals(vpranges.getStartRes(),
233		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
234	1	assertEquals(
235		vpranges.getStartSeq(),
236		Math.round((float) od.getBoxY() * alheight
237		/ od.getSequencesHeight()));
238
239		// overly large boxY value reset to sequenceHeight - boxHeight
240	1	mouseClick(od, 10, 520);
241	1	assertEquals(od.getBoxX(), 0);
242	1	assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
243	1	assertEquals(od.getBoxWidth(), boxWidth);
244	1	assertEquals(od.getBoxHeight(), boxHeight);
245	1	assertEquals(0,
246		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
247
248		// here (float) od.getBoxY() * alheight / od.getSequencesHeight() = 507.5
249		// and round rounds to 508; however we get 507 working with row values
250		// hence the subtraction of 1
251	1	assertEquals(
252		vpranges.getStartSeq(),
253		Math.round((float) od.getBoxY() * alheight
254		/ od.getSequencesHeight()) - 1);
255
256		// click past end of alignment, as above
257	1	mouseClick(od, 3000, 5);
258	1	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
259	1	assertEquals(od.getBoxWidth(), boxWidth);
260	1	assertEquals(od.getBoxHeight(), boxHeight);
261	1	assertEquals(vpranges.getStartRes(),
262		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
263	1	assertEquals(
264		vpranges.getStartSeq(),
265		Math.round((float) od.getBoxY() * alheight
266		/ od.getSequencesHeight()));
267
268		// move viewport so startRes non-zero and then mouseclick
269	1	moveViewportH(20);
270
271		// click at viewport position
272	1	int oldboxx = od.getBoxX();
273	1	int oldboxy = od.getBoxY();
274	1	mouseClick(od, od.getBoxX() + od.getBoxWidth() / 2 + 6,
275		od.getBoxY() + od.getBoxHeight() / 2 + 3);
276	1	assertEquals(od.getBoxX(), oldboxx + 6);
277	1	assertEquals(od.getBoxWidth(), boxWidth);
278	1	assertEquals(od.getBoxHeight(), boxHeight);
279	1	assertEquals(vpranges.getStartRes(),
280		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
281	1	assertEquals(od.getBoxY(), oldboxy + 3);
282	1	assertEquals(
283		vpranges.getStartSeq(),
284		Math.round((float) od.getBoxY() * alheight
285		/ od.getSequencesHeight()));
286
287		// click at top corner
288	1	mouseClick(od, 0, 0);
289	1	assertEquals(od.getBoxX(), 0);
290	1	assertEquals(vpranges.getStartRes(), 0);
291	1	assertEquals(od.getBoxY(), 0);
292	1	assertEquals(vpranges.getStartSeq(), 0);
293	1	assertEquals(od.getBoxWidth(), boxWidth);
294	1	assertEquals(od.getBoxHeight(), boxHeight);
295		}
296
297		/**
298		* Test setting of the box position, when there are hidden cols at the start
299		* of the alignment
300		*/
		100% Uncovered Elements: 0 (35) Complexity: 1 Complexity Density: 0.03 1PASS
301	1	@Test(groups = { "Functional" })...
302		public void testFromMouseWithHiddenColsAtStart()
303		{
304	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
305	1	assertEquals(od.getBoxX(), 0);
306	1	assertEquals(od.getBoxY(), 0);
307	1	assertEquals(od.getBoxWidth(), boxWidth);
308	1	assertEquals(vpranges.getStartRes(), 0);
309	1	assertEquals(vpranges.getStartSeq(), 0);
310
311		// hide cols at start and check updated box position is correct
312		// changes boxX but not boxwidth
313	1	int lastHiddenCol = 30;
314	1	hiddenCols.hideColumns(0, lastHiddenCol);
315
316	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
317	1	assertEquals(od.getBoxX(),
318		Math.round((float) (lastHiddenCol + 1) * od.getWidth()
319		/ alwidth));
320	1	assertEquals(od.getBoxWidth(), boxWidth);
321	1	assertEquals(od.getBoxHeight(), boxHeight);
322
323		// try to click in hidden cols, check box does not move
324	1	int xpos = 10;
325	1	mouseClick(od, xpos, 0);
326	1	assertEquals(
327		od.getBoxX(),
328		Math.round((float) (lastHiddenCol + 1) * od.getWidth()
329		/ alwidth));
330	1	assertEquals(od.getBoxY(), 0);
331	1	assertEquals(od.getBoxWidth(), boxWidth);
332	1	assertEquals(od.getBoxHeight(), boxHeight);
333	1	assertEquals(vpranges.getStartSeq(), 0);
334	1	assertEquals(vpranges.getStartRes(), 0);
335
336		// click to right of hidden columns, box moves to click point
337	1	mouseClick(od, 60 + boxWidth / 2, boxHeight / 2);
338	1	assertEquals(od.getBoxX(), 60);
339	1	assertEquals(od.getBoxY(), 0);
340	1	assertEquals(od.getBoxWidth(), boxWidth);
341	1	assertEquals(od.getBoxHeight(), boxHeight);
342	1	assertEquals(vpranges.getStartSeq(), 0);
343	1	assertEquals(vpranges.getStartRes(),
344		Math.round(
345		(float) 60 * alwidth / od.getWidth())
346		- (lastHiddenCol + 1));
347
348		// click to right of hidden columns such that box runs over right hand side
349		// of alignment
350		// box position is adjusted away from the edge
351		// overly large boxX value reset to width-boxWidth
352	1	xpos = 100;
353	1	mouseClick(od, xpos + boxWidth / 2, 5 + boxHeight / 2);
354	1	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
355	1	assertEquals(od.getBoxY(), 5);
356	1	assertEquals(od.getBoxWidth(), boxWidth);
357	1	assertEquals(od.getBoxHeight(), boxHeight);
358	1	assertEquals(vpranges.getStartRes(),
359		Math.round((float) od.getBoxX() * alwidth / od.getWidth())
360		- (lastHiddenCol + 1));
361	1	assertEquals(
362		vpranges.getStartSeq(),
363		Math.round((float) od.getBoxY() * alheight
364		/ od.getSequencesHeight()));
365		}
366
367		/**
368		* Test setting of the box position, when there are hidden cols in the middle
369		* of the alignment
370		*/
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
371	1	@Test(groups = { "Functional" })...
372		public void testFromMouseWithHiddenColsInMiddle()
373		{
374	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
375	1	assertEquals(od.getBoxX(), 0);
376	1	assertEquals(od.getBoxY(), 0);
377	1	assertEquals(od.getBoxWidth(), boxWidth);
378	1	assertEquals(vpranges.getStartRes(), 0);
379	1	assertEquals(vpranges.getStartSeq(), 0);
380
381		// hide columns 63-73, no change to box position or dimensions
382	1	int firstHidden = 63;
383	1	int lastHidden = 73;
384	1	hiddenCols.hideColumns(firstHidden, lastHidden);
385
386	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
387	1	assertEquals(od.getBoxX(), 0);
388	1	assertEquals(od.getBoxY(), 0);
389	1	assertEquals(od.getBoxWidth(), boxWidth);
390	1	assertEquals(vpranges.getStartRes(), 0);
391	1	assertEquals(vpranges.getStartSeq(), 0);
392
393		// move box so that it overlaps with hidden cols on one side
394		// box width changes, boxX and scrollCol as for unhidden case
395	1	int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
396		// between cols 60 and 70
397	1	mouseClick(od, xpos, boxHeight / 2);
398	1	assertEquals(od.getBoxX(), xpos - boxWidth / 2);
399	1	assertEquals(od.getBoxY(), 0);
400	1	assertEquals(
401		od.getBoxWidth(),
402		Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
403		* od.getWidth() / alwidth));
404	1	assertEquals(od.getBoxHeight(), boxHeight);
405	1	assertEquals(vpranges.getStartRes(),
406		Math.round((xpos - boxWidth / 2) * alwidth / od.getWidth())
407		+ 1); // +1 for rounding
408	1	assertEquals(vpranges.getStartSeq(), 0);
409
410		// move box so that it completely covers hidden cols
411		// box width changes, boxX and scrollCol as for hidden case
412	1	xpos = 24 + boxWidth / 2;
413	1	mouseClick(od, xpos, 0);
414	1	assertEquals(od.getBoxX(), 24);
415	1	assertEquals(od.getBoxY(), 0);
416	1	assertEquals(
417		od.getBoxWidth(),
418		Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
419		* od.getWidth() / alwidth));
420	1	assertEquals(od.getBoxHeight(), boxHeight);
421	1	assertEquals(vpranges.getStartRes(),
422		Math.round((float) 24 * alwidth / od.getWidth()));
423	1	assertEquals(vpranges.getStartSeq(), 0);
424
425		// move box so boxX is to right of hidden cols, but does not go beyond full
426		// width of alignment
427		// box width, boxX and scrollCol all as for non-hidden case
428	1	xpos = Math.round((float) 75 * od.getWidth() / alwidth) + boxWidth / 2;
429	1	mouseClick(od, xpos, boxHeight / 2);
430	1	assertEquals(od.getBoxX(), xpos - boxWidth / 2);
431	1	assertEquals(od.getBoxY(), 0);
432	1	assertEquals(od.getBoxWidth(), boxWidth);
433	1	assertEquals(od.getBoxHeight(), boxHeight);
434	1	assertEquals(vpranges.getStartSeq(), 0);
435	1	assertEquals(vpranges.getStartRes(),
436		75 - (lastHidden - firstHidden + 1));
437
438		// move box so it goes beyond full width of alignment
439		// boxX, scrollCol adjusted back, box width normal
440	1	xpos = 3000;
441	1	mouseClick(od, xpos, 5);
442	1	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
443	1	assertEquals(od.getBoxY(), 0);
444	1	assertEquals(od.getBoxWidth(), boxWidth);
445	1	assertEquals(od.getBoxHeight(), boxHeight);
446	1	assertEquals(
447		vpranges.getStartRes(),
448		Math.round(((float) od.getBoxX() * alwidth / od.getWidth())
449		- (lastHidden - firstHidden + 1)));
450	1	assertEquals(
451		vpranges.getStartSeq(),
452		Math.round((float) od.getBoxY() * alheight
453		/ od.getSequencesHeight()));
454
455		}
456
457		/**
458		* Test setting of the box position, when there are hidden cols at the end of
459		* the alignment
460		*/
		100% Uncovered Elements: 0 (42) Complexity: 1 Complexity Density: 0.02 1PASS
461	1	@Test(groups = { "Functional" })...
462		public void testFromMouseWithHiddenColsAtEnd()
463		{
464	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
465	1	assertEquals(od.getBoxX(), 0);
466	1	assertEquals(od.getBoxY(), 0);
467	1	assertEquals(od.getBoxWidth(), boxWidth);
468	1	assertEquals(vpranges.getStartRes(), 0);
469	1	assertEquals(vpranges.getStartSeq(), 0);
470
471		// hide columns 140-164, no change to box position or dimensions
472	1	int firstHidden = 140;
473	1	int lastHidden = 164;
474	1	hiddenCols.hideColumns(firstHidden, lastHidden);
475	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
476	1	assertEquals(od.getBoxX(), 0);
477	1	assertEquals(od.getBoxY(), 0);
478	1	assertEquals(od.getBoxWidth(), boxWidth);
479	1	assertEquals(vpranges.getStartRes(), 0);
480	1	assertEquals(vpranges.getStartSeq(), 0);
481
482		// click to left of hidden cols, without overlapping
483		// boxX, scrollCol and width as normal
484	1	int xpos = 30;
485	1	int ypos = 6;
486	1	testBoxIsAtClickPoint(xpos, ypos);
487	1	assertEquals(vpranges.getStartSeq(), Math
488		.round((float) (ypos - boxHeight / 2) * alheight
489		/ od.getHeight()));
490	1	assertEquals(vpranges.getStartRes(), Math.round(
491		(float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
492
493		// click to left of hidden cols, with overlap
494		// boxX and scrollCol adjusted for hidden cols, width normal
495	1	xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
496	1	mouseClick(od, xpos + boxWidth / 2, boxHeight / 2);
497	1	assertEquals(od.getBoxX(),
498		Math.round((float) (firstHidden - 1)
499		* od.getWidth() / alwidth)
500		- boxWidth + 1);
501	1	assertEquals(od.getBoxY(), 0);
502	1	assertEquals(od.getBoxWidth(), boxWidth);
503	1	assertEquals(od.getBoxHeight(), boxHeight);
504	1	assertEquals(vpranges.getStartRes(),
505		Math.round((float) (od.getBoxX()) * alwidth
506		/ od.getWidth()));
507	1	assertEquals(vpranges.getStartSeq(), 0);
508
509		// click in hidden cols
510		// boxX and scrollCol adjusted for hidden cols, width normal
511	1	xpos = 115;
512	1	assertEquals(od.getBoxX(),
513		Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
514		- boxWidth + 1);
515	1	assertEquals(od.getBoxY(), 0);
516	1	assertEquals(od.getBoxWidth(), boxWidth);
517	1	assertEquals(od.getBoxHeight(), boxHeight);
518	1	assertEquals(vpranges.getStartRes(),
519		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
520	1	assertEquals(vpranges.getStartSeq(), 0);
521
522		// click off end of alignment
523		// boxX and scrollCol adjusted for hidden cols, width normal
524	1	xpos = 3000;
525	1	assertEquals(od.getBoxX(),
526		Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
527		- boxWidth + 1);
528	1	assertEquals(od.getBoxY(), 0);
529	1	assertEquals(od.getBoxWidth(), boxWidth);
530	1	assertEquals(od.getBoxHeight(), boxHeight);
531	1	assertEquals(vpranges.getStartRes(),
532		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
533	1	assertEquals(vpranges.getStartSeq(), 0);
534		}
535
536		/**
537		* Test that the box position is set correctly when set from the viewport,
538		* with no hidden rows or columns
539		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
540	1	@Test(groups = { "Functional" })...
541		public void testSetBoxFromViewport()
542		{
543		// move viewport to start of alignment
544	1	moveViewport(0, 0);
545	1	assertEquals(od.getBoxX(), 0);
546	1	assertEquals(od.getBoxY(), 0);
547	1	assertEquals(od.getBoxWidth(), boxWidth);
548	1	assertEquals(od.getBoxHeight(), boxHeight);
549
550		// move viewport to right
551	1	moveViewportH(70);
552	1	assertEquals(od.getBoxX(),
553		Math.round((float) 70 * od.getWidth() / alwidth));
554	1	assertEquals(od.getBoxY(), 0);
555	1	assertEquals(od.getBoxWidth(), boxWidth);
556	1	assertEquals(od.getBoxHeight(), boxHeight);
557
558		// move viewport down
559	1	moveViewportV(100);
560	1	assertEquals(od.getBoxX(),
561		Math.round((float) 70 * od.getWidth() / alwidth));
562	1	assertEquals(od.getBoxY(),
563		Math.round(100 * od.getSequencesHeight() / alheight));
564	1	assertEquals(od.getBoxWidth(), boxWidth);
565	1	assertEquals(od.getBoxHeight(), boxHeight);
566
567		// move viewport to bottom right
568	1	moveViewport(98, 508);
569	1	assertEquals(od.getBoxX(),
570		Math.round((float) 98 * od.getWidth() / alwidth));
571	1	assertEquals(od.getBoxY(),
572		Math.round((float) 508 * od.getSequencesHeight() / alheight));
573	1	assertEquals(od.getBoxWidth(), boxWidth);
574	1	assertEquals(od.getBoxHeight(), boxHeight);
575		}
576
577		/**
578		* Test that the box position is set correctly when there are hidden columns
579		* at the start
580		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
581	1	@Test(groups = { "Functional" })...
582		public void testSetBoxFromViewportHiddenColsAtStart()
583		{
584	1	int firstHidden = 0;
585	1	int lastHidden = 20;
586	1	hiddenCols.hideColumns(firstHidden, lastHidden);
587
588		// move viewport to start of alignment
589	1	moveViewport(0, 0);
590	1	assertEquals(od.getBoxX(),
591		Math.round((float) (lastHidden + 1) * od.getWidth() / alwidth));
592	1	assertEquals(od.getBoxY(), 0);
593	1	assertEquals(od.getBoxWidth(), boxWidth);
594	1	assertEquals(od.getBoxHeight(), boxHeight);
595
596		// move viewport to end of alignment - need to make startRes by removing
597		// hidden cols because of how viewport/overview are implemented
598	1	moveViewport(98 - lastHidden - 1, 0);
599	1	assertEquals(od.getBoxX(),
600		Math.round((float) 98 * od.getWidth() / alwidth));
601	1	assertEquals(od.getBoxY(), 0);
602	1	assertEquals(od.getBoxWidth(), boxWidth);
603	1	assertEquals(od.getBoxHeight(), boxHeight);
604		}
605
606		/**
607		* Test that the box position is set correctly when there are hidden columns
608		* in the middle
609		*/
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
610	1	@Test(groups = { "Functional" })...
611		public void testSetBoxFromViewportHiddenColsInMiddle()
612		{
613	1	int firstHidden = 68;
614	1	int lastHidden = 78;
615	1	hiddenCols.hideColumns(firstHidden, lastHidden);
616
617		// move viewport before hidden columns
618	1	moveViewport(3, 0);
619
620	1	assertEquals(od.getBoxX(),
621		Math.round((float) 3 * od.getWidth() / alwidth));
622	1	assertEquals(od.getBoxY(), 0);
623	1	assertEquals(od.getBoxWidth(), boxWidth);
624	1	assertEquals(od.getBoxHeight(), boxHeight);
625
626		// move viewport to left of hidden columns with overlap
627	1	moveViewport(10, 0);
628	1	assertEquals(od.getBoxX(),
629		Math.round((float) 10 * od.getWidth() / alwidth));
630	1	assertEquals(od.getBoxY(), 0);
631	1	assertEquals(
632		od.getBoxWidth(),
633		boxWidth
634		+ Math.round((float) (lastHidden - firstHidden + 1)
635		* od.getWidth() / alwidth));
636	1	assertEquals(od.getBoxHeight(), boxHeight);
637
638		// move viewport to straddle hidden columns
639	1	moveViewport(63, 0);
640	1	assertEquals(od.getBoxX(),
641		Math.round((float) 63 * od.getWidth() / alwidth));
642	1	assertEquals(od.getBoxY(), 0);
643	1	assertEquals(
644		od.getBoxWidth(),
645		boxWidth
646		+ Math.round((lastHidden - firstHidden + 1)
647		* od.getWidth() / alwidth));
648	1	assertEquals(od.getBoxHeight(), boxHeight);
649
650		// move viewport to right of hidden columns, no overlap
651	1	moveViewport(80 - (lastHidden - firstHidden + 1), 0);
652	1	assertEquals(od.getBoxX(),
653		Math.round((float) 80 * od.getWidth() / alwidth));
654	1	assertEquals(od.getBoxY(), 0);
655	1	assertEquals(od.getBoxWidth(), boxWidth);
656	1	assertEquals(od.getBoxHeight(), boxHeight);
657
658		}
659
660		/**
661		* Test that the box position is set correctly when there are hidden columns
662		* at the end
663		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
664	1	@Test(groups = { "Functional" })...
665		public void testSetBoxFromViewportHiddenColsAtEnd()
666		{
667	1	int firstHidden = 152;
668	1	int lastHidden = 164;
669	1	hiddenCols.hideColumns(firstHidden, lastHidden);
670
671		// move viewport before hidden columns
672	1	moveViewport(3, 0);
673	1	assertEquals(od.getBoxX(),
674		Math.round((float) 3 * od.getWidth() / alwidth));
675	1	assertEquals(od.getBoxY(), 0);
676	1	assertEquals(od.getBoxWidth(), boxWidth);
677	1	assertEquals(od.getBoxHeight(), boxHeight);
678
679		// move viewport to hidden columns
680		// viewport can't actually extend into hidden cols,
681		// so move to the far right edge of the viewport
682	1	moveViewport(firstHidden - viewWidth, 0);
683	1	assertEquals(od.getBoxX(),
684		Math.round((float) (firstHidden - viewWidth)
685		* od.getWidth() / alwidth));
686	1	assertEquals(od.getBoxY(), 0);
687	1	assertEquals(od.getBoxWidth(), boxWidth);
688	1	assertEquals(od.getBoxHeight(), boxHeight);
689		}
690
691		/**
692		* Test that the box position is set correctly when there are hidden rows at
693		* the start
694		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
695	1	@Test(groups = { "Functional" })...
696		public void testSetBoxFromViewportHiddenRowsAtStart()
697		{
698	1	int firstHidden = 0;
699	1	int lastHidden = 20;
700	1	hideSequences(firstHidden, lastHidden);
701
702		// move viewport to start of alignment:
703		// box moves to below hidden rows, height remains same
704	1	moveViewport(0, 0);
705	1	assertEquals(od.getBoxX(), 0);
706	1	assertEquals(od.getBoxY(),
707		Math.round((float) (lastHidden + 1) * od.getSequencesHeight()
708		/ alheight));
709	1	assertEquals(od.getBoxWidth(), boxWidth);
710	1	assertEquals(od.getBoxHeight(), boxHeight);
711
712		// move viewport to end of alignment
713	1	moveViewport(0, 525 - viewHeight - lastHidden - 1);
714	1	assertEquals(od.getBoxX(), 0);
715	1	assertEquals(
716		od.getBoxY(),
717		Math.round((float) (525 - viewHeight) * od.getSequencesHeight()
718		/ alheight));
719	1	assertEquals(od.getBoxWidth(), boxWidth);
720	1	assertEquals(od.getBoxHeight(), boxHeight);
721		}
722
723		/**
724		* Test that the box position is set correctly when there are hidden rows in
725		* the middle
726		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
727	1	@Test(groups = { "Functional" })...
728		public void testSetBoxFromViewportHiddenRowsInMiddle()
729		{
730	1	int firstHidden = 200;
731	1	int lastHidden = 210;
732	1	hideSequences(firstHidden, lastHidden);
733
734		// move viewport to start of alignment:
735		// box, height etc as in non-hidden case
736	1	moveViewport(0, 0);
737	1	assertEquals(od.getBoxX(), 0);
738	1	assertEquals(od.getBoxY(), 0);
739	1	assertEquals(od.getBoxWidth(), boxWidth);
740	1	assertEquals(od.getBoxHeight(), boxHeight);
741
742		// move viewport to straddle hidden rows
743	1	moveViewport(0, 198);
744	1	assertEquals(od.getBoxX(), 0);
745	1	assertEquals(od.getBoxY(), Math.round ((float)198 * od.getSequencesHeight()
746		/ alheight));
747	1	assertEquals(od.getBoxWidth(), boxWidth);
748	1	assertEquals(
749		od.getBoxHeight(),
750		Math.round((float) (viewHeight + lastHidden - firstHidden + 1)
751		* od.getSequencesHeight() / alheight));
752		}
753
754		/**
755		* Test that the box position is set correctly when there are hidden rows at
756		* the bottom
757		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
758	1	@Test(groups = { "Functional" })...
759		public void testSetBoxFromViewportHiddenRowsAtEnd()
760		{
761	1	int firstHidden = 500;
762	1	int lastHidden = 524;
763	1	hideSequences(firstHidden, lastHidden);
764
765		// move viewport to start of alignment:
766		// box, height etc as in non-hidden case
767	1	moveViewport(0, 0);
768	1	assertEquals(od.getBoxX(), 0);
769	1	assertEquals(od.getBoxY(), 0);
770	1	assertEquals(od.getBoxWidth(), boxWidth);
771	1	assertEquals(od.getBoxHeight(), boxHeight);
772
773		// move viewport to end of alignment
774		// viewport sits above hidden rows and does not include them
775	1	moveViewport(0, firstHidden - viewHeight - 1);
776	1	assertEquals(od.getBoxX(), 0);
777	1	assertEquals(
778		od.getBoxY(),
779		Math.round((float) (firstHidden - viewHeight - 1)
780		* od.getSequencesHeight() / alheight));
781	1	assertEquals(od.getBoxWidth(), boxWidth);
782	1	assertEquals(od.getBoxHeight(), boxHeight);
783
784		}
785
786		/**
787		* Test setting of the box position, when there are hidden rows at the start
788		* of the alignment
789		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
790	1	@Test(groups = { "Functional" })...
791		public void testFromMouseWithHiddenRowsAtStart()
792		{
793	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
794	1	assertEquals(od.getBoxX(), 0);
795	1	assertEquals(od.getBoxY(), 0);
796	1	assertEquals(od.getBoxHeight(), boxHeight);
797	1	assertEquals(od.getBoxWidth(), boxWidth);
798	1	assertEquals(vpranges.getStartRes(), 0);
799	1	assertEquals(vpranges.getStartSeq(), 0);
800
801		// hide rows at start and check updated box position is correct
802		// changes boxY but not boxheight
803	1	int lastHiddenRow = 30;
804	1	hideSequences(0, lastHiddenRow);
805
806	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
807	1	assertEquals(od.getBoxX(), 0);
808	1	assertEquals(od.getBoxY(),
809		Math.round((float) (lastHiddenRow + 1)
810		* od.getSequencesHeight() / alheight));
811	1	assertEquals(od.getBoxWidth(), boxWidth);
812	1	assertEquals(od.getBoxHeight(), boxHeight);
813
814		// click in hidden rows - same result
815	1	mouseClick(od, 0, 0);
816	1	assertEquals(od.getBoxX(), 0);
817	1	assertEquals(
818		od.getBoxY(),
819		Math.round((float) (lastHiddenRow + 1)
820		* od.getSequencesHeight() / alheight));
821	1	assertEquals(od.getBoxWidth(), boxWidth);
822	1	assertEquals(od.getBoxHeight(), boxHeight);
823
824		// click below hidden rows
825	1	mouseClick(od, 0, 150 + boxHeight/2);
826	1	assertEquals(od.getBoxX(), 0);
827	1	assertEquals(od.getBoxY(), 150);
828	1	assertEquals(od.getBoxWidth(), boxWidth);
829	1	assertEquals(od.getBoxHeight(), boxHeight);
830		}
831
832		/**
833		* Test setting of the box position, when there are hidden rows at the middle
834		* of the alignment
835		*/
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
836	1	@Test(groups = { "Functional" })...
837		public void testFromMouseWithHiddenRowsInMiddle()
838		{
839	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
840
841	1	assertEquals(od.getBoxX(), 0);
842	1	assertEquals(od.getBoxY(), 0);
843	1	assertEquals(od.getBoxWidth(), boxWidth);
844	1	assertEquals(od.getBoxHeight(), boxHeight);
845	1	assertEquals(vpranges.getStartRes(), 0);
846	1	assertEquals(vpranges.getStartSeq(), 0);
847
848		// hide rows in middle and check updated box position is correct
849		// no changes
850	1	int firstHiddenRow = 50;
851	1	int lastHiddenRow = 54;
852	1	hideSequences(firstHiddenRow, lastHiddenRow);
853
854	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
855
856	1	assertEquals(od.getBoxX(), 0);
857	1	assertEquals(od.getBoxY(), 0);
858	1	assertEquals(od.getBoxWidth(), boxWidth);
859	1	assertEquals(od.getBoxHeight(), boxHeight);
860
861		// click above hidden rows, so that box overlaps
862	1	int rowpos = 35; // row value in residues
863	1	int centrepos = 43; // centre row
864	1	mouseClick(od, 0,
865		Math.round((float) centrepos * od.getSequencesHeight()
866		/ alheight));
867	1	assertEquals(od.getBoxX(), 0);
868	1	assertEquals(od.getBoxY(),
869		Math.round(
870		(float) rowpos * od.getSequencesHeight() / alheight));
871	1	assertEquals(od.getBoxWidth(), boxWidth);
872	1	assertEquals(
873		od.getBoxHeight(),
874		boxHeight
875		+ Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
876		* od.getSequencesHeight() / alheight));
877		}
878
879		/**
880		* Test setting of the box position, when there are hidden rows at the end of
881		* the alignment
882		*/
		100% Uncovered Elements: 0 (33) Complexity: 1 Complexity Density: 0.03 1PASS
883	1	@Test(groups = { "Functional" })...
884		public void testFromMouseWithHiddenRowsAtEnd()
885		{
886	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
887	1	assertEquals(od.getBoxX(), 0);
888	1	assertEquals(od.getBoxY(), 0);
889	1	assertEquals(od.getBoxWidth(), boxWidth);
890	1	assertEquals(od.getBoxHeight(), boxHeight);
891	1	assertEquals(vpranges.getStartRes(), 0);
892	1	assertEquals(vpranges.getStartSeq(), 0);
893
894		// hide rows at end and check updated box position is correct
895		// no changes
896	1	int firstHidden = 500;
897	1	int lastHidden = 524;
898	1	hideSequences(firstHidden, lastHidden);
899
900	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
901	1	assertEquals(od.getBoxX(), 0);
902	1	assertEquals(od.getBoxY(), 0);
903	1	assertEquals(od.getBoxWidth(), boxWidth);
904	1	assertEquals(od.getBoxHeight(), boxHeight);
905
906		// click above hidden rows, no overlap
907	1	int ypos = 40 + viewHeight / 2; // top is row 40
908	1	mouseClick(od, 0,
909		Math.round((float) ypos * od.getSequencesHeight() / alheight));
910	1	assertEquals(od.getBoxX(), 0);
911	1	assertEquals(od.getBoxY(),
912		Math.round((float) 40 * od.getSequencesHeight() / alheight));
913	1	assertEquals(od.getBoxWidth(), boxWidth);
914	1	assertEquals(od.getBoxHeight(), boxHeight);
915
916		// click above hidden rows so box overlaps
917		// boxY moved upwards, boxHeight remains same
918	1	ypos = 497 + viewHeight / 2; // row 497
919	1	mouseClick(od, 0,
920		Math.round((float) ypos * od.getSequencesHeight() / alheight));
921	1	assertEquals(od.getBoxX(), 0);
922	1	assertEquals(
923		od.getBoxY(),
924		Math.round((float) (firstHidden - viewHeight)
925		* od.getSequencesHeight() / alheight));
926	1	assertEquals(od.getBoxWidth(), boxWidth);
927	1	assertEquals(od.getBoxHeight(), boxHeight);
928
929		// click within hidden rows
930	1	ypos = 505 + boxHeight / 2;
931	1	mouseClick(od, 0,
932		Math.round((float) ypos * od.getSequencesHeight() / alheight));
933	1	assertEquals(od.getBoxX(), 0);
934	1	assertEquals(
935		od.getBoxY(),
936		Math.round((firstHidden - viewHeight) * od.getSequencesHeight()
937		/ alheight));
938	1	assertEquals(od.getBoxWidth(), boxWidth);
939	1	assertEquals(od.getBoxHeight(), boxHeight);
940		}
941
942		/**
943		* Test the function to determine if a point is in the overview's box or not
944		*/
		100% Uncovered Elements: 0 (34) Complexity: 1 Complexity Density: 0.03 1PASS
945	1	@Test(groups = { "Functional" })...
946		public void testPositionInBox()
947		{
948	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
949
950	1	assertFalse(od.isPositionInBox(0, 0));
951	1	assertTrue(od.isPositionInBox(10, 9));
952	1	assertFalse(od.isPositionInBox(0, 9));
953	1	assertFalse(od.isPositionInBox(9, 0));
954	1	assertFalse(od.isPositionInBox(75, 20));
955
956	1	assertTrue(od.isPositionInBox(47, 6));
957	1	assertFalse(od.isPositionInBox(48, 6));
958	1	assertTrue(od.isPositionInBox(47, 9));
959	1	assertFalse(od.isPositionInBox(47, 10));
960
961		// hide columns in the box area
962		// extends area where a point is considered to be in the box
963	1	hiddenCols.hideColumns(1, 4);
964	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
965	1	assertFalse(od.isPositionInBox(0, 0));
966	1	assertTrue(od.isPositionInBox(10, 9));
967	1	assertFalse(od.isPositionInBox(0, 9));
968	1	assertFalse(od.isPositionInBox(9, 0));
969	1	assertFalse(od.isPositionInBox(75, 20));
970
971	1	assertTrue(od.isPositionInBox(47, 6));
972	1	assertTrue(od.isPositionInBox(48, 6));
973	1	assertTrue(od.isPositionInBox(47, 9));
974	1	assertFalse(od.isPositionInBox(47, 10));
975
976		// hide sequences in box area
977		// extends area where a point is considered to be in the box
978	1	hideSequences(1, 3);
979	1	ColumnSelection cs = new ColumnSelection();
980	1	hiddenCols.revealAllHiddenColumns(cs);
981	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
982	1	assertFalse(od.isPositionInBox(0, 0));
983	1	assertTrue(od.isPositionInBox(10, 9));
984	1	assertFalse(od.isPositionInBox(0, 9));
985	1	assertFalse(od.isPositionInBox(9, 0));
986	1	assertFalse(od.isPositionInBox(75, 20));
987
988	1	assertTrue(od.isPositionInBox(47, 6));
989	1	assertFalse(od.isPositionInBox(48, 6));
990	1	assertTrue(od.isPositionInBox(47, 9));
991	1	assertTrue(od.isPositionInBox(47, 10));
992		}
993
994		/**
995		* Test the dragging functionality
996		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
997	1	@Test(groups = { "Functional" })...
998		public void testDragging()
999		{
1000	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
1001	1	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
1002	1	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
1003
1004		// updates require an OverviewPanel to exist which it doesn't here
1005		// so call setBoxPosition() as it would be called by the AlignmentPanel
1006		// normally
1007	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1008
1009		// corner moves 16 (20-4) right and 6 (22-16) up
1010	1	assertEquals(od.getBoxX(), 16);
1011	1	assertEquals(od.getBoxY(), 6);
1012
1013		// hide columns - box moves drag distance + hidden cols, vertically makes no
1014		// difference
1015	1	hiddenCols.hideColumns(1, 4);
1016	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
1017	1	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
1018	1	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
1019	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1020
1021		// corner moves 16 (20-4) + hiddenCols right and 6 (22-16) down
1022	1	assertEquals(od.getBoxX(),
1023		16 + Math.round((float) 4 * od.getWidth() / alwidth));
1024	1	assertEquals(od.getBoxY(), 6);
1025
1026		// hide sequences in box area
1027		// makes absolutely no difference
1028	1	hideSequences(1, 3);
1029	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
1030	1	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
1031	1	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
1032	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1033
1034		// corner moves 16 (20-4) + hiddenCols right and 6 (22-16) + hiddenRows down
1035	1	assertEquals(od.getBoxX(),
1036		16 + Math.round((float) 4 * od.getWidth() / alwidth));
1037	1	assertEquals(od.getBoxY(),
1038		6 + Math.round((float) 3 * od.getHeight() / alheight));
1039		}
1040
1041		/*
1042		* Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
1043		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1044	2	private void moveViewportH(int startRes)...
1045		{
1046	2	vpranges.setViewportStartAndWidth(startRes, viewWidth);
1047	2	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1048		}
1049
1050		/*
1051		* Move viewport vertically: startSeq and endSeq give new vertical extent. Horizontal extent stays the same.
1052		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1053	1	private void moveViewportV(int startSeq)...
1054		{
1055	1	vpranges.setViewportStartAndHeight(startSeq, viewHeight);
1056	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1057		}
1058
1059		/*
1060		* Move viewport horizontally and vertically.
1061		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
1062	34	private void moveViewport(int startRes, int startSeq)...
1063		{
1064	34	vpranges.setViewportStartAndWidth(startRes, viewWidth);
1065	34	vpranges.setViewportStartAndHeight(startSeq, viewHeight);
1066	34	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1067		}
1068
1069		/*
1070		* Mouse click as position x,y in overview window
1071		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1072	42	private void mouseClick(OverviewDimensions od, int x, int y)...
1073		{
1074	42	od.updateViewportFromMouse(x, y, al.getHiddenSequences(), hiddenCols);
1075
1076		// updates require an OverviewPanel to exist which it doesn't here
1077		// so call setBoxPosition() as it would be called by the AlignmentPanel
1078		// normally
1079	42	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1080		}
1081
1082		/*
1083		* Test that the box is positioned with the centre at xpos, ypos
1084		* and with the original width and height
1085		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
1086	1	private void testBoxIsAtClickPoint(int xpos, int ypos)...
1087		{
1088	1	mouseClick(od, xpos, ypos);
1089	1	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
1090	1	assertEquals(od.getBoxY() + od.getBoxHeight() / 2, ypos);
1091	1	assertEquals(od.getBoxWidth(), boxWidth);
1092	1	assertEquals(od.getBoxHeight(), boxHeight);
1093
1094		}
1095
1096		/*
1097		* Hide sequences between start and end
1098		*/
		100% Uncovered Elements: 0 (8) Complexity: 2 Complexity Density: 0.33
1099	9	private void hideSequences(int start, int end)...
1100		{
1101	9	SequenceI[] allseqs = al.getSequencesArray();
1102	9	SequenceGroup theseSeqs = new SequenceGroup();
1103
1104	164	for (int i = start; i <= end; i++)
1105		{
1106	155	theseSeqs.addSequence(allseqs[i], false);
1107	155	al.getHiddenSequences().hideSequence(allseqs[i]);
1108		}
1109
1110	9	hiddenRepSequences.put(allseqs[start], theseSeqs);
1111		}
1112
1113		/**
1114		* Test setting of the box position, when there are hidden rows at the start
1115		* of the alignment
1116		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
1117	1	@Test(groups = { "Functional" })...
1118		public void testFromMouseWithHiddenRowsAtStartWrapped()
1119		{
1120	1	vpranges.setWrappedMode(true);
1121	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
1122	1	assertEquals(od.getBoxX(), 0);
1123	1	assertEquals(od.getBoxY(), 0);
1124	1	assertEquals(od.getBoxHeight(), boxHeight);
1125	1	assertEquals(od.getBoxWidth(), boxWidth);
1126	1	assertEquals(vpranges.getStartRes(), 0);
1127	1	assertEquals(vpranges.getStartSeq(), 0);
1128
1129		// hide rows at start and check updated box position is correct
1130		// changes boxY but not boxheight
1131	1	int lastHiddenRow = 30;
1132	1	hideSequences(0, lastHiddenRow);
1133
1134	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1135	1	assertEquals(od.getBoxX(), 0);
1136	1	assertEquals(od.getBoxY(),
1137		Math.round((float) (lastHiddenRow + 1)
1138		* od.getSequencesHeight() / alheight));
1139	1	assertEquals(od.getBoxWidth(), boxWidth);
1140	1	assertEquals(od.getBoxHeight(), boxHeight);
1141
1142		// click in hidden rows - same result
1143	1	mouseClick(od, 0, 0);
1144	1	assertEquals(od.getBoxX(), 0);
1145	1	int boxY = od.getBoxY();
1146	1	assertEquals(
1147		boxY,
1148		Math.round((float) (lastHiddenRow + 1)
1149		* od.getSequencesHeight() / alheight));
1150	1	assertEquals(od.getBoxWidth(), boxWidth);
1151	1	assertEquals(od.getBoxHeight(), boxHeight);
1152
1153		// click below hidden rows
1154		// vertical move of overview box is suppressed in wrapped mode
1155	1	mouseClick(od, 0, 150);
1156	1	assertEquals(od.getBoxX(), 0);
1157	1	assertEquals(od.getBoxY(), boxY); // unchanged
1158	1	assertEquals(od.getBoxWidth(), boxWidth);
1159	1	assertEquals(od.getBoxHeight(), boxHeight);
1160		}
1161		}