Classes

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

Class OverviewDimensionsShowHiddenTest

Class OverviewDimensionsShowHiddenTest	Line # 45	Total Statements 538	Complexity 29	TOTAL Coverage 1.0100%
setUpAlignment() : void   setUpAlignment() : void	7070	2.02	1.01	1.0 1.0100%
setUp() : void   setUp() : void	7878	18.018	2.02	1.0 1.0100%
cleanUp() : void   cleanUp() : void	116116	1.01	1.01	1.0 1.0100%
testConstructor() : void   testConstructor() : void	126126	51.051	1.01	1.0 1.0100%
testSetBoxFromMouseClick() : void   testSetBoxFromMouseClick() : void	205205	55.055	1.01	1.0 1.0100%
testFromMouseWithHiddenColsAtStart() : void   testFromMouseWithHiddenColsAtStart() : void	299299	35.035	1.01	1.0 1.0100%
testFromMouseWithHiddenColsInMiddle() : void   testFromMouseWithHiddenColsInMiddle() : void	363363	47.047	1.01	1.0 1.0100%
testFromMouseWithHiddenColsAtEnd() : void   testFromMouseWithHiddenColsAtEnd() : void	448448	42.042	1.01	1.0 1.0100%
testSetBoxFromViewport() : void   testSetBoxFromViewport() : void	524524	20.020	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenColsAtStart() : void   testSetBoxFromViewportHiddenColsAtStart() : void	565565	13.013	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenColsInMiddle() : void   testSetBoxFromViewportHiddenColsInMiddle() : void	594594	23.023	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenColsAtEnd() : void   testSetBoxFromViewportHiddenColsAtEnd() : void	643643	13.013	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenRowsAtStart() : void   testSetBoxFromViewportHiddenRowsAtStart() : void	673673	13.013	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenRowsInMiddle() : void   testSetBoxFromViewportHiddenRowsInMiddle() : void	702702	13.013	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenRowsAtEnd() : void   testSetBoxFromViewportHiddenRowsAtEnd() : void	732732	13.013	1.01	1.0 1.0100%
testFromMouseWithHiddenRowsAtStart() : void   testFromMouseWithHiddenRowsAtStart() : void	763763	24.024	1.01	1.0 1.0100%
testFromMouseWithHiddenRowsInMiddle() : void   testFromMouseWithHiddenRowsInMiddle() : void	806806	22.022	1.01	1.0 1.0100%
testFromMouseWithHiddenRowsAtEnd() : void   testFromMouseWithHiddenRowsAtEnd() : void	850850	33.033	1.01	1.0 1.0100%
testPositionInBox() : void   testPositionInBox() : void	908908	34.034	1.01	1.0 1.0100%
testDragging() : void   testDragging() : void	960960	20.020	1.01	1.0 1.0100%
moveViewportH(int) : void   moveViewportH(int) : void	10071007	2.02	1.01	1.0 1.0100%
moveViewportV(int) : void   moveViewportV(int) : void	10161016	2.02	1.01	1.0 1.0100%
moveViewport(int,int) : void   moveViewport(int,int) : void	10251025	3.03	1.01	1.0 1.0100%
mouseClick(OverviewDimensions,int,int) : void   mouseClick(OverviewDimensions,int,int) : void	10351035	2.02	1.01	1.0 1.0100%
testBoxIsAtClickPoint(int,int) : void   testBoxIsAtClickPoint(int,int) : void	10491049	5.05	1.01	1.0 1.0100%
hideSequences(int,int) : void   hideSequences(int,int) : void	10621062	6.06	2.02	1.0 1.0100%
testFromMouseWithHiddenRowsAtStartWrapped() : void   testFromMouseWithHiddenRowsAtStartWrapped() : void	10801080	26.026	1.01	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.testConstructorjalview.viewmodel.OverviewDimensionsShowHiddenTest.testConstructor	1PASS
	0.091388404	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenColsAtEndjalview.viewmodel.OverviewDimensionsShowHiddenTest.testFromMouseWithHiddenColsAtEnd	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.testSetBoxFromViewportHiddenRowsAtStartjalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsAtStart	1PASS
	0.04745167	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsAtEndjalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsAtEnd	1PASS
	0.04745167	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsInMiddlejalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenRowsInMiddle	1PASS
	0.031634446	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenColsAtEndjalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenColsAtEnd	1PASS
	0.031634446	jalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenColsAtStartjalview.viewmodel.OverviewDimensionsShowHiddenTest.testSetBoxFromViewportHiddenColsAtStart	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
49		OverviewDimensionsShowHidden od;
50
51		// cached widths and heights
52		int boxWidth;
53
54		int boxHeight;
55
56		int viewHeight;
57
58		int viewWidth;
59
60		int alheight;
61
62		int alwidth;
63
64		ViewportRanges vpranges;
65
66		Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<>();
67
68		HiddenColumns hiddenCols = new HiddenColumns();
69
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
70	1	@BeforeClass(alwaysRun = true)...
71		public void setUpAlignment()
72		{
73		// create random alignment
74	1	AlignmentGenerator gen = new AlignmentGenerator(false);
75	1	al = gen.generate(157, 525, 123, 5, 5);
76		}
77
		100% Uncovered Elements: 0 (20) Complexity: 2 Complexity Density: 0.11
78	18	@BeforeMethod(alwaysRun = true)...
79		public void setUp()
80		{
81	18	if (!hiddenRepSequences.isEmpty())
82		{
83	16	al.getHiddenSequences().showAll(hiddenRepSequences);
84		}
85	18	ColumnSelection colsel = new ColumnSelection();
86	18	hiddenCols.revealAllHiddenColumns(colsel);
87
88	18	vpranges = new ViewportRanges(al);
89	18	vpranges.setViewportStartAndHeight(0, 18);
90	18	vpranges.setViewportStartAndWidth(0, 63);
91
92	18	viewHeight = vpranges.getEndSeq() - vpranges.getStartSeq() + 1;
93	18	viewWidth = vpranges.getEndRes() - vpranges.getStartRes() + 1;
94
95	18	HiddenColumns hiddenCols = new HiddenColumns();
96
97	18	od = new OverviewDimensionsShowHidden(vpranges, true);
98		// Initial box sizing - default path through code
99	18	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
100
101	18	mouseClick(od, 0, 0);
102	18	moveViewport(0, 0);
103
104		// calculate before hidden columns so we get absolute values
105	18	alheight = vpranges.getAbsoluteAlignmentHeight();
106	18	alwidth = vpranges.getAbsoluteAlignmentWidth();
107
108	18	boxWidth = Math.round(
109		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
110		* od.getWidth() / alwidth);
111	18	boxHeight = Math.round(
112		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
113		* od.getSequencesHeight() / alheight);
114		}
115
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
116	1	@AfterClass(alwaysRun = true)...
117		public void cleanUp()
118		{
119	1	al = null;
120		}
121
122		/**
123		* Test that the OverviewDimensions constructor sets width and height
124		* correctly
125		*/
		100% Uncovered Elements: 0 (51) Complexity: 1 Complexity Density: 0.02 1PASS
126	1	@Test(groups = { "Functional" })...
127		public void testConstructor()
128		{
129	1	SequenceI seqa = new Sequence("Seq1", "ABC");
130	1	SequenceI seqb = new Sequence("Seq2", "ABC");
131	1	SequenceI seqc = new Sequence("Seq3", "ABC");
132	1	SequenceI seqd = new Sequence("Seq4", "ABC");
133	1	SequenceI seqe = new Sequence("Seq5",
134		"ABCABCABCABCABCABCABCABCBACBACBACBAC");
135
136	1	int defaultGraphHeight = 20;
137	1	int maxWidth = 400;
138	1	int minWidth = 120;
139	1	int maxSeqHeight = 300;
140	1	int minSeqHeight = 40;
141
142		// test for alignment with width > height
143	1	SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
144	1	Alignment al1 = new Alignment(seqs1);
145	1	ViewportRanges props = new ViewportRanges(al1);
146
147	1	OverviewDimensions od = new OverviewDimensionsShowHidden(props, true);
148	1	int scaledHeight = 267;
149	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
150	1	assertEquals(od.getSequencesHeight(), scaledHeight);
151	1	assertEquals(od.getWidth(), maxWidth);
152	1	assertEquals(od.getHeight(), scaledHeight + defaultGraphHeight);
153
154		// test for alignment with width < height
155	1	SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
156	1	Alignment al2 = new Alignment(seqs2);
157	1	props = new ViewportRanges(al2);
158
159	1	od = new OverviewDimensionsShowHidden(props, true);
160	1	int scaledWidth = 300;
161	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
162	1	assertEquals(od.getSequencesHeight(), maxSeqHeight);
163	1	assertEquals(od.getWidth(), scaledWidth);
164	1	assertEquals(od.getHeight(), scaledWidth + defaultGraphHeight);
165
166		// test for alignment with width > height and sequence height scaled below
167		// min value
168	1	SequenceI[] seqs3 = new SequenceI[] { seqe };
169	1	Alignment al3 = new Alignment(seqs3);
170	1	props = new ViewportRanges(al3);
171
172	1	od = new OverviewDimensionsShowHidden(props, true);
173	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
174	1	assertEquals(od.getSequencesHeight(), minSeqHeight);
175	1	assertEquals(od.getWidth(), maxWidth);
176	1	assertEquals(od.getHeight(), minSeqHeight + defaultGraphHeight);
177
178		// test for alignment with width < height and width scaled below min value
179	1	SequenceI[] seqs4 = new SequenceI[] { seqa, seqb, seqc, seqd, seqa,
180		seqb, seqc, seqd, seqa, seqb, seqc, seqd, seqa, seqb, seqc, seqd };
181	1	Alignment al4 = new Alignment(seqs4);
182	1	props = new ViewportRanges(al4);
183
184	1	od = new OverviewDimensionsShowHidden(props, true);
185	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
186	1	assertEquals(od.getSequencesHeight(), maxSeqHeight);
187	1	assertEquals(od.getWidth(), minWidth);
188	1	assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);
189
190	1	Alignment al5 = new Alignment(seqs4);
191	1	props = new ViewportRanges(al5);
192
193	1	od = new OverviewDimensionsShowHidden(props, false);
194	1	assertEquals(od.getGraphHeight(), 0);
195	1	assertEquals(od.getSequencesHeight(), maxSeqHeight);
196	1	assertEquals(od.getWidth(), minWidth);
197	1	assertEquals(od.getHeight(), maxSeqHeight);
198		}
199
200		/**
201		* Test that validation after mouse adjustments to boxX and boxY sets box
202		* dimensions and scroll values correctly, when there are no hidden rows or
203		* columns.
204		*/
		100% Uncovered Elements: 0 (55) Complexity: 1 Complexity Density: 0.02 1PASS
205	1	@Test(groups = { "Functional" })...
206		public void testSetBoxFromMouseClick()
207		{
208	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
209	1	assertEquals(od.getBoxX(), 0);
210	1	assertEquals(od.getBoxY(), 0);
211	1	assertEquals(od.getBoxWidth(), boxWidth);
212	1	assertEquals(vpranges.getStartRes(), 0);
213	1	assertEquals(vpranges.getStartSeq(), 0);
214
215		// negative boxX value reset to 0
216	1	mouseClick(od, -5, 10);
217	1	assertEquals(od.getBoxX(), 0);
218	1	assertEquals(od.getBoxWidth(), boxWidth);
219	1	assertEquals(od.getBoxHeight(), boxHeight);
220	1	assertEquals(vpranges.getStartSeq() + vpranges.getViewportHeight() / 2,
221		Math.round((float) 10 * alheight / od.getSequencesHeight()));
222	1	assertEquals(vpranges.getStartRes(), 0);
223
224		// negative boxY value reset to 0
225	1	mouseClick(od, 6, -2);
226	1	assertEquals(od.getBoxY(), 0);
227	1	assertEquals(od.getBoxWidth(), boxWidth);
228	1	assertEquals(od.getBoxHeight(), boxHeight);
229	1	assertEquals(vpranges.getStartRes(), 0);
230	1	assertEquals(vpranges.getStartSeq(), 0);
231
232		// overly large boxX value reset to width-boxWidth
233	1	mouseClick(od, 101, 6);
234	1	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
235	1	assertEquals(od.getBoxY(), 1);
236	1	assertEquals(od.getBoxWidth(), boxWidth);
237	1	assertEquals(od.getBoxHeight(), boxHeight);
238	1	assertEquals(vpranges.getStartRes(),
239		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
240	1	assertEquals(vpranges.getStartSeq(), Math.round(
241		(float) od.getBoxY() * alheight / od.getSequencesHeight()));
242
243		// overly large boxY value reset to sequenceHeight - boxHeight
244	1	mouseClick(od, 10, 520);
245	1	assertEquals(od.getBoxX(), 0);
246	1	assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
247	1	assertEquals(od.getBoxWidth(), boxWidth);
248	1	assertEquals(od.getBoxHeight(), boxHeight);
249	1	assertEquals(0,
250		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
251
252		// here (float) od.getBoxY() * alheight / od.getSequencesHeight() = 507.5
253		// and round rounds to 508; however we get 507 working with row values
254		// hence the subtraction of 1
255	1	assertEquals(vpranges.getStartSeq(), Math.round(
256		(float) od.getBoxY() * alheight / od.getSequencesHeight()) - 1);
257
258		// click past end of alignment, as above
259	1	mouseClick(od, 3000, 5);
260	1	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
261	1	assertEquals(od.getBoxWidth(), boxWidth);
262	1	assertEquals(od.getBoxHeight(), boxHeight);
263	1	assertEquals(vpranges.getStartRes(),
264		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
265	1	assertEquals(vpranges.getStartSeq(), Math.round(
266		(float) od.getBoxY() * alheight / 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(vpranges.getStartSeq(), Math.round(
283		(float) od.getBoxY() * alheight / od.getSequencesHeight()));
284
285		// click at top corner
286	1	mouseClick(od, 0, 0);
287	1	assertEquals(od.getBoxX(), 0);
288	1	assertEquals(vpranges.getStartRes(), 0);
289	1	assertEquals(od.getBoxY(), 0);
290	1	assertEquals(vpranges.getStartSeq(), 0);
291	1	assertEquals(od.getBoxWidth(), boxWidth);
292	1	assertEquals(od.getBoxHeight(), boxHeight);
293		}
294
295		/**
296		* Test setting of the box position, when there are hidden cols at the start
297		* of the alignment
298		*/
		100% Uncovered Elements: 0 (35) Complexity: 1 Complexity Density: 0.03 1PASS
299	1	@Test(groups = { "Functional" })...
300		public void testFromMouseWithHiddenColsAtStart()
301		{
302	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
303	1	assertEquals(od.getBoxX(), 0);
304	1	assertEquals(od.getBoxY(), 0);
305	1	assertEquals(od.getBoxWidth(), boxWidth);
306	1	assertEquals(vpranges.getStartRes(), 0);
307	1	assertEquals(vpranges.getStartSeq(), 0);
308
309		// hide cols at start and check updated box position is correct
310		// changes boxX but not boxwidth
311	1	int lastHiddenCol = 30;
312	1	hiddenCols.hideColumns(0, lastHiddenCol);
313
314	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
315	1	assertEquals(od.getBoxX(), Math
316		.round((float) (lastHiddenCol + 1) * od.getWidth() / alwidth));
317	1	assertEquals(od.getBoxWidth(), boxWidth);
318	1	assertEquals(od.getBoxHeight(), boxHeight);
319
320		// try to click in hidden cols, check box does not move
321	1	int xpos = 10;
322	1	mouseClick(od, xpos, 0);
323	1	assertEquals(od.getBoxX(), Math
324		.round((float) (lastHiddenCol + 1) * od.getWidth() / alwidth));
325	1	assertEquals(od.getBoxY(), 0);
326	1	assertEquals(od.getBoxWidth(), boxWidth);
327	1	assertEquals(od.getBoxHeight(), boxHeight);
328	1	assertEquals(vpranges.getStartSeq(), 0);
329	1	assertEquals(vpranges.getStartRes(), 0);
330
331		// click to right of hidden columns, box moves to click point
332	1	mouseClick(od, 60 + boxWidth / 2, boxHeight / 2);
333	1	assertEquals(od.getBoxX(), 60);
334	1	assertEquals(od.getBoxY(), 0);
335	1	assertEquals(od.getBoxWidth(), boxWidth);
336	1	assertEquals(od.getBoxHeight(), boxHeight);
337	1	assertEquals(vpranges.getStartSeq(), 0);
338	1	assertEquals(vpranges.getStartRes(),
339		Math.round((float) 60 * alwidth / od.getWidth())
340		- (lastHiddenCol + 1));
341
342		// click to right of hidden columns such that box runs over right hand side
343		// of alignment
344		// box position is adjusted away from the edge
345		// overly large boxX value reset to width-boxWidth
346	1	xpos = 100;
347	1	mouseClick(od, xpos + boxWidth / 2, 5 + boxHeight / 2);
348	1	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
349	1	assertEquals(od.getBoxY(), 5);
350	1	assertEquals(od.getBoxWidth(), boxWidth);
351	1	assertEquals(od.getBoxHeight(), boxHeight);
352	1	assertEquals(vpranges.getStartRes(),
353		Math.round((float) od.getBoxX() * alwidth / od.getWidth())
354		- (lastHiddenCol + 1));
355	1	assertEquals(vpranges.getStartSeq(), Math.round(
356		(float) od.getBoxY() * alheight / od.getSequencesHeight()));
357		}
358
359		/**
360		* Test setting of the box position, when there are hidden cols in the middle
361		* of the alignment
362		*/
		100% Uncovered Elements: 0 (47) Complexity: 1 Complexity Density: 0.02 1PASS
363	1	@Test(groups = { "Functional" })...
364		public void testFromMouseWithHiddenColsInMiddle()
365		{
366	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
367	1	assertEquals(od.getBoxX(), 0);
368	1	assertEquals(od.getBoxY(), 0);
369	1	assertEquals(od.getBoxWidth(), boxWidth);
370	1	assertEquals(vpranges.getStartRes(), 0);
371	1	assertEquals(vpranges.getStartSeq(), 0);
372
373		// hide columns 63-73, no change to box position or dimensions
374	1	int firstHidden = 63;
375	1	int lastHidden = 73;
376	1	hiddenCols.hideColumns(firstHidden, lastHidden);
377
378	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
379	1	assertEquals(od.getBoxX(), 0);
380	1	assertEquals(od.getBoxY(), 0);
381	1	assertEquals(od.getBoxWidth(), boxWidth);
382	1	assertEquals(vpranges.getStartRes(), 0);
383	1	assertEquals(vpranges.getStartSeq(), 0);
384
385		// move box so that it overlaps with hidden cols on one side
386		// box width changes, boxX and scrollCol as for unhidden case
387	1	int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
388		// between cols 60 and 70
389	1	mouseClick(od, xpos, boxHeight / 2);
390	1	assertEquals(od.getBoxX(), xpos - boxWidth / 2);
391	1	assertEquals(od.getBoxY(), 0);
392	1	assertEquals(od.getBoxWidth(),
393		Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
394		* od.getWidth() / alwidth));
395	1	assertEquals(od.getBoxHeight(), boxHeight);
396	1	assertEquals(vpranges.getStartRes(),
397		Math.round((xpos - boxWidth / 2) * alwidth / od.getWidth())
398		+ 1); // +1 for rounding
399	1	assertEquals(vpranges.getStartSeq(), 0);
400
401		// move box so that it completely covers hidden cols
402		// box width changes, boxX and scrollCol as for hidden case
403	1	xpos = 24 + boxWidth / 2;
404	1	mouseClick(od, xpos, 0);
405	1	assertEquals(od.getBoxX(), 24);
406	1	assertEquals(od.getBoxY(), 0);
407	1	assertEquals(od.getBoxWidth(),
408		Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
409		* od.getWidth() / alwidth));
410	1	assertEquals(od.getBoxHeight(), boxHeight);
411	1	assertEquals(vpranges.getStartRes(),
412		Math.round((float) 24 * alwidth / od.getWidth()));
413	1	assertEquals(vpranges.getStartSeq(), 0);
414
415		// move box so boxX is to right of hidden cols, but does not go beyond full
416		// width of alignment
417		// box width, boxX and scrollCol all as for non-hidden case
418	1	xpos = Math.round((float) 75 * od.getWidth() / alwidth) + boxWidth / 2;
419	1	mouseClick(od, xpos, boxHeight / 2);
420	1	assertEquals(od.getBoxX(), xpos - boxWidth / 2);
421	1	assertEquals(od.getBoxY(), 0);
422	1	assertEquals(od.getBoxWidth(), boxWidth);
423	1	assertEquals(od.getBoxHeight(), boxHeight);
424	1	assertEquals(vpranges.getStartSeq(), 0);
425	1	assertEquals(vpranges.getStartRes(),
426		75 - (lastHidden - firstHidden + 1));
427
428		// move box so it goes beyond full width of alignment
429		// boxX, scrollCol adjusted back, box width normal
430	1	xpos = 3000;
431	1	mouseClick(od, xpos, 5);
432	1	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
433	1	assertEquals(od.getBoxY(), 0);
434	1	assertEquals(od.getBoxWidth(), boxWidth);
435	1	assertEquals(od.getBoxHeight(), boxHeight);
436	1	assertEquals(vpranges.getStartRes(),
437		Math.round(((float) od.getBoxX() * alwidth / od.getWidth())
438		- (lastHidden - firstHidden + 1)));
439	1	assertEquals(vpranges.getStartSeq(), Math.round(
440		(float) od.getBoxY() * alheight / od.getSequencesHeight()));
441
442		}
443
444		/**
445		* Test setting of the box position, when there are hidden cols at the end of
446		* the alignment
447		*/
		100% Uncovered Elements: 0 (42) Complexity: 1 Complexity Density: 0.02 1PASS
448	1	@Test(groups = { "Functional" })...
449		public void testFromMouseWithHiddenColsAtEnd()
450		{
451	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
452	1	assertEquals(od.getBoxX(), 0);
453	1	assertEquals(od.getBoxY(), 0);
454	1	assertEquals(od.getBoxWidth(), boxWidth);
455	1	assertEquals(vpranges.getStartRes(), 0);
456	1	assertEquals(vpranges.getStartSeq(), 0);
457
458		// hide columns 140-164, no change to box position or dimensions
459	1	int firstHidden = 140;
460	1	int lastHidden = 164;
461	1	hiddenCols.hideColumns(firstHidden, lastHidden);
462	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
463	1	assertEquals(od.getBoxX(), 0);
464	1	assertEquals(od.getBoxY(), 0);
465	1	assertEquals(od.getBoxWidth(), boxWidth);
466	1	assertEquals(vpranges.getStartRes(), 0);
467	1	assertEquals(vpranges.getStartSeq(), 0);
468
469		// click to left of hidden cols, without overlapping
470		// boxX, scrollCol and width as normal
471	1	int xpos = 30;
472	1	int ypos = 6;
473	1	testBoxIsAtClickPoint(xpos, ypos);
474	1	assertEquals(vpranges.getStartSeq(), Math.round(
475		(float) (ypos - boxHeight / 2) * alheight / od.getHeight()));
476	1	assertEquals(vpranges.getStartRes(), Math.round(
477		(float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
478
479		// click to left of hidden cols, with overlap
480		// boxX and scrollCol adjusted for hidden cols, width normal
481	1	xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
482	1	mouseClick(od, xpos + boxWidth / 2, boxHeight / 2);
483	1	assertEquals(od.getBoxX(),
484		Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
485		- boxWidth + 1);
486	1	assertEquals(od.getBoxY(), 0);
487	1	assertEquals(od.getBoxWidth(), boxWidth);
488	1	assertEquals(od.getBoxHeight(), boxHeight);
489	1	assertEquals(vpranges.getStartRes(),
490		Math.round((float) (od.getBoxX()) * alwidth / od.getWidth()));
491	1	assertEquals(vpranges.getStartSeq(), 0);
492
493		// click in hidden cols
494		// boxX and scrollCol adjusted for hidden cols, width normal
495	1	xpos = 115;
496	1	assertEquals(od.getBoxX(),
497		Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
498		- boxWidth + 1);
499	1	assertEquals(od.getBoxY(), 0);
500	1	assertEquals(od.getBoxWidth(), boxWidth);
501	1	assertEquals(od.getBoxHeight(), boxHeight);
502	1	assertEquals(vpranges.getStartRes(),
503		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
504	1	assertEquals(vpranges.getStartSeq(), 0);
505
506		// click off end of alignment
507		// boxX and scrollCol adjusted for hidden cols, width normal
508	1	xpos = 3000;
509	1	assertEquals(od.getBoxX(),
510		Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
511		- boxWidth + 1);
512	1	assertEquals(od.getBoxY(), 0);
513	1	assertEquals(od.getBoxWidth(), boxWidth);
514	1	assertEquals(od.getBoxHeight(), boxHeight);
515	1	assertEquals(vpranges.getStartRes(),
516		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
517	1	assertEquals(vpranges.getStartSeq(), 0);
518		}
519
520		/**
521		* Test that the box position is set correctly when set from the viewport,
522		* with no hidden rows or columns
523		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
524	1	@Test(groups = { "Functional" })...
525		public void testSetBoxFromViewport()
526		{
527		// move viewport to start of alignment
528	1	moveViewport(0, 0);
529	1	assertEquals(od.getBoxX(), 0);
530	1	assertEquals(od.getBoxY(), 0);
531	1	assertEquals(od.getBoxWidth(), boxWidth);
532	1	assertEquals(od.getBoxHeight(), boxHeight);
533
534		// move viewport to right
535	1	moveViewportH(70);
536	1	assertEquals(od.getBoxX(),
537		Math.round((float) 70 * od.getWidth() / alwidth));
538	1	assertEquals(od.getBoxY(), 0);
539	1	assertEquals(od.getBoxWidth(), boxWidth);
540	1	assertEquals(od.getBoxHeight(), boxHeight);
541
542		// move viewport down
543	1	moveViewportV(100);
544	1	assertEquals(od.getBoxX(),
545		Math.round((float) 70 * od.getWidth() / alwidth));
546	1	assertEquals(od.getBoxY(),
547		Math.round(100 * od.getSequencesHeight() / alheight));
548	1	assertEquals(od.getBoxWidth(), boxWidth);
549	1	assertEquals(od.getBoxHeight(), boxHeight);
550
551		// move viewport to bottom right
552	1	moveViewport(98, 508);
553	1	assertEquals(od.getBoxX(),
554		Math.round((float) 98 * od.getWidth() / alwidth));
555	1	assertEquals(od.getBoxY(),
556		Math.round((float) 508 * od.getSequencesHeight() / alheight));
557	1	assertEquals(od.getBoxWidth(), boxWidth);
558	1	assertEquals(od.getBoxHeight(), boxHeight);
559		}
560
561		/**
562		* Test that the box position is set correctly when there are hidden columns
563		* at the start
564		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
565	1	@Test(groups = { "Functional" })...
566		public void testSetBoxFromViewportHiddenColsAtStart()
567		{
568	1	int firstHidden = 0;
569	1	int lastHidden = 20;
570	1	hiddenCols.hideColumns(firstHidden, lastHidden);
571
572		// move viewport to start of alignment
573	1	moveViewport(0, 0);
574	1	assertEquals(od.getBoxX(),
575		Math.round((float) (lastHidden + 1) * od.getWidth() / alwidth));
576	1	assertEquals(od.getBoxY(), 0);
577	1	assertEquals(od.getBoxWidth(), boxWidth);
578	1	assertEquals(od.getBoxHeight(), boxHeight);
579
580		// move viewport to end of alignment - need to make startRes by removing
581		// hidden cols because of how viewport/overview are implemented
582	1	moveViewport(98 - lastHidden - 1, 0);
583	1	assertEquals(od.getBoxX(),
584		Math.round((float) 98 * od.getWidth() / alwidth));
585	1	assertEquals(od.getBoxY(), 0);
586	1	assertEquals(od.getBoxWidth(), boxWidth);
587	1	assertEquals(od.getBoxHeight(), boxHeight);
588		}
589
590		/**
591		* Test that the box position is set correctly when there are hidden columns
592		* in the middle
593		*/
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
594	1	@Test(groups = { "Functional" })...
595		public void testSetBoxFromViewportHiddenColsInMiddle()
596		{
597	1	int firstHidden = 68;
598	1	int lastHidden = 78;
599	1	hiddenCols.hideColumns(firstHidden, lastHidden);
600
601		// move viewport before hidden columns
602	1	moveViewport(3, 0);
603
604	1	assertEquals(od.getBoxX(),
605		Math.round((float) 3 * od.getWidth() / alwidth));
606	1	assertEquals(od.getBoxY(), 0);
607	1	assertEquals(od.getBoxWidth(), boxWidth);
608	1	assertEquals(od.getBoxHeight(), boxHeight);
609
610		// move viewport to left of hidden columns with overlap
611	1	moveViewport(10, 0);
612	1	assertEquals(od.getBoxX(),
613		Math.round((float) 10 * od.getWidth() / alwidth));
614	1	assertEquals(od.getBoxY(), 0);
615	1	assertEquals(od.getBoxWidth(),
616		boxWidth + Math.round((float) (lastHidden - firstHidden + 1)
617		* od.getWidth() / alwidth));
618	1	assertEquals(od.getBoxHeight(), boxHeight);
619
620		// move viewport to straddle hidden columns
621	1	moveViewport(63, 0);
622	1	assertEquals(od.getBoxX(),
623		Math.round((float) 63 * od.getWidth() / alwidth));
624	1	assertEquals(od.getBoxY(), 0);
625	1	assertEquals(od.getBoxWidth(), boxWidth + Math.round(
626		(lastHidden - firstHidden + 1) * od.getWidth() / alwidth));
627	1	assertEquals(od.getBoxHeight(), boxHeight);
628
629		// move viewport to right of hidden columns, no overlap
630	1	moveViewport(80 - (lastHidden - firstHidden + 1), 0);
631	1	assertEquals(od.getBoxX(),
632		Math.round((float) 80 * od.getWidth() / alwidth));
633	1	assertEquals(od.getBoxY(), 0);
634	1	assertEquals(od.getBoxWidth(), boxWidth);
635	1	assertEquals(od.getBoxHeight(), boxHeight);
636
637		}
638
639		/**
640		* Test that the box position is set correctly when there are hidden columns
641		* at the end
642		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
643	1	@Test(groups = { "Functional" })...
644		public void testSetBoxFromViewportHiddenColsAtEnd()
645		{
646	1	int firstHidden = 152;
647	1	int lastHidden = 164;
648	1	hiddenCols.hideColumns(firstHidden, lastHidden);
649
650		// move viewport before hidden columns
651	1	moveViewport(3, 0);
652	1	assertEquals(od.getBoxX(),
653		Math.round((float) 3 * od.getWidth() / alwidth));
654	1	assertEquals(od.getBoxY(), 0);
655	1	assertEquals(od.getBoxWidth(), boxWidth);
656	1	assertEquals(od.getBoxHeight(), boxHeight);
657
658		// move viewport to hidden columns
659		// viewport can't actually extend into hidden cols,
660		// so move to the far right edge of the viewport
661	1	moveViewport(firstHidden - viewWidth, 0);
662	1	assertEquals(od.getBoxX(), Math.round(
663		(float) (firstHidden - viewWidth) * od.getWidth() / alwidth));
664	1	assertEquals(od.getBoxY(), 0);
665	1	assertEquals(od.getBoxWidth(), boxWidth);
666	1	assertEquals(od.getBoxHeight(), boxHeight);
667		}
668
669		/**
670		* Test that the box position is set correctly when there are hidden rows at
671		* the start
672		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
673	1	@Test(groups = { "Functional" })...
674		public void testSetBoxFromViewportHiddenRowsAtStart()
675		{
676	1	int firstHidden = 0;
677	1	int lastHidden = 20;
678	1	hideSequences(firstHidden, lastHidden);
679
680		// move viewport to start of alignment:
681		// box moves to below hidden rows, height remains same
682	1	moveViewport(0, 0);
683	1	assertEquals(od.getBoxX(), 0);
684	1	assertEquals(od.getBoxY(), Math.round(
685		(float) (lastHidden + 1) * od.getSequencesHeight() / alheight));
686	1	assertEquals(od.getBoxWidth(), boxWidth);
687	1	assertEquals(od.getBoxHeight(), boxHeight);
688
689		// move viewport to end of alignment
690	1	moveViewport(0, 525 - viewHeight - lastHidden - 1);
691	1	assertEquals(od.getBoxX(), 0);
692	1	assertEquals(od.getBoxY(), Math.round((float) (525 - viewHeight)
693		* od.getSequencesHeight() / alheight));
694	1	assertEquals(od.getBoxWidth(), boxWidth);
695	1	assertEquals(od.getBoxHeight(), boxHeight);
696		}
697
698		/**
699		* Test that the box position is set correctly when there are hidden rows in
700		* the middle
701		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
702	1	@Test(groups = { "Functional" })...
703		public void testSetBoxFromViewportHiddenRowsInMiddle()
704		{
705	1	int firstHidden = 200;
706	1	int lastHidden = 210;
707	1	hideSequences(firstHidden, lastHidden);
708
709		// move viewport to start of alignment:
710		// box, height etc as in non-hidden case
711	1	moveViewport(0, 0);
712	1	assertEquals(od.getBoxX(), 0);
713	1	assertEquals(od.getBoxY(), 0);
714	1	assertEquals(od.getBoxWidth(), boxWidth);
715	1	assertEquals(od.getBoxHeight(), boxHeight);
716
717		// move viewport to straddle hidden rows
718	1	moveViewport(0, 198);
719	1	assertEquals(od.getBoxX(), 0);
720	1	assertEquals(od.getBoxY(),
721		Math.round((float) 198 * od.getSequencesHeight() / alheight));
722	1	assertEquals(od.getBoxWidth(), boxWidth);
723	1	assertEquals(od.getBoxHeight(),
724		Math.round((float) (viewHeight + lastHidden - firstHidden + 1)
725		* od.getSequencesHeight() / alheight));
726		}
727
728		/**
729		* Test that the box position is set correctly when there are hidden rows at
730		* the bottom
731		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
732	1	@Test(groups = { "Functional" })...
733		public void testSetBoxFromViewportHiddenRowsAtEnd()
734		{
735	1	int firstHidden = 500;
736	1	int lastHidden = 524;
737	1	hideSequences(firstHidden, lastHidden);
738
739		// move viewport to start of alignment:
740		// box, height etc as in non-hidden case
741	1	moveViewport(0, 0);
742	1	assertEquals(od.getBoxX(), 0);
743	1	assertEquals(od.getBoxY(), 0);
744	1	assertEquals(od.getBoxWidth(), boxWidth);
745	1	assertEquals(od.getBoxHeight(), boxHeight);
746
747		// move viewport to end of alignment
748		// viewport sits above hidden rows and does not include them
749	1	moveViewport(0, firstHidden - viewHeight - 1);
750	1	assertEquals(od.getBoxX(), 0);
751	1	assertEquals(od.getBoxY(),
752		Math.round((float) (firstHidden - viewHeight - 1)
753		* od.getSequencesHeight() / alheight));
754	1	assertEquals(od.getBoxWidth(), boxWidth);
755	1	assertEquals(od.getBoxHeight(), boxHeight);
756
757		}
758
759		/**
760		* Test setting of the box position, when there are hidden rows at the start
761		* of the alignment
762		*/
		100% Uncovered Elements: 0 (24) Complexity: 1 Complexity Density: 0.04 1PASS
763	1	@Test(groups = { "Functional" })...
764		public void testFromMouseWithHiddenRowsAtStart()
765		{
766	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
767	1	assertEquals(od.getBoxX(), 0);
768	1	assertEquals(od.getBoxY(), 0);
769	1	assertEquals(od.getBoxHeight(), boxHeight);
770	1	assertEquals(od.getBoxWidth(), boxWidth);
771	1	assertEquals(vpranges.getStartRes(), 0);
772	1	assertEquals(vpranges.getStartSeq(), 0);
773
774		// hide rows at start and check updated box position is correct
775		// changes boxY but not boxheight
776	1	int lastHiddenRow = 30;
777	1	hideSequences(0, lastHiddenRow);
778
779	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
780	1	assertEquals(od.getBoxX(), 0);
781	1	assertEquals(od.getBoxY(), Math.round((float) (lastHiddenRow + 1)
782		* od.getSequencesHeight() / alheight));
783	1	assertEquals(od.getBoxWidth(), boxWidth);
784	1	assertEquals(od.getBoxHeight(), boxHeight);
785
786		// click in hidden rows - same result
787	1	mouseClick(od, 0, 0);
788	1	assertEquals(od.getBoxX(), 0);
789	1	assertEquals(od.getBoxY(), Math.round((float) (lastHiddenRow + 1)
790		* od.getSequencesHeight() / alheight));
791	1	assertEquals(od.getBoxWidth(), boxWidth);
792	1	assertEquals(od.getBoxHeight(), boxHeight);
793
794		// click below hidden rows
795	1	mouseClick(od, 0, 150 + boxHeight / 2);
796	1	assertEquals(od.getBoxX(), 0);
797	1	assertEquals(od.getBoxY(), 150);
798	1	assertEquals(od.getBoxWidth(), boxWidth);
799	1	assertEquals(od.getBoxHeight(), boxHeight);
800		}
801
802		/**
803		* Test setting of the box position, when there are hidden rows at the middle
804		* of the alignment
805		*/
		100% Uncovered Elements: 0 (22) Complexity: 1 Complexity Density: 0.05 1PASS
806	1	@Test(groups = { "Functional" })...
807		public void testFromMouseWithHiddenRowsInMiddle()
808		{
809	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
810
811	1	assertEquals(od.getBoxX(), 0);
812	1	assertEquals(od.getBoxY(), 0);
813	1	assertEquals(od.getBoxWidth(), boxWidth);
814	1	assertEquals(od.getBoxHeight(), boxHeight);
815	1	assertEquals(vpranges.getStartRes(), 0);
816	1	assertEquals(vpranges.getStartSeq(), 0);
817
818		// hide rows in middle and check updated box position is correct
819		// no changes
820	1	int firstHiddenRow = 50;
821	1	int lastHiddenRow = 54;
822	1	hideSequences(firstHiddenRow, lastHiddenRow);
823
824	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
825
826	1	assertEquals(od.getBoxX(), 0);
827	1	assertEquals(od.getBoxY(), 0);
828	1	assertEquals(od.getBoxWidth(), boxWidth);
829	1	assertEquals(od.getBoxHeight(), boxHeight);
830
831		// click above hidden rows, so that box overlaps
832	1	int rowpos = 35; // row value in residues
833	1	int centrepos = 43; // centre row
834	1	mouseClick(od, 0, Math
835		.round((float) centrepos * od.getSequencesHeight() / alheight));
836	1	assertEquals(od.getBoxX(), 0);
837	1	assertEquals(od.getBoxY(), Math
838		.round((float) rowpos * od.getSequencesHeight() / alheight));
839	1	assertEquals(od.getBoxWidth(), boxWidth);
840	1	assertEquals(od.getBoxHeight(),
841		boxHeight + Math
842		.round((float) (lastHiddenRow - firstHiddenRow + 1)
843		* od.getSequencesHeight() / alheight));
844		}
845
846		/**
847		* Test setting of the box position, when there are hidden rows at the end of
848		* the alignment
849		*/
		100% Uncovered Elements: 0 (33) Complexity: 1 Complexity Density: 0.03 1PASS
850	1	@Test(groups = { "Functional" })...
851		public void testFromMouseWithHiddenRowsAtEnd()
852		{
853	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
854	1	assertEquals(od.getBoxX(), 0);
855	1	assertEquals(od.getBoxY(), 0);
856	1	assertEquals(od.getBoxWidth(), boxWidth);
857	1	assertEquals(od.getBoxHeight(), boxHeight);
858	1	assertEquals(vpranges.getStartRes(), 0);
859	1	assertEquals(vpranges.getStartSeq(), 0);
860
861		// hide rows at end and check updated box position is correct
862		// no changes
863	1	int firstHidden = 500;
864	1	int lastHidden = 524;
865	1	hideSequences(firstHidden, lastHidden);
866
867	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
868	1	assertEquals(od.getBoxX(), 0);
869	1	assertEquals(od.getBoxY(), 0);
870	1	assertEquals(od.getBoxWidth(), boxWidth);
871	1	assertEquals(od.getBoxHeight(), boxHeight);
872
873		// click above hidden rows, no overlap
874	1	int ypos = 40 + viewHeight / 2; // top is row 40
875	1	mouseClick(od, 0,
876		Math.round((float) ypos * od.getSequencesHeight() / alheight));
877	1	assertEquals(od.getBoxX(), 0);
878	1	assertEquals(od.getBoxY(),
879		Math.round((float) 40 * od.getSequencesHeight() / alheight));
880	1	assertEquals(od.getBoxWidth(), boxWidth);
881	1	assertEquals(od.getBoxHeight(), boxHeight);
882
883		// click above hidden rows so box overlaps
884		// boxY moved upwards, boxHeight remains same
885	1	ypos = 497 + viewHeight / 2; // row 497
886	1	mouseClick(od, 0,
887		Math.round((float) ypos * od.getSequencesHeight() / alheight));
888	1	assertEquals(od.getBoxX(), 0);
889	1	assertEquals(od.getBoxY(), Math.round((float) (firstHidden - viewHeight)
890		* od.getSequencesHeight() / alheight));
891	1	assertEquals(od.getBoxWidth(), boxWidth);
892	1	assertEquals(od.getBoxHeight(), boxHeight);
893
894		// click within hidden rows
895	1	ypos = 505 + boxHeight / 2;
896	1	mouseClick(od, 0,
897		Math.round((float) ypos * od.getSequencesHeight() / alheight));
898	1	assertEquals(od.getBoxX(), 0);
899	1	assertEquals(od.getBoxY(), Math.round((firstHidden - viewHeight)
900		* od.getSequencesHeight() / alheight));
901	1	assertEquals(od.getBoxWidth(), boxWidth);
902	1	assertEquals(od.getBoxHeight(), boxHeight);
903		}
904
905		/**
906		* Test the function to determine if a point is in the overview's box or not
907		*/
		100% Uncovered Elements: 0 (34) Complexity: 1 Complexity Density: 0.03 1PASS
908	1	@Test(groups = { "Functional" })...
909		public void testPositionInBox()
910		{
911	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
912
913	1	assertFalse(od.isPositionInBox(0, 0));
914	1	assertTrue(od.isPositionInBox(10, 9));
915	1	assertFalse(od.isPositionInBox(0, 9));
916	1	assertFalse(od.isPositionInBox(9, 0));
917	1	assertFalse(od.isPositionInBox(75, 20));
918
919	1	assertTrue(od.isPositionInBox(47, 6));
920	1	assertFalse(od.isPositionInBox(48, 6));
921	1	assertTrue(od.isPositionInBox(47, 9));
922	1	assertFalse(od.isPositionInBox(47, 10));
923
924		// hide columns in the box area
925		// extends area where a point is considered to be in the box
926	1	hiddenCols.hideColumns(1, 4);
927	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
928	1	assertFalse(od.isPositionInBox(0, 0));
929	1	assertTrue(od.isPositionInBox(10, 9));
930	1	assertFalse(od.isPositionInBox(0, 9));
931	1	assertFalse(od.isPositionInBox(9, 0));
932	1	assertFalse(od.isPositionInBox(75, 20));
933
934	1	assertTrue(od.isPositionInBox(47, 6));
935	1	assertTrue(od.isPositionInBox(48, 6));
936	1	assertTrue(od.isPositionInBox(47, 9));
937	1	assertFalse(od.isPositionInBox(47, 10));
938
939		// hide sequences in box area
940		// extends area where a point is considered to be in the box
941	1	hideSequences(1, 3);
942	1	ColumnSelection cs = new ColumnSelection();
943	1	hiddenCols.revealAllHiddenColumns(cs);
944	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
945	1	assertFalse(od.isPositionInBox(0, 0));
946	1	assertTrue(od.isPositionInBox(10, 9));
947	1	assertFalse(od.isPositionInBox(0, 9));
948	1	assertFalse(od.isPositionInBox(9, 0));
949	1	assertFalse(od.isPositionInBox(75, 20));
950
951	1	assertTrue(od.isPositionInBox(47, 6));
952	1	assertFalse(od.isPositionInBox(48, 6));
953	1	assertTrue(od.isPositionInBox(47, 9));
954	1	assertTrue(od.isPositionInBox(47, 10));
955		}
956
957		/**
958		* Test the dragging functionality
959		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
960	1	@Test(groups = { "Functional" })...
961		public void testDragging()
962		{
963	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
964	1	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
965	1	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
966
967		// updates require an OverviewPanel to exist which it doesn't here
968		// so call setBoxPosition() as it would be called by the AlignmentPanel
969		// normally
970	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
971
972		// corner moves 16 (20-4) right and 6 (22-16) up
973	1	assertEquals(od.getBoxX(), 16);
974	1	assertEquals(od.getBoxY(), 6);
975
976		// hide columns - box moves drag distance + hidden cols, vertically makes no
977		// difference
978	1	hiddenCols.hideColumns(1, 4);
979	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
980	1	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
981	1	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
982	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
983
984		// corner moves 16 (20-4) + hiddenCols right and 6 (22-16) down
985	1	assertEquals(od.getBoxX(),
986		16 + Math.round((float) 4 * od.getWidth() / alwidth));
987	1	assertEquals(od.getBoxY(), 6);
988
989		// hide sequences in box area
990		// makes absolutely no difference
991	1	hideSequences(1, 3);
992	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
993	1	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
994	1	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
995	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
996
997		// corner moves 16 (20-4) + hiddenCols right and 6 (22-16) + hiddenRows down
998	1	assertEquals(od.getBoxX(),
999		16 + Math.round((float) 4 * od.getWidth() / alwidth));
1000	1	assertEquals(od.getBoxY(),
1001		6 + Math.round((float) 3 * od.getHeight() / alheight));
1002		}
1003
1004		/*
1005		* Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
1006		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1007	2	private void moveViewportH(int startRes)...
1008		{
1009	2	vpranges.setViewportStartAndWidth(startRes, viewWidth);
1010	2	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1011		}
1012
1013		/*
1014		* Move viewport vertically: startSeq and endSeq give new vertical extent. Horizontal extent stays the same.
1015		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1016	1	private void moveViewportV(int startSeq)...
1017		{
1018	1	vpranges.setViewportStartAndHeight(startSeq, viewHeight);
1019	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1020		}
1021
1022		/*
1023		* Move viewport horizontally and vertically.
1024		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
1025	34	private void moveViewport(int startRes, int startSeq)...
1026		{
1027	34	vpranges.setViewportStartAndWidth(startRes, viewWidth);
1028	34	vpranges.setViewportStartAndHeight(startSeq, viewHeight);
1029	34	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1030		}
1031
1032		/*
1033		* Mouse click as position x,y in overview window
1034		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1035	42	private void mouseClick(OverviewDimensions od, int x, int y)...
1036		{
1037	42	od.updateViewportFromMouse(x, y, al.getHiddenSequences(), hiddenCols);
1038
1039		// updates require an OverviewPanel to exist which it doesn't here
1040		// so call setBoxPosition() as it would be called by the AlignmentPanel
1041		// normally
1042	42	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1043		}
1044
1045		/*
1046		* Test that the box is positioned with the centre at xpos, ypos
1047		* and with the original width and height
1048		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
1049	1	private void testBoxIsAtClickPoint(int xpos, int ypos)...
1050		{
1051	1	mouseClick(od, xpos, ypos);
1052	1	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
1053	1	assertEquals(od.getBoxY() + od.getBoxHeight() / 2, ypos);
1054	1	assertEquals(od.getBoxWidth(), boxWidth);
1055	1	assertEquals(od.getBoxHeight(), boxHeight);
1056
1057		}
1058
1059		/*
1060		* Hide sequences between start and end
1061		*/
		100% Uncovered Elements: 0 (8) Complexity: 2 Complexity Density: 0.33
1062	9	private void hideSequences(int start, int end)...
1063		{
1064	9	SequenceI[] allseqs = al.getSequencesArray();
1065	9	SequenceGroup theseSeqs = new SequenceGroup();
1066
1067	164	for (int i = start; i <= end; i++)
1068		{
1069	155	theseSeqs.addSequence(allseqs[i], false);
1070	155	al.getHiddenSequences().hideSequence(allseqs[i]);
1071		}
1072
1073	9	hiddenRepSequences.put(allseqs[start], theseSeqs);
1074		}
1075
1076		/**
1077		* Test setting of the box position, when there are hidden rows at the start
1078		* of the alignment
1079		*/
		100% Uncovered Elements: 0 (26) Complexity: 1 Complexity Density: 0.04 1PASS
1080	1	@Test(groups = { "Functional" })...
1081		public void testFromMouseWithHiddenRowsAtStartWrapped()
1082		{
1083	1	vpranges.setWrappedMode(true);
1084	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
1085	1	assertEquals(od.getBoxX(), 0);
1086	1	assertEquals(od.getBoxY(), 0);
1087	1	assertEquals(od.getBoxHeight(), boxHeight);
1088	1	assertEquals(od.getBoxWidth(), boxWidth);
1089	1	assertEquals(vpranges.getStartRes(), 0);
1090	1	assertEquals(vpranges.getStartSeq(), 0);
1091
1092		// hide rows at start and check updated box position is correct
1093		// changes boxY but not boxheight
1094	1	int lastHiddenRow = 30;
1095	1	hideSequences(0, lastHiddenRow);
1096
1097	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1098	1	assertEquals(od.getBoxX(), 0);
1099	1	assertEquals(od.getBoxY(), Math.round((float) (lastHiddenRow + 1)
1100		* od.getSequencesHeight() / alheight));
1101	1	assertEquals(od.getBoxWidth(), boxWidth);
1102	1	assertEquals(od.getBoxHeight(), boxHeight);
1103
1104		// click in hidden rows - same result
1105	1	mouseClick(od, 0, 0);
1106	1	assertEquals(od.getBoxX(), 0);
1107	1	int boxY = od.getBoxY();
1108	1	assertEquals(boxY, Math.round((float) (lastHiddenRow + 1)
1109		* od.getSequencesHeight() / alheight));
1110	1	assertEquals(od.getBoxWidth(), boxWidth);
1111	1	assertEquals(od.getBoxHeight(), boxHeight);
1112
1113		// click below hidden rows
1114		// vertical move of overview box is suppressed in wrapped mode
1115	1	mouseClick(od, 0, 150);
1116	1	assertEquals(od.getBoxX(), 0);
1117	1	assertEquals(od.getBoxY(), boxY); // unchanged
1118	1	assertEquals(od.getBoxWidth(), boxWidth);
1119	1	assertEquals(od.getBoxHeight(), boxHeight);
1120		}
1121		}