Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
OverviewDimensionsHideHiddenTest	45	496	28	0	1.0100%	Show methods

Class OverviewDimensionsHideHiddenTest

Class OverviewDimensionsHideHiddenTest	Line # 45	Total Statements 496	Complexity 28	Uncovered Elements 0	TOTAL Coverage 1.0100%
setUpAlignment() : void   setUpAlignment() : void	6565	2.02	1.01	0.00	1.0 1.0100%
setUp() : void   setUp() : void	7373	18.018	2.02	0.00	1.0 1.0100%
cleanUp() : void   cleanUp() : void	111111	1.01	1.01	0.00	1.0 1.0100%
testConstructor() : void   testConstructor() : void	121121	51.051	1.01	0.00	1.0 1.0100%
testSetBoxFromMouseClick() : void   testSetBoxFromMouseClick() : void	200200	55.055	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenColsAtStart() : void   testFromMouseWithHiddenColsAtStart() : void	302302	20.020	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenColsInMiddle() : void   testFromMouseWithHiddenColsInMiddle() : void	343343	51.051	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenColsAtEnd() : void   testFromMouseWithHiddenColsAtEnd() : void	428428	33.033	1.01	0.00	1.0 1.0100%
testSetBoxFromViewport() : void   testSetBoxFromViewport() : void	486486	20.020	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenColsAtStart() : void   testSetBoxFromViewportHiddenColsAtStart() : void	527527	13.013	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenColsInMiddle() : void   testSetBoxFromViewportHiddenColsInMiddle() : void	556556	23.023	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenColsAtEnd() : void   testSetBoxFromViewportHiddenColsAtEnd() : void	603603	13.013	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenRowsAtStart() : void   testSetBoxFromViewportHiddenRowsAtStart() : void	634634	17.017	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenRowsInMiddle() : void   testSetBoxFromViewportHiddenRowsInMiddle() : void	676676	17.017	1.01	0.00	1.0 1.0100%
testSetBoxFromViewportHiddenRowsAtEnd() : void   testSetBoxFromViewportHiddenRowsAtEnd() : void	715715	17.017	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenRowsAtStart() : void   testFromMouseWithHiddenRowsAtStart() : void	758758	23.023	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenRowsInMiddle() : void   testFromMouseWithHiddenRowsInMiddle() : void	802802	31.031	1.01	0.00	1.0 1.0100%
testFromMouseWithHiddenRowsAtEnd() : void   testFromMouseWithHiddenRowsAtEnd() : void	863863	31.031	1.01	0.00	1.0 1.0100%
testPositionInBox() : void   testPositionInBox() : void	925925	20.020	1.01	0.00	1.0 1.0100%
testDragging() : void   testDragging() : void	960960	20.020	1.01	0.00	1.0 1.0100%
moveViewportH(int) : void   moveViewportH(int) : void	10051005	2.02	1.01	0.00	1.0 1.0100%
moveViewportV(int) : void   moveViewportV(int) : void	10141014	2.02	1.01	0.00	1.0 1.0100%
moveViewport(int,int) : void   moveViewport(int,int) : void	10231023	3.03	1.01	0.00	1.0 1.0100%
mouseClick(OverviewDimensions,int,int) : void   mouseClick(OverviewDimensions,int,int) : void	10331033	2.02	1.01	0.00	1.0 1.0100%
testBoxIsAtClickPoint(int,int) : void   testBoxIsAtClickPoint(int,int) : void	10471047	5.05	1.01	0.00	1.0 1.0100%
hideSequences(int,int) : void   hideSequences(int,int) : void	10601060	6.06	2.02	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.117870726	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromMouseClickjalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromMouseClick	1PASS
	0.11596958	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenColsInMiddlejalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenColsInMiddle	1PASS
	0.09885932	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testConstructorjalview.viewmodel.OverviewDimensionsHideHiddenTest.testConstructor	1PASS
	0.08365019	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenRowsAtEndjalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenRowsAtEnd	1PASS
	0.08365019	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenRowsInMiddlejalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenRowsInMiddle	1PASS
	0.08174905	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenColsAtEndjalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenColsAtEnd	1PASS
	0.06844106	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenRowsAtStartjalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenRowsAtStart	1PASS
	0.058935363	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportjalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewport	1PASS
	0.058935363	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsAtStartjalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsAtStart	1PASS
	0.058935363	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsAtEndjalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsAtEnd	1PASS
	0.058935363	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsInMiddlejalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsInMiddle	1PASS
	0.05703422	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testPositionInBoxjalview.viewmodel.OverviewDimensionsHideHiddenTest.testPositionInBox	1PASS
	0.05703422	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenColsAtStartjalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenColsAtStart	1PASS
	0.05703422	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testDraggingjalview.viewmodel.OverviewDimensionsHideHiddenTest.testDragging	1PASS
	0.05323194	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenColsInMiddlejalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenColsInMiddle	1PASS
	0.03422053	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenColsAtStartjalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenColsAtStart	1PASS
	0.03422053	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenColsAtEndjalview.viewmodel.OverviewDimensionsHideHiddenTest.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 (526) Complexity: 28 Complexity Density: 0.06
45		public class OverviewDimensionsHideHiddenTest
46		{
47		AlignmentI al;
48
49		OverviewDimensionsHideHidden od;
50
51		// cached widths and heights
52		int boxWidth;
53		int boxHeight;
54		int viewHeight;
55		int viewWidth;
56		int alheight;
57		int alwidth;
58
59		ViewportRanges vpranges;
60
61		Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<>();
62
63		HiddenColumns hiddenCols = new HiddenColumns();
64
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
65	1	@BeforeClass(alwaysRun = true)...
66		public void setUpAlignment()
67		{
68		// create random alignment
69	1	AlignmentGenerator gen = new AlignmentGenerator(false);
70	1	al = gen.generate(157, 525, 123, 5, 5);
71		}
72
		100% Uncovered Elements: 0 (20) Complexity: 2 Complexity Density: 0.11
73	17	@BeforeMethod(alwaysRun = true)...
74		public void setUp()
75		{
76	17	if (!hiddenRepSequences.isEmpty())
77		{
78	15	al.getHiddenSequences().showAll(hiddenRepSequences);
79		}
80	17	ColumnSelection colsel = new ColumnSelection();
81	17	hiddenCols.revealAllHiddenColumns(colsel);
82
83	17	vpranges = new ViewportRanges(al);
84	17	vpranges.setViewportStartAndHeight(0, 18);
85	17	vpranges.setViewportStartAndWidth(0, 63);
86
87	17	viewHeight = vpranges.getEndSeq() - vpranges.getStartSeq() + 1;
88	17	viewWidth = vpranges.getEndRes() - vpranges.getStartRes() + 1;
89
90	17	HiddenColumns hiddenCols = new HiddenColumns();
91
92	17	od = new OverviewDimensionsHideHidden(vpranges, true);
93		// Initial box sizing - default path through code
94	17	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
95
96	17	mouseClick(od, 0, 0);
97	17	moveViewport(0, 0);
98
99		// calculate with visible values
100	17	alheight = vpranges.getVisibleAlignmentHeight();
101	17	alwidth = vpranges.getVisibleAlignmentWidth();
102
103	17	boxWidth = Math.round((float) (vpranges.getEndRes()
104		- vpranges.getStartRes() + 1)
105		* od.getWidth() / alwidth);
106	17	boxHeight = Math.round((float) (vpranges.getEndSeq()
107		- vpranges.getStartSeq() + 1)
108		* od.getSequencesHeight() / alheight);
109		}
110
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
111	1	@AfterClass(alwaysRun = true)...
112		public void cleanUp()
113		{
114	1	al = null;
115		}
116
117		/**
118		* Test that the OverviewDimensions constructor sets width and height
119		* correctly
120		*/
		100% Uncovered Elements: 0 (51) Complexity: 1 Complexity Density: 0.02 1PASS
121	1	@Test(groups = { "Functional" })...
122		public void testConstructor()
123		{
124	1	SequenceI seqa = new Sequence("Seq1", "ABC");
125	1	SequenceI seqb = new Sequence("Seq2", "ABC");
126	1	SequenceI seqc = new Sequence("Seq3", "ABC");
127	1	SequenceI seqd = new Sequence("Seq4", "ABC");
128	1	SequenceI seqe = new Sequence("Seq5",
129		"ABCABCABCABCABCABCABCABCBACBACBACBAC");
130
131	1	int defaultGraphHeight = 20;
132	1	int maxWidth = 400;
133	1	int minWidth = 120;
134	1	int maxSeqHeight = 300;
135	1	int minSeqHeight = 40;
136
137		// test for alignment with width > height
138	1	SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
139	1	Alignment al1 = new Alignment(seqs1);
140	1	ViewportRanges props = new ViewportRanges(al1);
141
142	1	OverviewDimensions od = new OverviewDimensionsHideHidden(props, true);
143	1	int scaledHeight = 267;
144	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
145	1	assertEquals(od.getSequencesHeight(), scaledHeight);
146	1	assertEquals(od.getWidth(), maxWidth);
147	1	assertEquals(od.getHeight(), scaledHeight + defaultGraphHeight);
148
149		// test for alignment with width < height
150	1	SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
151	1	Alignment al2 = new Alignment(seqs2);
152	1	props = new ViewportRanges(al2);
153
154	1	od = new OverviewDimensionsHideHidden(props, true);
155	1	int scaledWidth = 300;
156	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
157	1	assertEquals(od.getSequencesHeight(), maxSeqHeight);
158	1	assertEquals(od.getWidth(), scaledWidth);
159	1	assertEquals(od.getHeight(), scaledWidth + defaultGraphHeight);
160
161		// test for alignment with width > height and sequence height scaled below
162		// min value
163	1	SequenceI[] seqs3 = new SequenceI[] { seqe };
164	1	Alignment al3 = new Alignment(seqs3);
165	1	props = new ViewportRanges(al3);
166
167	1	od = new OverviewDimensionsHideHidden(props, true);
168	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
169	1	assertEquals(od.getSequencesHeight(), minSeqHeight);
170	1	assertEquals(od.getWidth(), maxWidth);
171	1	assertEquals(od.getHeight(), minSeqHeight + defaultGraphHeight);
172
173		// test for alignment with width < height and width scaled below min value
174	1	SequenceI[] seqs4 = new SequenceI[] { seqa, seqb, seqc, seqd, seqa,
175		seqb, seqc, seqd, seqa, seqb, seqc, seqd, seqa, seqb, seqc, seqd };
176	1	Alignment al4 = new Alignment(seqs4);
177	1	props = new ViewportRanges(al4);
178
179	1	od = new OverviewDimensionsHideHidden(props, true);
180	1	assertEquals(od.getGraphHeight(), defaultGraphHeight);
181	1	assertEquals(od.getSequencesHeight(), maxSeqHeight);
182	1	assertEquals(od.getWidth(), minWidth);
183	1	assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);
184
185	1	Alignment al5 = new Alignment(seqs4);
186	1	props = new ViewportRanges(al5);
187
188	1	od = new OverviewDimensionsHideHidden(props, false);
189	1	assertEquals(od.getGraphHeight(), 0);
190	1	assertEquals(od.getSequencesHeight(), maxSeqHeight);
191	1	assertEquals(od.getWidth(), minWidth);
192	1	assertEquals(od.getHeight(), maxSeqHeight);
193		}
194
195		/**
196		* Test that validation after mouse adjustments to boxX and boxY sets box
197		* dimensions and scroll values correctly, when there are no hidden rows or
198		* columns.
199		*/
		100% Uncovered Elements: 0 (55) Complexity: 1 Complexity Density: 0.02 1PASS
200	1	@Test(groups = { "Functional" })...
201		public void testSetBoxFromMouseClick()
202		{
203	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
204	1	assertEquals(od.getBoxX(), 0);
205	1	assertEquals(od.getBoxY(), 0);
206	1	assertEquals(od.getBoxWidth(), boxWidth);
207	1	assertEquals(vpranges.getStartRes(), 0);
208	1	assertEquals(vpranges.getStartSeq(), 0);
209
210		// negative boxX value reset to 0
211	1	mouseClick(od, -5, 10);
212	1	assertEquals(od.getBoxX(), 0);
213	1	assertEquals(od.getBoxWidth(), boxWidth);
214	1	assertEquals(od.getBoxHeight(), boxHeight);
215	1	assertEquals(vpranges.getStartSeq() + vpranges.getViewportHeight() / 2,
216		Math.round((float) 10 * alheight / od.getSequencesHeight()));
217	1	assertEquals(vpranges.getStartRes(), 0);
218
219		// negative boxY value reset to 0
220	1	mouseClick(od, 6, -2);
221	1	assertEquals(od.getBoxY(), 0);
222	1	assertEquals(od.getBoxWidth(), boxWidth);
223	1	assertEquals(od.getBoxHeight(), boxHeight);
224	1	assertEquals(vpranges.getStartRes(), 0);
225	1	assertEquals(vpranges.getStartSeq(), 0);
226
227		// overly large boxX value reset to width-boxWidth
228	1	mouseClick(od, 101, 6);
229	1	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
230	1	assertEquals(od.getBoxY(), 1);
231	1	assertEquals(od.getBoxWidth(), boxWidth);
232	1	assertEquals(od.getBoxHeight(), boxHeight);
233	1	assertEquals(vpranges.getStartRes(),
234		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
235	1	assertEquals(
236		vpranges.getStartSeq(),
237		Math.round((float) od.getBoxY() * alheight
238		/ od.getSequencesHeight()));
239
240		// overly large boxY value reset to sequenceHeight - boxHeight
241	1	mouseClick(od, 10, 520);
242	1	assertEquals(od.getBoxX(), 0);
243	1	assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
244	1	assertEquals(od.getBoxWidth(), boxWidth);
245	1	assertEquals(od.getBoxHeight(), boxHeight);
246	1	assertEquals(vpranges.getStartRes(),
247		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
248
249		// here (float) od.getBoxY() * alheight / od.getSequencesHeight() = 507.5
250		// and round rounds to 508; however we get 507 working with row values
251		// hence the subtraction of 1
252	1	assertEquals(
253		vpranges.getStartSeq(),
254		Math.round((float) od.getBoxY() * alheight
255		/ od.getSequencesHeight()) - 1);
256
257		// click past end of alignment, as above
258	1	mouseClick(od, 3000, 5);
259	1	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
260	1	assertEquals(od.getBoxWidth(), boxWidth);
261	1	assertEquals(od.getBoxHeight(), boxHeight);
262	1	assertEquals(vpranges.getStartRes(),
263		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
264	1	assertEquals(
265		vpranges.getStartSeq(),
266		Math.round((float) od.getBoxY() * alheight
267		/ od.getSequencesHeight()));
268
269		// move viewport so startRes non-zero and then mouseclick
270	1	moveViewportH(20);
271
272		// click at viewport position
273	1	int oldboxx = od.getBoxX();
274	1	int oldboxy = od.getBoxY();
275	1	mouseClick(od, od.getBoxX() + od.getBoxWidth() / 2 + 6,
276		od.getBoxY() + od.getBoxHeight() / 2 + 3);
277	1	assertEquals(od.getBoxX(), oldboxx + 6);
278	1	assertEquals(od.getBoxWidth(), boxWidth);
279	1	assertEquals(od.getBoxHeight(), boxHeight);
280	1	assertEquals(vpranges.getStartRes(),
281		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
282	1	assertEquals(od.getBoxY(), oldboxy + 3);
283	1	assertEquals(
284		vpranges.getStartSeq(),
285		Math.round((float) od.getBoxY() * alheight
286		/ od.getSequencesHeight()));
287
288		// click at top corner
289	1	mouseClick(od, 0, 0);
290	1	assertEquals(od.getBoxX(), 0);
291	1	assertEquals(vpranges.getStartRes(), 0);
292	1	assertEquals(od.getBoxY(), 0);
293	1	assertEquals(vpranges.getStartSeq(), 0);
294	1	assertEquals(od.getBoxWidth(), boxWidth);
295	1	assertEquals(od.getBoxHeight(), boxHeight);
296		}
297
298		/**
299		* Test setting of the box position, when there are hidden cols at the start
300		* of the alignment
301		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
302	1	@Test(groups = { "Functional" })...
303		public void testFromMouseWithHiddenColsAtStart()
304		{
305	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
306	1	assertEquals(od.getBoxX(), 0);
307	1	assertEquals(od.getBoxY(), 0);
308	1	assertEquals(od.getBoxWidth(), boxWidth);
309	1	assertEquals(vpranges.getStartRes(), 0);
310	1	assertEquals(vpranges.getStartSeq(), 0);
311
312		// hide cols at start and check updated box position is correct
313	1	int lastHiddenCol = 30;
314	1	hiddenCols.hideColumns(0, lastHiddenCol);
315
316	1	testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
317
318		// click to right of hidden columns, box moves to click point
319	1	testBoxIsAtClickPoint(41 + boxWidth / 2, boxHeight / 2);
320	1	assertEquals(vpranges.getStartSeq(), 0);
321	1	assertEquals(vpranges.getStartRes(),
322		Math.round((float) 41 * alwidth / od.getWidth()));
323
324		// click to right of hidden columns such that box runs over right hand side
325		// of alignment
326		// box position is adjusted away from the edge
327		// overly large boxX value reset to width-boxWidth
328	1	int xpos = 100 + boxWidth / 2;
329	1	mouseClick(od, xpos, boxHeight / 2);
330	1	assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
331	1	assertEquals(od.getBoxY(), 0);
332	1	assertEquals(od.getBoxWidth(), boxWidth);
333	1	assertEquals(od.getBoxHeight(), boxHeight);
334	1	assertEquals(vpranges.getStartRes(),
335		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
336	1	assertEquals(vpranges.getStartSeq(), 0);
337		}
338
339		/**
340		* Test setting of the box position, when there are hidden cols in the middle
341		* of the alignment
342		*/
		100% Uncovered Elements: 0 (51) Complexity: 1 Complexity Density: 0.02 1PASS
343	1	@Test(groups = { "Functional" })...
344		public void testFromMouseWithHiddenColsInMiddle()
345		{
346	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
347	1	testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
348	1	assertEquals(od.getBoxX(), 0);
349	1	assertEquals(od.getBoxY(), 0);
350	1	assertEquals(od.getBoxWidth(), boxWidth);
351	1	assertEquals(vpranges.getStartRes(), 0);
352	1	assertEquals(vpranges.getStartSeq(), 0);
353
354		// hide columns 63-73, no change to box position or dimensions
355	1	int firstHidden = 63;
356	1	int lastHidden = 73;
357	1	hiddenCols.hideColumns(firstHidden, lastHidden);
358
359	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
360	1	testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
361	1	assertEquals(od.getBoxX(), 0);
362	1	assertEquals(od.getBoxY(), 0);
363	1	assertEquals(od.getBoxWidth(), boxWidth);
364	1	assertEquals(vpranges.getStartRes(), 0);
365	1	assertEquals(vpranges.getStartSeq(), 0);
366
367		// move box so that it overlaps with hidden cols on one side
368		// box width, boxX and scrollCol as for unhidden case
369	1	int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
370		// between cols 60 and 70
371	1	mouseClick(od, xpos, boxHeight / 2);
372	1	testBoxIsAtClickPoint(xpos, boxHeight / 2);
373	1	assertEquals(vpranges.getStartRes(), 1 + // rounding
374		Math.round((xpos - boxWidth / 2) * alwidth / od.getWidth()));
375	1	assertEquals(vpranges.getStartSeq(), 0);
376
377		// move box so that it completely covers hidden cols
378		// box width, boxX and scrollCol as for unhidden case
379	1	xpos = 33;
380	1	mouseClick(od, xpos, boxHeight / 2);
381	1	testBoxIsAtClickPoint(xpos, boxHeight / 2);
382	1	assertEquals(vpranges.getStartRes(),
383		Math.round((float) (xpos - boxWidth / 2) * alwidth
384		/ od.getWidth()));
385	1	assertEquals(vpranges.getStartSeq(), 0);
386
387		// move box so boxX is in hidden cols, box overhangs at right
388		// boxX and scrollCol at left of hidden area, box width unchanged
389	1	xpos = Math.round((float) 50 * od.getWidth() / alwidth) + boxWidth / 2;
390	1	mouseClick(od, xpos, boxHeight / 2);
391	1	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
392	1	assertEquals(od.getBoxY(), 0);
393	1	assertEquals(od.getBoxWidth(), boxWidth);
394	1	assertEquals(od.getBoxHeight(), boxHeight);
395	1	assertEquals(vpranges.getStartRes(), 50);
396	1	assertEquals(vpranges.getStartSeq(), 0);
397
398		// move box so boxX is to right of hidden cols, but does not go beyond full
399		// width of alignment
400		// box width, boxX and scrollCol all as for non-hidden case
401	1	xpos = Math.round((float) 75 * od.getWidth() / alwidth) + boxWidth / 2;
402	1	mouseClick(od, xpos, boxHeight / 2);
403	1	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
404	1	assertEquals(od.getBoxY(), 0);
405	1	assertEquals(od.getBoxWidth(), boxWidth);
406	1	assertEquals(od.getBoxHeight(), boxHeight);
407	1	assertEquals(vpranges.getStartSeq(), 0);
408	1	assertEquals(vpranges.getStartRes(), 75);
409
410		// move box so it goes beyond full width of alignment
411		// boxX, scrollCol adjusted back, box width normal
412	1	xpos = 3000;
413	1	mouseClick(od, xpos, boxHeight / 2);
414	1	assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
415	1	assertEquals(od.getBoxY(), 0);
416	1	assertEquals(od.getBoxWidth(), boxWidth);
417	1	assertEquals(od.getBoxHeight(), boxHeight);
418	1	assertEquals(vpranges.getStartRes(),
419		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
420	1	assertEquals(vpranges.getStartSeq(), 0);
421
422		}
423
424		/**
425		* Test setting of the box position, when there are hidden cols at the end of
426		* the alignment
427		*/
		100% Uncovered Elements: 0 (33) Complexity: 1 Complexity Density: 0.03 1PASS
428	1	@Test(groups = { "Functional" })...
429		public void testFromMouseWithHiddenColsAtEnd()
430		{
431	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
432	1	assertEquals(od.getBoxX(), 0);
433	1	assertEquals(od.getBoxY(), 0);
434	1	assertEquals(od.getBoxWidth(), boxWidth);
435	1	assertEquals(vpranges.getStartRes(), 0);
436	1	assertEquals(vpranges.getStartSeq(), 0);
437
438		// hide columns 140-164, no change to box position or dimensions
439	1	int firstHidden = 140;
440	1	int lastHidden = 164;
441	1	hiddenCols.hideColumns(firstHidden, lastHidden);
442	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
443	1	assertEquals(od.getBoxX(), 0);
444	1	assertEquals(od.getBoxY(), 0);
445	1	assertEquals(od.getBoxWidth(), boxWidth);
446	1	assertEquals(vpranges.getStartRes(), 0);
447	1	assertEquals(vpranges.getStartSeq(), 0);
448
449		// click to left of hidden cols, without overlapping
450		// boxX, scrollCol and width as normal
451	1	int xpos = 30;
452	1	int ypos = 6;
453	1	testBoxIsAtClickPoint(xpos, ypos);
454	1	assertEquals(vpranges.getStartSeq(), Math.round(
455		(float) (ypos - boxHeight / 2) * alheight / od.getHeight()));
456	1	assertEquals(vpranges.getStartRes(), Math.round(
457		(float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
458
459		// click to left of hidden cols, with overlap
460		// boxX and scrollCol adjusted for hidden cols, width normal
461	1	xpos = Math.round((float) 144 * od.getWidth() / alwidth) - boxWidth;
462	1	mouseClick(od, xpos, boxHeight / 2);
463	1	testBoxIsAtClickPoint(xpos, boxHeight / 2);
464	1	assertEquals(vpranges.getStartRes(),
465		Math.round((float) (xpos - boxWidth / 2) * alwidth
466		/ od.getWidth()));
467	1	assertEquals(vpranges.getStartSeq(), 0);
468
469		// click off end of alignment
470		// boxX and scrollCol adjusted backwards, width normal
471	1	xpos = 3000;
472	1	mouseClick(od, xpos, 0);
473	1	assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
474	1	assertEquals(od.getBoxY(), 0);
475	1	assertEquals(od.getBoxWidth(), boxWidth);
476	1	assertEquals(od.getBoxHeight(), boxHeight);
477	1	assertEquals(vpranges.getStartRes(),
478		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
479	1	assertEquals(vpranges.getStartSeq(), 0);
480		}
481
482		/**
483		* Test that the box position is set correctly when set from the viewport,
484		* with no hidden rows or columns
485		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
486	1	@Test(groups = { "Functional" })...
487		public void testSetBoxFromViewport()
488		{
489		// move viewport to start of alignment
490	1	moveViewport(0, 0);
491	1	assertEquals(od.getBoxX(), 0);
492	1	assertEquals(od.getBoxY(), 0);
493	1	assertEquals(od.getBoxWidth(), boxWidth);
494	1	assertEquals(od.getBoxHeight(), boxHeight);
495
496		// move viewport to right
497	1	moveViewportH(70);
498	1	assertEquals(od.getBoxX(),
499		Math.round((float) 70 * od.getWidth() / alwidth));
500	1	assertEquals(od.getBoxY(), 0);
501	1	assertEquals(od.getBoxWidth(), boxWidth);
502	1	assertEquals(od.getBoxHeight(), boxHeight);
503
504		// move viewport down
505	1	moveViewportV(100);
506	1	assertEquals(od.getBoxX(),
507		Math.round((float) 70 * od.getWidth() / alwidth));
508	1	assertEquals(od.getBoxY(),
509		Math.round(100 * od.getSequencesHeight() / alheight));
510	1	assertEquals(od.getBoxWidth(), boxWidth);
511	1	assertEquals(od.getBoxHeight(), boxHeight);
512
513		// move viewport to bottom right
514	1	moveViewport(98, 508);
515	1	assertEquals(od.getBoxX(),
516		Math.round((float) 98 * od.getWidth() / alwidth));
517	1	assertEquals(od.getBoxY(),
518		Math.round((float) 508 * od.getSequencesHeight() / alheight));
519	1	assertEquals(od.getBoxWidth(), boxWidth);
520	1	assertEquals(od.getBoxHeight(), boxHeight);
521		}
522
523		/**
524		* Test that the box position is set correctly when there are hidden columns
525		* at the start
526		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
527	1	@Test(groups = { "Functional" })...
528		public void testSetBoxFromViewportHiddenColsAtStart()
529		{
530	1	int firstHidden = 0;
531	1	int lastHidden = 20;
532	1	hiddenCols.hideColumns(firstHidden, lastHidden);
533
534		// move viewport to start of alignment
535	1	moveViewport(0, 0);
536	1	assertEquals(od.getBoxX(), 0);
537	1	assertEquals(od.getBoxY(), 0);
538	1	assertEquals(od.getBoxWidth(), boxWidth);
539	1	assertEquals(od.getBoxHeight(), boxHeight);
540
541		// move viewport to end of alignment - need to make startRes by removing
542		// hidden cols because of how viewport/overview are implemented
543	1	moveViewport(98 - lastHidden - 1, 0);
544	1	assertEquals(od.getBoxX(),
545		Math.round((float) (98 - lastHidden - 1) * od.getWidth()
546		/ alwidth));
547	1	assertEquals(od.getBoxY(), 0);
548	1	assertEquals(od.getBoxWidth(), boxWidth);
549	1	assertEquals(od.getBoxHeight(), boxHeight);
550		}
551
552		/**
553		* Test that the box position is set correctly when there are hidden columns
554		* in the middle
555		*/
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
556	1	@Test(groups = { "Functional" })...
557		public void testSetBoxFromViewportHiddenColsInMiddle()
558		{
559	1	int firstHidden = 68;
560	1	int lastHidden = 78;
561	1	hiddenCols.hideColumns(firstHidden, lastHidden);
562
563		// move viewport before hidden columns
564	1	moveViewport(3, 0);
565
566	1	assertEquals(od.getBoxX(),
567		Math.round((float) 3 * od.getWidth() / alwidth));
568	1	assertEquals(od.getBoxY(), 0);
569	1	assertEquals(od.getBoxWidth(), boxWidth);
570	1	assertEquals(od.getBoxHeight(), boxHeight);
571
572		// move viewport to left of hidden columns with overlap
573	1	moveViewport(10, 0);
574	1	assertEquals(od.getBoxX(),
575		Math.round((float) 10 * 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 straddle hidden columns
581	1	moveViewport(63, 0);
582	1	assertEquals(od.getBoxX(),
583		Math.round((float) 63 * od.getWidth() / alwidth));
584	1	assertEquals(od.getBoxY(), 0);
585	1	assertEquals(od.getBoxWidth(), boxWidth);
586	1	assertEquals(od.getBoxHeight(), boxHeight);
587
588		// move viewport to right of hidden columns, no overlap
589	1	moveViewport(80 - (lastHidden - firstHidden + 1), 0);
590	1	assertEquals(od.getBoxX(),
591		Math.round((float) (80 - (lastHidden - firstHidden + 1))
592		* od.getWidth() / alwidth));
593	1	assertEquals(od.getBoxY(), 0);
594	1	assertEquals(od.getBoxWidth(), boxWidth);
595	1	assertEquals(od.getBoxHeight(), boxHeight);
596
597		}
598
599		/**
600		* Test that the box position is set correctly when there are hidden columns
601		* at the end
602		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
603	1	@Test(groups = { "Functional" })...
604		public void testSetBoxFromViewportHiddenColsAtEnd()
605		{
606	1	int firstHidden = 152;
607	1	int lastHidden = 164;
608	1	hiddenCols.hideColumns(firstHidden, lastHidden);
609
610		// move viewport before hidden columns
611	1	moveViewport(3, 0);
612	1	assertEquals(od.getBoxX(),
613		Math.round((float) 3 * od.getWidth() / alwidth));
614	1	assertEquals(od.getBoxY(), 0);
615	1	assertEquals(od.getBoxWidth(), boxWidth);
616	1	assertEquals(od.getBoxHeight(), boxHeight);
617
618		// move viewport to hidden columns
619		// viewport can't actually extend into hidden cols,
620		// so move to the far right edge of the viewport
621	1	moveViewport(firstHidden - viewWidth, 0);
622	1	assertEquals(od.getBoxX(),
623		Math.round((float) (firstHidden - viewWidth)
624		* od.getWidth() / alwidth));
625	1	assertEquals(od.getBoxY(), 0);
626	1	assertEquals(od.getBoxWidth(), boxWidth);
627	1	assertEquals(od.getBoxHeight(), boxHeight);
628		}
629
630		/**
631		* Test that the box position is set correctly when there are hidden rows at
632		* the start
633		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
634	1	@Test(groups = { "Functional" })...
635		public void testSetBoxFromViewportHiddenRowsAtStart()
636		{
637	1	int firstHidden = 0;
638	1	int lastHidden = 20;
639	1	hideSequences(firstHidden, lastHidden);
640
641		// calculate with visible values
642	1	alheight = vpranges.getVisibleAlignmentHeight();
643	1	alwidth = vpranges.getVisibleAlignmentWidth();
644
645	1	boxWidth = Math.round((float) (vpranges.getEndRes()
646		- vpranges.getStartRes() + 1)
647		* od.getWidth() / alwidth);
648	1	boxHeight = Math.round((float) (vpranges.getEndSeq()
649		- vpranges.getStartSeq() + 1)
650		* od.getSequencesHeight() / alheight);
651
652		// move viewport to start of alignment:
653		// box moves to below hidden rows, height remains same
654	1	moveViewport(0, 0);
655	1	assertEquals(od.getBoxX(), 0);
656	1	assertEquals(od.getBoxY(), 0);
657	1	assertEquals(od.getBoxWidth(), boxWidth);
658	1	assertEquals(od.getBoxHeight(), boxHeight);
659
660		// move viewport to end of alignment
661	1	moveViewport(0, 525 - viewHeight - lastHidden - 1);
662	1	assertEquals(od.getBoxX(), 0);
663	1	assertEquals(
664		od.getBoxY(),
665		Math.round((float) (525 - viewHeight - lastHidden - 1)
666		* od.getSequencesHeight()
667		/ alheight));
668	1	assertEquals(od.getBoxWidth(), boxWidth);
669	1	assertEquals(od.getBoxHeight(), boxHeight);
670		}
671
672		/**
673		* Test that the box position is set correctly when there are hidden rows in
674		* the middle
675		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
676	1	@Test(groups = { "Functional" })...
677		public void testSetBoxFromViewportHiddenRowsInMiddle()
678		{
679	1	int firstHidden = 200;
680	1	int lastHidden = 210;
681	1	hideSequences(firstHidden, lastHidden);
682
683		// calculate with visible values
684	1	alheight = vpranges.getVisibleAlignmentHeight();
685	1	alwidth = vpranges.getVisibleAlignmentWidth();
686
687	1	boxWidth = Math.round((float) (vpranges.getEndRes()
688		- vpranges.getStartRes() + 1)
689		* od.getWidth() / alwidth);
690	1	boxHeight = Math.round((float) (vpranges.getEndSeq()
691		- vpranges.getStartSeq() + 1)
692		* od.getSequencesHeight() / alheight);
693
694		// move viewport to start of alignment:
695		// box, height etc as in non-hidden case
696	1	moveViewport(0, 0);
697	1	assertEquals(od.getBoxX(), 0);
698	1	assertEquals(od.getBoxY(), 0);
699	1	assertEquals(od.getBoxWidth(), boxWidth);
700	1	assertEquals(od.getBoxHeight(), boxHeight);
701
702		// move viewport to straddle hidden rows
703	1	moveViewport(0, 198);
704	1	assertEquals(od.getBoxX(), 0);
705	1	assertEquals(od.getBoxY(), Math.round ((float)198 * od.getSequencesHeight()
706		/ alheight));
707	1	assertEquals(od.getBoxWidth(), boxWidth);
708	1	assertEquals(od.getBoxHeight(), boxHeight);
709		}
710
711		/**
712		* Test that the box position is set correctly when there are hidden rows at
713		* the bottom
714		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
715	1	@Test(groups = { "Functional" })...
716		public void testSetBoxFromViewportHiddenRowsAtEnd()
717		{
718	1	int firstHidden = 500;
719	1	int lastHidden = 524;
720	1	hideSequences(firstHidden, lastHidden);
721
722		// calculate with visible values
723	1	alheight = vpranges.getVisibleAlignmentHeight();
724	1	alwidth = vpranges.getVisibleAlignmentWidth();
725
726	1	boxWidth = Math.round((float) (vpranges.getEndRes()
727		- vpranges.getStartRes() + 1)
728		* od.getWidth() / alwidth);
729	1	boxHeight = Math.round((float) (vpranges.getEndSeq()
730		- vpranges.getStartSeq() + 1)
731		* od.getSequencesHeight() / alheight);
732
733		// move viewport to start of alignment:
734		// box, height etc as in non-hidden case
735	1	moveViewport(0, 0);
736	1	assertEquals(od.getBoxX(), 0);
737	1	assertEquals(od.getBoxY(), 0);
738	1	assertEquals(od.getBoxWidth(), boxWidth);
739	1	assertEquals(od.getBoxHeight(), boxHeight);
740
741		// move viewport to end of alignment
742		// viewport sits above hidden rows and does not include them
743	1	moveViewport(0, firstHidden - viewHeight - 1);
744	1	assertEquals(od.getBoxX(), 0);
745	1	assertEquals(
746		od.getBoxY(),
747		Math.round((float) (firstHidden - viewHeight - 1)
748		* od.getSequencesHeight() / alheight));
749	1	assertEquals(od.getBoxWidth(), boxWidth);
750	1	assertEquals(od.getBoxHeight(), boxHeight);
751
752		}
753
754		/**
755		* Test setting of the box position, when there are hidden rows at the start
756		* of the alignment
757		*/
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
758	1	@Test(groups = { "Functional" })...
759		public void testFromMouseWithHiddenRowsAtStart()
760		{
761	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
762	1	assertEquals(od.getBoxX(), 0);
763	1	assertEquals(od.getBoxY(), 0);
764	1	assertEquals(od.getBoxHeight(), boxHeight);
765	1	assertEquals(od.getBoxWidth(), boxWidth);
766	1	assertEquals(vpranges.getStartRes(), 0);
767	1	assertEquals(vpranges.getStartSeq(), 0);
768
769		// hide rows at start and check updated box position is correct
770	1	int lastHiddenRow = 30;
771	1	hideSequences(0, lastHiddenRow);
772
773		// calculate with visible values
774	1	alheight = vpranges.getVisibleAlignmentHeight();
775	1	alwidth = vpranges.getVisibleAlignmentWidth();
776
777	1	boxWidth = Math.round((float) (vpranges.getEndRes()
778		- vpranges.getStartRes() + 1)
779		* od.getWidth() / alwidth);
780	1	boxHeight = Math.round((float) (vpranges.getEndSeq()
781		- vpranges.getStartSeq() + 1)
782		* od.getSequencesHeight() / alheight);
783
784	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
785	1	assertEquals(od.getBoxX(), 0);
786	1	assertEquals(od.getBoxY(), 0);
787	1	assertEquals(od.getBoxWidth(), boxWidth);
788	1	assertEquals(od.getBoxHeight(), boxHeight);
789
790		// click below hidden rows
791	1	mouseClick(od, 0, 151 + boxHeight / 2);
792	1	assertEquals(od.getBoxX(), 0);
793	1	assertEquals(od.getBoxY(), 151);
794	1	assertEquals(od.getBoxWidth(), boxWidth);
795	1	assertEquals(od.getBoxHeight(), boxHeight);
796		}
797
798		/**
799		* Test setting of the box position, when there are hidden rows at the middle
800		* of the alignment
801		*/
		100% Uncovered Elements: 0 (31) Complexity: 1 Complexity Density: 0.03 1PASS
802	1	@Test(groups = { "Functional" })...
803		public void testFromMouseWithHiddenRowsInMiddle()
804		{
805	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
806
807	1	assertEquals(od.getBoxX(), 0);
808	1	assertEquals(od.getBoxY(), 0);
809	1	assertEquals(od.getBoxWidth(), boxWidth);
810	1	assertEquals(od.getBoxHeight(), boxHeight);
811	1	assertEquals(vpranges.getStartRes(), 0);
812	1	assertEquals(vpranges.getStartSeq(), 0);
813
814		// hide rows in middle and check updated box position is correct
815		// no changes
816	1	int firstHiddenRow = 50;
817	1	int lastHiddenRow = 54;
818	1	hideSequences(firstHiddenRow, lastHiddenRow);
819
820		// calculate with visible values
821	1	alheight = vpranges.getVisibleAlignmentHeight();
822	1	alwidth = vpranges.getVisibleAlignmentWidth();
823
824	1	boxWidth = Math.round((float) (vpranges.getEndRes()
825		- vpranges.getStartRes() + 1)
826		* od.getWidth() / alwidth);
827	1	boxHeight = Math.round((float) (vpranges.getEndSeq()
828		- vpranges.getStartSeq() + 1)
829		* od.getSequencesHeight() / alheight);
830
831	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
832
833	1	assertEquals(od.getBoxX(), 0);
834	1	assertEquals(od.getBoxY(), 0);
835	1	assertEquals(od.getBoxWidth(), boxWidth);
836	1	assertEquals(od.getBoxHeight(), boxHeight);
837
838		// click above hidden rows, so that box overlaps
839	1	int ypos = 35 + viewHeight / 2; // row value in residues
840	1	mouseClick(od, 0,
841		Math.round((float) ypos * od.getSequencesHeight() / alheight));
842	1	assertEquals(od.getBoxX(), 0);
843	1	assertEquals(od.getBoxY(),
844		Math.round((float) 35 * od.getSequencesHeight() / alheight));
845	1	assertEquals(od.getBoxWidth(), boxWidth);
846	1	assertEquals(od.getBoxHeight(), boxHeight);
847
848		// click so that box straddles hidden rows
849	1	ypos = 45 + viewHeight / 2; // row value in residues
850	1	mouseClick(od, 0,
851		Math.round((float) ypos * od.getSequencesHeight() / alheight));
852	1	assertEquals(od.getBoxX(), 0);
853	1	assertEquals(od.getBoxY(),
854		Math.round((float) 45 * od.getSequencesHeight() / alheight));
855	1	assertEquals(od.getBoxWidth(), boxWidth);
856	1	assertEquals(od.getBoxHeight(), boxHeight);
857		}
858
859		/**
860		* Test setting of the box position, when there are hidden rows at the end of
861		* the alignment
862		*/
		100% Uncovered Elements: 0 (31) Complexity: 1 Complexity Density: 0.03 1PASS
863	1	@Test(groups = { "Functional" })...
864		public void testFromMouseWithHiddenRowsAtEnd()
865		{
866	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
867	1	assertEquals(od.getBoxX(), 0);
868	1	assertEquals(od.getBoxY(), 0);
869	1	assertEquals(od.getBoxWidth(), boxWidth);
870	1	assertEquals(od.getBoxHeight(), boxHeight);
871	1	assertEquals(vpranges.getStartRes(), 0);
872	1	assertEquals(vpranges.getStartSeq(), 0);
873
874		// hide rows at end and check updated box position is correct
875		// no changes
876	1	int firstHidden = 500;
877	1	int lastHidden = 524;
878	1	hideSequences(firstHidden, lastHidden);
879
880		// calculate with visible values
881	1	alheight = vpranges.getVisibleAlignmentHeight();
882	1	alwidth = vpranges.getVisibleAlignmentWidth();
883
884	1	boxWidth = Math.round((float) (vpranges.getEndRes()
885		- vpranges.getStartRes() + 1)
886		* od.getWidth() / alwidth);
887	1	boxHeight = Math.round((float) (vpranges.getEndSeq()
888		- vpranges.getStartSeq() + 1)
889		* od.getSequencesHeight() / alheight);
890
891	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
892	1	assertEquals(od.getBoxX(), 0);
893	1	assertEquals(od.getBoxY(), 0);
894	1	assertEquals(od.getBoxWidth(), boxWidth);
895	1	assertEquals(od.getBoxHeight(), boxHeight);
896
897		// click above hidden rows
898	1	int ypos = 41 + viewHeight / 2; // row 41
899	1	mouseClick(od, 0,
900		Math.round((float) ypos * od.getSequencesHeight() / alheight));
901	1	assertEquals(od.getBoxX(), 0);
902	1	assertEquals(od.getBoxY(),
903		Math.round((float) 41 * od.getSequencesHeight() / alheight));
904	1	assertEquals(od.getBoxWidth(), boxWidth);
905	1	assertEquals(od.getBoxHeight(), boxHeight);
906
907		// click above hidden rows so box overlaps
908		// boxY, boxHeight remains same
909	1	ypos = 497 + viewHeight / 2; // row 497
910	1	mouseClick(od, 0,
911		Math.round((float) ypos * od.getSequencesHeight() / alheight));
912	1	assertEquals(od.getBoxX(), 0);
913	1	assertEquals(
914		od.getBoxY(),
915		Math.round((float) firstHidden * od.getSequencesHeight()
916		/ alheight)
917		- boxHeight);
918	1	assertEquals(od.getBoxWidth(), boxWidth);
919	1	assertEquals(od.getBoxHeight(), boxHeight);
920		}
921
922		/**
923		* Test the function to determine if a point is in the overview's box or not
924		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
925	1	@Test(groups = { "Functional" })...
926		public void testPositionInBox()
927		{
928	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
929
930	1	assertFalse(od.isPositionInBox(0, 0));
931	1	assertTrue(od.isPositionInBox(10, 9));
932	1	assertFalse(od.isPositionInBox(0, 9));
933	1	assertFalse(od.isPositionInBox(9, 0));
934	1	assertFalse(od.isPositionInBox(75, 20));
935
936		// hide columns in the box area
937		// makes absolutely no difference
938	1	hiddenCols.hideColumns(1, 4);
939	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
940	1	assertFalse(od.isPositionInBox(0, 0));
941	1	assertTrue(od.isPositionInBox(10, 9));
942	1	assertFalse(od.isPositionInBox(0, 9));
943	1	assertFalse(od.isPositionInBox(9, 0));
944	1	assertFalse(od.isPositionInBox(75, 20));
945
946		// hide sequences in box area
947		// makes absolutely no difference
948	1	hideSequences(1, 3);
949	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
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
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(),
965		hiddenCols);
966	1	od.adjustViewportFromMouse(20, 22,
967		al.getHiddenSequences(), hiddenCols);
968
969		// updates require an OverviewPanel to exist which it doesn't here
970		// so call setBoxPosition() as it would be called by the AlignmentPanel
971		// normally
972	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
973
974		// corner moves 16 (20-4) right and 6 (22-16) up
975	1	assertEquals(od.getBoxX(), 16);
976	1	assertEquals(od.getBoxY(), 6);
977
978		// hide columns - makes no difference
979	1	hiddenCols.hideColumns(1, 4);
980	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
981	1	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
982	1	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
983	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
984
985		// corner moves 16 (20-4) right and 6 (22-16) up
986	1	assertEquals(od.getBoxX(), 16);
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) right and 6 (22-16) up
998	1	assertEquals(od.getBoxX(), 16);
999	1	assertEquals(od.getBoxY(), 6);
1000		}
1001
1002		/*
1003		* Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
1004		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1005	2	private void moveViewportH(int startRes)...
1006		{
1007	2	vpranges.setViewportStartAndWidth(startRes, viewWidth);
1008	2	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1009		}
1010
1011		/*
1012		* Move viewport vertically: startSeq and endSeq give new vertical extent. Horizontal extent stays the same.
1013		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1014	1	private void moveViewportV(int startSeq)...
1015		{
1016	1	vpranges.setViewportStartAndHeight(startSeq, viewHeight);
1017	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1018		}
1019
1020		/*
1021		* Move viewport horizontally and vertically.
1022		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
1023	33	private void moveViewport(int startRes, int startSeq)...
1024		{
1025	33	vpranges.setViewportStartAndWidth(startRes, viewWidth);
1026	33	vpranges.setViewportStartAndHeight(startSeq, viewHeight);
1027	33	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1028		}
1029
1030		/*
1031		* Mouse click as position x,y in overview window
1032		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1033	45	private void mouseClick(OverviewDimensions od, int x, int y)...
1034		{
1035	45	od.updateViewportFromMouse(x, y, al.getHiddenSequences(), hiddenCols);
1036
1037		// updates require an OverviewPanel to exist which it doesn't here
1038		// so call setBoxPosition() as it would be called by the AlignmentPanel
1039		// normally
1040	45	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1041		}
1042
1043		/*
1044		* Test that the box is positioned with the top left corner at xpos, ypos
1045		* and with the original width and height
1046		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
1047	8	private void testBoxIsAtClickPoint(int xpos, int ypos)...
1048		{
1049	8	mouseClick(od, xpos, ypos);
1050	8	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
1051	8	assertEquals(od.getBoxY() + od.getBoxHeight() / 2, ypos);
1052	8	assertEquals(od.getBoxWidth(), boxWidth);
1053	8	assertEquals(od.getBoxHeight(), boxHeight);
1054
1055		}
1056
1057		/*
1058		* Hide sequences between start and end
1059		*/
		100% Uncovered Elements: 0 (8) Complexity: 2 Complexity Density: 0.33
1060	8	private void hideSequences(int start, int end)...
1061		{
1062	8	SequenceI[] allseqs = al.getSequencesArray();
1063	8	SequenceGroup theseSeqs = new SequenceGroup();
1064
1065	132	for (int i = start; i <= end; i++)
1066		{
1067	124	theseSeqs.addSequence(allseqs[i], false);
1068	124	al.getHiddenSequences().hideSequence(allseqs[i]);
1069		}
1070
1071	8	hiddenRepSequences.put(allseqs[start], theseSeqs);
1072		}
1073		}