Classes

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

Class OverviewDimensionsHideHiddenTest

Class OverviewDimensionsHideHiddenTest	Line # 45	Total Statements 496	Complexity 28	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	20.020	1.01	1.0 1.0100%
testFromMouseWithHiddenColsInMiddle() : void   testFromMouseWithHiddenColsInMiddle() : void	340340	51.051	1.01	1.0 1.0100%
testFromMouseWithHiddenColsAtEnd() : void   testFromMouseWithHiddenColsAtEnd() : void	424424	33.033	1.01	1.0 1.0100%
testSetBoxFromViewport() : void   testSetBoxFromViewport() : void	481481	20.020	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenColsAtStart() : void   testSetBoxFromViewportHiddenColsAtStart() : void	522522	13.013	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenColsInMiddle() : void   testSetBoxFromViewportHiddenColsInMiddle() : void	550550	23.023	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenColsAtEnd() : void   testSetBoxFromViewportHiddenColsAtEnd() : void	597597	13.013	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenRowsAtStart() : void   testSetBoxFromViewportHiddenRowsAtStart() : void	627627	17.017	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenRowsInMiddle() : void   testSetBoxFromViewportHiddenRowsInMiddle() : void	667667	17.017	1.01	1.0 1.0100%
testSetBoxFromViewportHiddenRowsAtEnd() : void   testSetBoxFromViewportHiddenRowsAtEnd() : void	706706	17.017	1.01	1.0 1.0100%
testFromMouseWithHiddenRowsAtStart() : void   testFromMouseWithHiddenRowsAtStart() : void	748748	23.023	1.01	1.0 1.0100%
testFromMouseWithHiddenRowsInMiddle() : void   testFromMouseWithHiddenRowsInMiddle() : void	792792	31.031	1.01	1.0 1.0100%
testFromMouseWithHiddenRowsAtEnd() : void   testFromMouseWithHiddenRowsAtEnd() : void	853853	31.031	1.01	1.0 1.0100%
testPositionInBox() : void   testPositionInBox() : void	913913	20.020	1.01	1.0 1.0100%
testDragging() : void   testDragging() : void	948948	20.020	1.01	1.0 1.0100%
moveViewportH(int) : void   moveViewportH(int) : void	991991	2.02	1.01	1.0 1.0100%
moveViewportV(int) : void   moveViewportV(int) : void	10001000	2.02	1.01	1.0 1.0100%
moveViewport(int,int) : void   moveViewport(int,int) : void	10091009	3.03	1.01	1.0 1.0100%
mouseClick(OverviewDimensions,int,int) : void   mouseClick(OverviewDimensions,int,int) : void	10191019	2.02	1.01	1.0 1.0100%
testBoxIsAtClickPoint(int,int) : void   testBoxIsAtClickPoint(int,int) : void	10331033	5.05	1.01	1.0 1.0100%
hideSequences(int,int) : void   hideSequences(int,int) : void	10461046	6.06	2.02	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.testSetBoxFromViewportHiddenRowsAtEndjalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsAtEnd	1PASS
	0.058935363	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsAtStartjalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsAtStart	1PASS
	0.058935363	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsInMiddlejalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenRowsInMiddle	1PASS
	0.058935363	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportjalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewport	1PASS
	0.05703422	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testDraggingjalview.viewmodel.OverviewDimensionsHideHiddenTest.testDragging	1PASS
	0.05703422	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testPositionInBoxjalview.viewmodel.OverviewDimensionsHideHiddenTest.testPositionInBox	1PASS
	0.05703422	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenColsAtStartjalview.viewmodel.OverviewDimensionsHideHiddenTest.testFromMouseWithHiddenColsAtStart	1PASS
	0.05323194	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenColsInMiddlejalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenColsInMiddle	1PASS
	0.03422053	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenColsAtEndjalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenColsAtEnd	1PASS
	0.03422053	jalview.viewmodel.OverviewDimensionsHideHiddenTest.testSetBoxFromViewportHiddenColsAtStartjalview.viewmodel.OverviewDimensionsHideHiddenTest.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 (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
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	17	@BeforeMethod(alwaysRun = true)...
79		public void setUp()
80		{
81	17	if (!hiddenRepSequences.isEmpty())
82		{
83	15	al.getHiddenSequences().showAll(hiddenRepSequences);
84		}
85	17	ColumnSelection colsel = new ColumnSelection();
86	17	hiddenCols.revealAllHiddenColumns(colsel);
87
88	17	vpranges = new ViewportRanges(al);
89	17	vpranges.setViewportStartAndHeight(0, 18);
90	17	vpranges.setViewportStartAndWidth(0, 63);
91
92	17	viewHeight = vpranges.getEndSeq() - vpranges.getStartSeq() + 1;
93	17	viewWidth = vpranges.getEndRes() - vpranges.getStartRes() + 1;
94
95	17	HiddenColumns hiddenCols = new HiddenColumns();
96
97	17	od = new OverviewDimensionsHideHidden(vpranges, true);
98		// Initial box sizing - default path through code
99	17	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
100
101	17	mouseClick(od, 0, 0);
102	17	moveViewport(0, 0);
103
104		// calculate with visible values
105	17	alheight = vpranges.getVisibleAlignmentHeight();
106	17	alwidth = vpranges.getVisibleAlignmentWidth();
107
108	17	boxWidth = Math.round(
109		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
110		* od.getWidth() / alwidth);
111	17	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 OverviewDimensionsHideHidden(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 OverviewDimensionsHideHidden(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 OverviewDimensionsHideHidden(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 OverviewDimensionsHideHidden(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 OverviewDimensionsHideHidden(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(vpranges.getStartRes(),
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 (20) Complexity: 1 Complexity Density: 0.05 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	1	int lastHiddenCol = 30;
311	1	hiddenCols.hideColumns(0, lastHiddenCol);
312
313	1	testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
314
315		// click to right of hidden columns, box moves to click point
316	1	testBoxIsAtClickPoint(41 + boxWidth / 2, boxHeight / 2);
317	1	assertEquals(vpranges.getStartSeq(), 0);
318	1	assertEquals(vpranges.getStartRes(),
319		Math.round((float) 41 * alwidth / od.getWidth()));
320
321		// click to right of hidden columns such that box runs over right hand side
322		// of alignment
323		// box position is adjusted away from the edge
324		// overly large boxX value reset to width-boxWidth
325	1	int xpos = 100 + boxWidth / 2;
326	1	mouseClick(od, xpos, boxHeight / 2);
327	1	assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
328	1	assertEquals(od.getBoxY(), 0);
329	1	assertEquals(od.getBoxWidth(), boxWidth);
330	1	assertEquals(od.getBoxHeight(), boxHeight);
331	1	assertEquals(vpranges.getStartRes(),
332		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
333	1	assertEquals(vpranges.getStartSeq(), 0);
334		}
335
336		/**
337		* Test setting of the box position, when there are hidden cols in the middle
338		* of the alignment
339		*/
		100% Uncovered Elements: 0 (51) Complexity: 1 Complexity Density: 0.02 1PASS
340	1	@Test(groups = { "Functional" })...
341		public void testFromMouseWithHiddenColsInMiddle()
342		{
343	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
344	1	testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
345	1	assertEquals(od.getBoxX(), 0);
346	1	assertEquals(od.getBoxY(), 0);
347	1	assertEquals(od.getBoxWidth(), boxWidth);
348	1	assertEquals(vpranges.getStartRes(), 0);
349	1	assertEquals(vpranges.getStartSeq(), 0);
350
351		// hide columns 63-73, no change to box position or dimensions
352	1	int firstHidden = 63;
353	1	int lastHidden = 73;
354	1	hiddenCols.hideColumns(firstHidden, lastHidden);
355
356	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
357	1	testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
358	1	assertEquals(od.getBoxX(), 0);
359	1	assertEquals(od.getBoxY(), 0);
360	1	assertEquals(od.getBoxWidth(), boxWidth);
361	1	assertEquals(vpranges.getStartRes(), 0);
362	1	assertEquals(vpranges.getStartSeq(), 0);
363
364		// move box so that it overlaps with hidden cols on one side
365		// box width, boxX and scrollCol as for unhidden case
366	1	int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
367		// between cols 60 and 70
368	1	mouseClick(od, xpos, boxHeight / 2);
369	1	testBoxIsAtClickPoint(xpos, boxHeight / 2);
370	1	assertEquals(vpranges.getStartRes(), 1 + // rounding
371		Math.round((xpos - boxWidth / 2) * alwidth / od.getWidth()));
372	1	assertEquals(vpranges.getStartSeq(), 0);
373
374		// move box so that it completely covers hidden cols
375		// box width, boxX and scrollCol as for unhidden case
376	1	xpos = 33;
377	1	mouseClick(od, xpos, boxHeight / 2);
378	1	testBoxIsAtClickPoint(xpos, boxHeight / 2);
379	1	assertEquals(vpranges.getStartRes(), Math.round(
380		(float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
381	1	assertEquals(vpranges.getStartSeq(), 0);
382
383		// move box so boxX is in hidden cols, box overhangs at right
384		// boxX and scrollCol at left of hidden area, box width unchanged
385	1	xpos = Math.round((float) 50 * od.getWidth() / alwidth) + boxWidth / 2;
386	1	mouseClick(od, xpos, boxHeight / 2);
387	1	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
388	1	assertEquals(od.getBoxY(), 0);
389	1	assertEquals(od.getBoxWidth(), boxWidth);
390	1	assertEquals(od.getBoxHeight(), boxHeight);
391	1	assertEquals(vpranges.getStartRes(), 50);
392	1	assertEquals(vpranges.getStartSeq(), 0);
393
394		// move box so boxX is to right of hidden cols, but does not go beyond full
395		// width of alignment
396		// box width, boxX and scrollCol all as for non-hidden case
397	1	xpos = Math.round((float) 75 * od.getWidth() / alwidth) + boxWidth / 2;
398	1	mouseClick(od, xpos, boxHeight / 2);
399	1	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
400	1	assertEquals(od.getBoxY(), 0);
401	1	assertEquals(od.getBoxWidth(), boxWidth);
402	1	assertEquals(od.getBoxHeight(), boxHeight);
403	1	assertEquals(vpranges.getStartSeq(), 0);
404	1	assertEquals(vpranges.getStartRes(), 75);
405
406		// move box so it goes beyond full width of alignment
407		// boxX, scrollCol adjusted back, box width normal
408	1	xpos = 3000;
409	1	mouseClick(od, xpos, boxHeight / 2);
410	1	assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
411	1	assertEquals(od.getBoxY(), 0);
412	1	assertEquals(od.getBoxWidth(), boxWidth);
413	1	assertEquals(od.getBoxHeight(), boxHeight);
414	1	assertEquals(vpranges.getStartRes(),
415		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
416	1	assertEquals(vpranges.getStartSeq(), 0);
417
418		}
419
420		/**
421		* Test setting of the box position, when there are hidden cols at the end of
422		* the alignment
423		*/
		100% Uncovered Elements: 0 (33) Complexity: 1 Complexity Density: 0.03 1PASS
424	1	@Test(groups = { "Functional" })...
425		public void testFromMouseWithHiddenColsAtEnd()
426		{
427	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
428	1	assertEquals(od.getBoxX(), 0);
429	1	assertEquals(od.getBoxY(), 0);
430	1	assertEquals(od.getBoxWidth(), boxWidth);
431	1	assertEquals(vpranges.getStartRes(), 0);
432	1	assertEquals(vpranges.getStartSeq(), 0);
433
434		// hide columns 140-164, no change to box position or dimensions
435	1	int firstHidden = 140;
436	1	int lastHidden = 164;
437	1	hiddenCols.hideColumns(firstHidden, lastHidden);
438	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
439	1	assertEquals(od.getBoxX(), 0);
440	1	assertEquals(od.getBoxY(), 0);
441	1	assertEquals(od.getBoxWidth(), boxWidth);
442	1	assertEquals(vpranges.getStartRes(), 0);
443	1	assertEquals(vpranges.getStartSeq(), 0);
444
445		// click to left of hidden cols, without overlapping
446		// boxX, scrollCol and width as normal
447	1	int xpos = 30;
448	1	int ypos = 6;
449	1	testBoxIsAtClickPoint(xpos, ypos);
450	1	assertEquals(vpranges.getStartSeq(), Math.round(
451		(float) (ypos - boxHeight / 2) * alheight / od.getHeight()));
452	1	assertEquals(vpranges.getStartRes(), Math.round(
453		(float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
454
455		// click to left of hidden cols, with overlap
456		// boxX and scrollCol adjusted for hidden cols, width normal
457	1	xpos = Math.round((float) 144 * od.getWidth() / alwidth) - boxWidth;
458	1	mouseClick(od, xpos, boxHeight / 2);
459	1	testBoxIsAtClickPoint(xpos, boxHeight / 2);
460	1	assertEquals(vpranges.getStartRes(), Math.round(
461		(float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
462	1	assertEquals(vpranges.getStartSeq(), 0);
463
464		// click off end of alignment
465		// boxX and scrollCol adjusted backwards, width normal
466	1	xpos = 3000;
467	1	mouseClick(od, xpos, 0);
468	1	assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
469	1	assertEquals(od.getBoxY(), 0);
470	1	assertEquals(od.getBoxWidth(), boxWidth);
471	1	assertEquals(od.getBoxHeight(), boxHeight);
472	1	assertEquals(vpranges.getStartRes(),
473		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
474	1	assertEquals(vpranges.getStartSeq(), 0);
475		}
476
477		/**
478		* Test that the box position is set correctly when set from the viewport,
479		* with no hidden rows or columns
480		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
481	1	@Test(groups = { "Functional" })...
482		public void testSetBoxFromViewport()
483		{
484		// move viewport to start of alignment
485	1	moveViewport(0, 0);
486	1	assertEquals(od.getBoxX(), 0);
487	1	assertEquals(od.getBoxY(), 0);
488	1	assertEquals(od.getBoxWidth(), boxWidth);
489	1	assertEquals(od.getBoxHeight(), boxHeight);
490
491		// move viewport to right
492	1	moveViewportH(70);
493	1	assertEquals(od.getBoxX(),
494		Math.round((float) 70 * od.getWidth() / alwidth));
495	1	assertEquals(od.getBoxY(), 0);
496	1	assertEquals(od.getBoxWidth(), boxWidth);
497	1	assertEquals(od.getBoxHeight(), boxHeight);
498
499		// move viewport down
500	1	moveViewportV(100);
501	1	assertEquals(od.getBoxX(),
502		Math.round((float) 70 * od.getWidth() / alwidth));
503	1	assertEquals(od.getBoxY(),
504		Math.round(100 * od.getSequencesHeight() / alheight));
505	1	assertEquals(od.getBoxWidth(), boxWidth);
506	1	assertEquals(od.getBoxHeight(), boxHeight);
507
508		// move viewport to bottom right
509	1	moveViewport(98, 508);
510	1	assertEquals(od.getBoxX(),
511		Math.round((float) 98 * od.getWidth() / alwidth));
512	1	assertEquals(od.getBoxY(),
513		Math.round((float) 508 * od.getSequencesHeight() / alheight));
514	1	assertEquals(od.getBoxWidth(), boxWidth);
515	1	assertEquals(od.getBoxHeight(), boxHeight);
516		}
517
518		/**
519		* Test that the box position is set correctly when there are hidden columns
520		* at the start
521		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
522	1	@Test(groups = { "Functional" })...
523		public void testSetBoxFromViewportHiddenColsAtStart()
524		{
525	1	int firstHidden = 0;
526	1	int lastHidden = 20;
527	1	hiddenCols.hideColumns(firstHidden, lastHidden);
528
529		// move viewport to start of alignment
530	1	moveViewport(0, 0);
531	1	assertEquals(od.getBoxX(), 0);
532	1	assertEquals(od.getBoxY(), 0);
533	1	assertEquals(od.getBoxWidth(), boxWidth);
534	1	assertEquals(od.getBoxHeight(), boxHeight);
535
536		// move viewport to end of alignment - need to make startRes by removing
537		// hidden cols because of how viewport/overview are implemented
538	1	moveViewport(98 - lastHidden - 1, 0);
539	1	assertEquals(od.getBoxX(), Math.round(
540		(float) (98 - lastHidden - 1) * od.getWidth() / alwidth));
541	1	assertEquals(od.getBoxY(), 0);
542	1	assertEquals(od.getBoxWidth(), boxWidth);
543	1	assertEquals(od.getBoxHeight(), boxHeight);
544		}
545
546		/**
547		* Test that the box position is set correctly when there are hidden columns
548		* in the middle
549		*/
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
550	1	@Test(groups = { "Functional" })...
551		public void testSetBoxFromViewportHiddenColsInMiddle()
552		{
553	1	int firstHidden = 68;
554	1	int lastHidden = 78;
555	1	hiddenCols.hideColumns(firstHidden, lastHidden);
556
557		// move viewport before hidden columns
558	1	moveViewport(3, 0);
559
560	1	assertEquals(od.getBoxX(),
561		Math.round((float) 3 * od.getWidth() / alwidth));
562	1	assertEquals(od.getBoxY(), 0);
563	1	assertEquals(od.getBoxWidth(), boxWidth);
564	1	assertEquals(od.getBoxHeight(), boxHeight);
565
566		// move viewport to left of hidden columns with overlap
567	1	moveViewport(10, 0);
568	1	assertEquals(od.getBoxX(),
569		Math.round((float) 10 * od.getWidth() / alwidth));
570	1	assertEquals(od.getBoxY(), 0);
571	1	assertEquals(od.getBoxWidth(), boxWidth);
572	1	assertEquals(od.getBoxHeight(), boxHeight);
573
574		// move viewport to straddle hidden columns
575	1	moveViewport(63, 0);
576	1	assertEquals(od.getBoxX(),
577		Math.round((float) 63 * od.getWidth() / alwidth));
578	1	assertEquals(od.getBoxY(), 0);
579	1	assertEquals(od.getBoxWidth(), boxWidth);
580	1	assertEquals(od.getBoxHeight(), boxHeight);
581
582		// move viewport to right of hidden columns, no overlap
583	1	moveViewport(80 - (lastHidden - firstHidden + 1), 0);
584	1	assertEquals(od.getBoxX(),
585		Math.round((float) (80 - (lastHidden - firstHidden + 1))
586		* od.getWidth() / alwidth));
587	1	assertEquals(od.getBoxY(), 0);
588	1	assertEquals(od.getBoxWidth(), boxWidth);
589	1	assertEquals(od.getBoxHeight(), boxHeight);
590
591		}
592
593		/**
594		* Test that the box position is set correctly when there are hidden columns
595		* at the end
596		*/
		100% Uncovered Elements: 0 (13) Complexity: 1 Complexity Density: 0.08 1PASS
597	1	@Test(groups = { "Functional" })...
598		public void testSetBoxFromViewportHiddenColsAtEnd()
599		{
600	1	int firstHidden = 152;
601	1	int lastHidden = 164;
602	1	hiddenCols.hideColumns(firstHidden, lastHidden);
603
604		// move viewport before hidden columns
605	1	moveViewport(3, 0);
606	1	assertEquals(od.getBoxX(),
607		Math.round((float) 3 * od.getWidth() / alwidth));
608	1	assertEquals(od.getBoxY(), 0);
609	1	assertEquals(od.getBoxWidth(), boxWidth);
610	1	assertEquals(od.getBoxHeight(), boxHeight);
611
612		// move viewport to hidden columns
613		// viewport can't actually extend into hidden cols,
614		// so move to the far right edge of the viewport
615	1	moveViewport(firstHidden - viewWidth, 0);
616	1	assertEquals(od.getBoxX(), Math.round(
617		(float) (firstHidden - viewWidth) * od.getWidth() / alwidth));
618	1	assertEquals(od.getBoxY(), 0);
619	1	assertEquals(od.getBoxWidth(), boxWidth);
620	1	assertEquals(od.getBoxHeight(), boxHeight);
621		}
622
623		/**
624		* Test that the box position is set correctly when there are hidden rows at
625		* the start
626		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
627	1	@Test(groups = { "Functional" })...
628		public void testSetBoxFromViewportHiddenRowsAtStart()
629		{
630	1	int firstHidden = 0;
631	1	int lastHidden = 20;
632	1	hideSequences(firstHidden, lastHidden);
633
634		// calculate with visible values
635	1	alheight = vpranges.getVisibleAlignmentHeight();
636	1	alwidth = vpranges.getVisibleAlignmentWidth();
637
638	1	boxWidth = Math.round(
639		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
640		* od.getWidth() / alwidth);
641	1	boxHeight = Math.round(
642		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
643		* od.getSequencesHeight() / alheight);
644
645		// move viewport to start of alignment:
646		// box moves to below hidden rows, height remains same
647	1	moveViewport(0, 0);
648	1	assertEquals(od.getBoxX(), 0);
649	1	assertEquals(od.getBoxY(), 0);
650	1	assertEquals(od.getBoxWidth(), boxWidth);
651	1	assertEquals(od.getBoxHeight(), boxHeight);
652
653		// move viewport to end of alignment
654	1	moveViewport(0, 525 - viewHeight - lastHidden - 1);
655	1	assertEquals(od.getBoxX(), 0);
656	1	assertEquals(od.getBoxY(),
657		Math.round((float) (525 - viewHeight - lastHidden - 1)
658		* od.getSequencesHeight() / alheight));
659	1	assertEquals(od.getBoxWidth(), boxWidth);
660	1	assertEquals(od.getBoxHeight(), boxHeight);
661		}
662
663		/**
664		* Test that the box position is set correctly when there are hidden rows in
665		* the middle
666		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
667	1	@Test(groups = { "Functional" })...
668		public void testSetBoxFromViewportHiddenRowsInMiddle()
669		{
670	1	int firstHidden = 200;
671	1	int lastHidden = 210;
672	1	hideSequences(firstHidden, lastHidden);
673
674		// calculate with visible values
675	1	alheight = vpranges.getVisibleAlignmentHeight();
676	1	alwidth = vpranges.getVisibleAlignmentWidth();
677
678	1	boxWidth = Math.round(
679		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
680		* od.getWidth() / alwidth);
681	1	boxHeight = Math.round(
682		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
683		* od.getSequencesHeight() / alheight);
684
685		// move viewport to start of alignment:
686		// box, height etc as in non-hidden case
687	1	moveViewport(0, 0);
688	1	assertEquals(od.getBoxX(), 0);
689	1	assertEquals(od.getBoxY(), 0);
690	1	assertEquals(od.getBoxWidth(), boxWidth);
691	1	assertEquals(od.getBoxHeight(), boxHeight);
692
693		// move viewport to straddle hidden rows
694	1	moveViewport(0, 198);
695	1	assertEquals(od.getBoxX(), 0);
696	1	assertEquals(od.getBoxY(),
697		Math.round((float) 198 * od.getSequencesHeight() / alheight));
698	1	assertEquals(od.getBoxWidth(), boxWidth);
699	1	assertEquals(od.getBoxHeight(), boxHeight);
700		}
701
702		/**
703		* Test that the box position is set correctly when there are hidden rows at
704		* the bottom
705		*/
		100% Uncovered Elements: 0 (17) Complexity: 1 Complexity Density: 0.06 1PASS
706	1	@Test(groups = { "Functional" })...
707		public void testSetBoxFromViewportHiddenRowsAtEnd()
708		{
709	1	int firstHidden = 500;
710	1	int lastHidden = 524;
711	1	hideSequences(firstHidden, lastHidden);
712
713		// calculate with visible values
714	1	alheight = vpranges.getVisibleAlignmentHeight();
715	1	alwidth = vpranges.getVisibleAlignmentWidth();
716
717	1	boxWidth = Math.round(
718		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
719		* od.getWidth() / alwidth);
720	1	boxHeight = Math.round(
721		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
722		* od.getSequencesHeight() / alheight);
723
724		// move viewport to start of alignment:
725		// box, height etc as in non-hidden case
726	1	moveViewport(0, 0);
727	1	assertEquals(od.getBoxX(), 0);
728	1	assertEquals(od.getBoxY(), 0);
729	1	assertEquals(od.getBoxWidth(), boxWidth);
730	1	assertEquals(od.getBoxHeight(), boxHeight);
731
732		// move viewport to end of alignment
733		// viewport sits above hidden rows and does not include them
734	1	moveViewport(0, firstHidden - viewHeight - 1);
735	1	assertEquals(od.getBoxX(), 0);
736	1	assertEquals(od.getBoxY(),
737		Math.round((float) (firstHidden - viewHeight - 1)
738		* od.getSequencesHeight() / alheight));
739	1	assertEquals(od.getBoxWidth(), boxWidth);
740	1	assertEquals(od.getBoxHeight(), boxHeight);
741
742		}
743
744		/**
745		* Test setting of the box position, when there are hidden rows at the start
746		* of the alignment
747		*/
		100% Uncovered Elements: 0 (23) Complexity: 1 Complexity Density: 0.04 1PASS
748	1	@Test(groups = { "Functional" })...
749		public void testFromMouseWithHiddenRowsAtStart()
750		{
751	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
752	1	assertEquals(od.getBoxX(), 0);
753	1	assertEquals(od.getBoxY(), 0);
754	1	assertEquals(od.getBoxHeight(), boxHeight);
755	1	assertEquals(od.getBoxWidth(), boxWidth);
756	1	assertEquals(vpranges.getStartRes(), 0);
757	1	assertEquals(vpranges.getStartSeq(), 0);
758
759		// hide rows at start and check updated box position is correct
760	1	int lastHiddenRow = 30;
761	1	hideSequences(0, lastHiddenRow);
762
763		// calculate with visible values
764	1	alheight = vpranges.getVisibleAlignmentHeight();
765	1	alwidth = vpranges.getVisibleAlignmentWidth();
766
767	1	boxWidth = Math.round(
768		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
769		* od.getWidth() / alwidth);
770	1	boxHeight = Math.round(
771		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
772		* od.getSequencesHeight() / alheight);
773
774	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
775	1	assertEquals(od.getBoxX(), 0);
776	1	assertEquals(od.getBoxY(), 0);
777	1	assertEquals(od.getBoxWidth(), boxWidth);
778	1	assertEquals(od.getBoxHeight(), boxHeight);
779
780		// click below hidden rows
781	1	mouseClick(od, 0, 151 + boxHeight / 2);
782	1	assertEquals(od.getBoxX(), 0);
783	1	assertEquals(od.getBoxY(), 151);
784	1	assertEquals(od.getBoxWidth(), boxWidth);
785	1	assertEquals(od.getBoxHeight(), boxHeight);
786		}
787
788		/**
789		* Test setting of the box position, when there are hidden rows at the middle
790		* of the alignment
791		*/
		100% Uncovered Elements: 0 (31) Complexity: 1 Complexity Density: 0.03 1PASS
792	1	@Test(groups = { "Functional" })...
793		public void testFromMouseWithHiddenRowsInMiddle()
794		{
795	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
796
797	1	assertEquals(od.getBoxX(), 0);
798	1	assertEquals(od.getBoxY(), 0);
799	1	assertEquals(od.getBoxWidth(), boxWidth);
800	1	assertEquals(od.getBoxHeight(), boxHeight);
801	1	assertEquals(vpranges.getStartRes(), 0);
802	1	assertEquals(vpranges.getStartSeq(), 0);
803
804		// hide rows in middle and check updated box position is correct
805		// no changes
806	1	int firstHiddenRow = 50;
807	1	int lastHiddenRow = 54;
808	1	hideSequences(firstHiddenRow, lastHiddenRow);
809
810		// calculate with visible values
811	1	alheight = vpranges.getVisibleAlignmentHeight();
812	1	alwidth = vpranges.getVisibleAlignmentWidth();
813
814	1	boxWidth = Math.round(
815		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
816		* od.getWidth() / alwidth);
817	1	boxHeight = Math.round(
818		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
819		* od.getSequencesHeight() / alheight);
820
821	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
822
823	1	assertEquals(od.getBoxX(), 0);
824	1	assertEquals(od.getBoxY(), 0);
825	1	assertEquals(od.getBoxWidth(), boxWidth);
826	1	assertEquals(od.getBoxHeight(), boxHeight);
827
828		// click above hidden rows, so that box overlaps
829	1	int ypos = 35 + viewHeight / 2; // row value in residues
830	1	mouseClick(od, 0,
831		Math.round((float) ypos * od.getSequencesHeight() / alheight));
832	1	assertEquals(od.getBoxX(), 0);
833	1	assertEquals(od.getBoxY(),
834		Math.round((float) 35 * od.getSequencesHeight() / alheight));
835	1	assertEquals(od.getBoxWidth(), boxWidth);
836	1	assertEquals(od.getBoxHeight(), boxHeight);
837
838		// click so that box straddles hidden rows
839	1	ypos = 45 + 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) 45 * od.getSequencesHeight() / alheight));
845	1	assertEquals(od.getBoxWidth(), boxWidth);
846	1	assertEquals(od.getBoxHeight(), boxHeight);
847		}
848
849		/**
850		* Test setting of the box position, when there are hidden rows at the end of
851		* the alignment
852		*/
		100% Uncovered Elements: 0 (31) Complexity: 1 Complexity Density: 0.03 1PASS
853	1	@Test(groups = { "Functional" })...
854		public void testFromMouseWithHiddenRowsAtEnd()
855		{
856	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
857	1	assertEquals(od.getBoxX(), 0);
858	1	assertEquals(od.getBoxY(), 0);
859	1	assertEquals(od.getBoxWidth(), boxWidth);
860	1	assertEquals(od.getBoxHeight(), boxHeight);
861	1	assertEquals(vpranges.getStartRes(), 0);
862	1	assertEquals(vpranges.getStartSeq(), 0);
863
864		// hide rows at end and check updated box position is correct
865		// no changes
866	1	int firstHidden = 500;
867	1	int lastHidden = 524;
868	1	hideSequences(firstHidden, lastHidden);
869
870		// calculate with visible values
871	1	alheight = vpranges.getVisibleAlignmentHeight();
872	1	alwidth = vpranges.getVisibleAlignmentWidth();
873
874	1	boxWidth = Math.round(
875		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
876		* od.getWidth() / alwidth);
877	1	boxHeight = Math.round(
878		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
879		* od.getSequencesHeight() / alheight);
880
881	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
882	1	assertEquals(od.getBoxX(), 0);
883	1	assertEquals(od.getBoxY(), 0);
884	1	assertEquals(od.getBoxWidth(), boxWidth);
885	1	assertEquals(od.getBoxHeight(), boxHeight);
886
887		// click above hidden rows
888	1	int ypos = 41 + viewHeight / 2; // row 41
889	1	mouseClick(od, 0,
890		Math.round((float) ypos * od.getSequencesHeight() / alheight));
891	1	assertEquals(od.getBoxX(), 0);
892	1	assertEquals(od.getBoxY(),
893		Math.round((float) 41 * od.getSequencesHeight() / alheight));
894	1	assertEquals(od.getBoxWidth(), boxWidth);
895	1	assertEquals(od.getBoxHeight(), boxHeight);
896
897		// click above hidden rows so box overlaps
898		// boxY, boxHeight remains same
899	1	ypos = 497 + viewHeight / 2; // row 497
900	1	mouseClick(od, 0,
901		Math.round((float) ypos * od.getSequencesHeight() / alheight));
902	1	assertEquals(od.getBoxX(), 0);
903	1	assertEquals(od.getBoxY(), Math
904		.round((float) firstHidden * od.getSequencesHeight() / alheight)
905		- boxHeight);
906	1	assertEquals(od.getBoxWidth(), boxWidth);
907	1	assertEquals(od.getBoxHeight(), boxHeight);
908		}
909
910		/**
911		* Test the function to determine if a point is in the overview's box or not
912		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
913	1	@Test(groups = { "Functional" })...
914		public void testPositionInBox()
915		{
916	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
917
918	1	assertFalse(od.isPositionInBox(0, 0));
919	1	assertTrue(od.isPositionInBox(10, 9));
920	1	assertFalse(od.isPositionInBox(0, 9));
921	1	assertFalse(od.isPositionInBox(9, 0));
922	1	assertFalse(od.isPositionInBox(75, 20));
923
924		// hide columns in the box area
925		// makes absolutely no difference
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		// hide sequences in box area
935		// makes absolutely no difference
936	1	hideSequences(1, 3);
937	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
938	1	assertFalse(od.isPositionInBox(0, 0));
939	1	assertTrue(od.isPositionInBox(10, 9));
940	1	assertFalse(od.isPositionInBox(0, 9));
941	1	assertFalse(od.isPositionInBox(9, 0));
942	1	assertFalse(od.isPositionInBox(75, 20));
943		}
944
945		/**
946		* Test the dragging functionality
947		*/
		100% Uncovered Elements: 0 (20) Complexity: 1 Complexity Density: 0.05 1PASS
948	1	@Test(groups = { "Functional" })...
949		public void testDragging()
950		{
951	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
952	1	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
953	1	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
954
955		// updates require an OverviewPanel to exist which it doesn't here
956		// so call setBoxPosition() as it would be called by the AlignmentPanel
957		// normally
958	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
959
960		// corner moves 16 (20-4) right and 6 (22-16) up
961	1	assertEquals(od.getBoxX(), 16);
962	1	assertEquals(od.getBoxY(), 6);
963
964		// hide columns - makes no difference
965	1	hiddenCols.hideColumns(1, 4);
966	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
967	1	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
968	1	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
969	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
970
971		// corner moves 16 (20-4) right and 6 (22-16) up
972	1	assertEquals(od.getBoxX(), 16);
973	1	assertEquals(od.getBoxY(), 6);
974
975		// hide sequences in box area
976		// makes absolutely no difference
977	1	hideSequences(1, 3);
978	1	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
979	1	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
980	1	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
981	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
982
983		// corner moves 16 (20-4) right and 6 (22-16) up
984	1	assertEquals(od.getBoxX(), 16);
985	1	assertEquals(od.getBoxY(), 6);
986		}
987
988		/*
989		* Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
990		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
991	2	private void moveViewportH(int startRes)...
992		{
993	2	vpranges.setViewportStartAndWidth(startRes, viewWidth);
994	2	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
995		}
996
997		/*
998		* Move viewport vertically: startSeq and endSeq give new vertical extent. Horizontal extent stays the same.
999		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1000	1	private void moveViewportV(int startSeq)...
1001		{
1002	1	vpranges.setViewportStartAndHeight(startSeq, viewHeight);
1003	1	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1004		}
1005
1006		/*
1007		* Move viewport horizontally and vertically.
1008		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
1009	33	private void moveViewport(int startRes, int startSeq)...
1010		{
1011	33	vpranges.setViewportStartAndWidth(startRes, viewWidth);
1012	33	vpranges.setViewportStartAndHeight(startSeq, viewHeight);
1013	33	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1014		}
1015
1016		/*
1017		* Mouse click as position x,y in overview window
1018		*/
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
1019	45	private void mouseClick(OverviewDimensions od, int x, int y)...
1020		{
1021	45	od.updateViewportFromMouse(x, y, al.getHiddenSequences(), hiddenCols);
1022
1023		// updates require an OverviewPanel to exist which it doesn't here
1024		// so call setBoxPosition() as it would be called by the AlignmentPanel
1025		// normally
1026	45	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1027		}
1028
1029		/*
1030		* Test that the box is positioned with the top left corner at xpos, ypos
1031		* and with the original width and height
1032		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
1033	8	private void testBoxIsAtClickPoint(int xpos, int ypos)...
1034		{
1035	8	mouseClick(od, xpos, ypos);
1036	8	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
1037	8	assertEquals(od.getBoxY() + od.getBoxHeight() / 2, ypos);
1038	8	assertEquals(od.getBoxWidth(), boxWidth);
1039	8	assertEquals(od.getBoxHeight(), boxHeight);
1040
1041		}
1042
1043		/*
1044		* Hide sequences between start and end
1045		*/
		100% Uncovered Elements: 0 (8) Complexity: 2 Complexity Density: 0.33
1046	8	private void hideSequences(int start, int end)...
1047		{
1048	8	SequenceI[] allseqs = al.getSequencesArray();
1049	8	SequenceGroup theseSeqs = new SequenceGroup();
1050
1051	132	for (int i = start; i <= end; i++)
1052		{
1053	124	theseSeqs.addSequence(allseqs[i], false);
1054	124	al.getHiddenSequences().hideSequence(allseqs[i]);
1055		}
1056
1057	8	hiddenRepSequences.put(allseqs[start], theseSeqs);
1058		}
1059		}