Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewDimensionsHideHiddenTest	45	496	28	0.00%	Show methods

Class OverviewDimensionsHideHiddenTest

Class OverviewDimensionsHideHiddenTest	Line # 45	Total Statements 496	Complexity 28	TOTAL Coverage 0.00%
setUpAlignment() : void   setUpAlignment() : void	7070	2.02	1.01	0.0 0.00%
setUp() : void   setUp() : void	7878	18.018	2.02	0.0 0.00%
cleanUp() : void   cleanUp() : void	116116	1.01	1.01	0.0 0.00%
testConstructor() : void   testConstructor() : void	126126	51.051	1.01	0.0 0.00%
testSetBoxFromMouseClick() : void   testSetBoxFromMouseClick() : void	205205	55.055	1.01	0.0 0.00%
testFromMouseWithHiddenColsAtStart() : void   testFromMouseWithHiddenColsAtStart() : void	299299	20.020	1.01	0.0 0.00%
testFromMouseWithHiddenColsInMiddle() : void   testFromMouseWithHiddenColsInMiddle() : void	340340	51.051	1.01	0.0 0.00%
testFromMouseWithHiddenColsAtEnd() : void   testFromMouseWithHiddenColsAtEnd() : void	424424	33.033	1.01	0.0 0.00%
testSetBoxFromViewport() : void   testSetBoxFromViewport() : void	481481	20.020	1.01	0.0 0.00%
testSetBoxFromViewportHiddenColsAtStart() : void   testSetBoxFromViewportHiddenColsAtStart() : void	522522	13.013	1.01	0.0 0.00%
testSetBoxFromViewportHiddenColsInMiddle() : void   testSetBoxFromViewportHiddenColsInMiddle() : void	550550	23.023	1.01	0.0 0.00%
testSetBoxFromViewportHiddenColsAtEnd() : void   testSetBoxFromViewportHiddenColsAtEnd() : void	597597	13.013	1.01	0.0 0.00%
testSetBoxFromViewportHiddenRowsAtStart() : void   testSetBoxFromViewportHiddenRowsAtStart() : void	627627	17.017	1.01	0.0 0.00%
testSetBoxFromViewportHiddenRowsInMiddle() : void   testSetBoxFromViewportHiddenRowsInMiddle() : void	667667	17.017	1.01	0.0 0.00%
testSetBoxFromViewportHiddenRowsAtEnd() : void   testSetBoxFromViewportHiddenRowsAtEnd() : void	706706	17.017	1.01	0.0 0.00%
testFromMouseWithHiddenRowsAtStart() : void   testFromMouseWithHiddenRowsAtStart() : void	748748	23.023	1.01	0.0 0.00%
testFromMouseWithHiddenRowsInMiddle() : void   testFromMouseWithHiddenRowsInMiddle() : void	792792	31.031	1.01	0.0 0.00%
testFromMouseWithHiddenRowsAtEnd() : void   testFromMouseWithHiddenRowsAtEnd() : void	853853	31.031	1.01	0.0 0.00%
testPositionInBox() : void   testPositionInBox() : void	913913	20.020	1.01	0.0 0.00%
testDragging() : void   testDragging() : void	948948	20.020	1.01	0.0 0.00%
moveViewportH(int) : void   moveViewportH(int) : void	991991	2.02	1.01	0.0 0.00%
moveViewportV(int) : void   moveViewportV(int) : void	10001000	2.02	1.01	0.0 0.00%
moveViewport(int,int) : void   moveViewport(int,int) : void	10091009	3.03	1.01	0.0 0.00%
mouseClick(OverviewDimensions,int,int) : void   mouseClick(OverviewDimensions,int,int) : void	10191019	2.02	1.01	0.0 0.00%
testBoxIsAtClickPoint(int,int) : void   testBoxIsAtClickPoint(int,int) : void	10331033	5.05	1.01	0.0 0.00%
hideSequences(int,int) : void   hideSequences(int,int) : void	10461046	6.06	2.02	0.0 0.00%

 

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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)
		0% Uncovered Elements: 526 (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
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
70	0	@BeforeClass(alwaysRun = true)...
71		public void setUpAlignment()
72		{
73		// create random alignment
74	0	AlignmentGenerator gen = new AlignmentGenerator(false);
75	0	al = gen.generate(157, 525, 123, 5, 5);
76		}
77
		0% Uncovered Elements: 20 (20) Complexity: 2 Complexity Density: 0.11
78	0	@BeforeMethod(alwaysRun = true)...
79		public void setUp()
80		{
81	0	if (!hiddenRepSequences.isEmpty())
82		{
83	0	al.getHiddenSequences().showAll(hiddenRepSequences);
84		}
85	0	ColumnSelection colsel = new ColumnSelection();
86	0	hiddenCols.revealAllHiddenColumns(colsel);
87
88	0	vpranges = new ViewportRanges(al);
89	0	vpranges.setViewportStartAndHeight(0, 18);
90	0	vpranges.setViewportStartAndWidth(0, 63);
91
92	0	viewHeight = vpranges.getEndSeq() - vpranges.getStartSeq() + 1;
93	0	viewWidth = vpranges.getEndRes() - vpranges.getStartRes() + 1;
94
95	0	HiddenColumns hiddenCols = new HiddenColumns();
96
97	0	od = new OverviewDimensionsHideHidden(vpranges, true);
98		// Initial box sizing - default path through code
99	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
100
101	0	mouseClick(od, 0, 0);
102	0	moveViewport(0, 0);
103
104		// calculate with visible values
105	0	alheight = vpranges.getVisibleAlignmentHeight();
106	0	alwidth = vpranges.getVisibleAlignmentWidth();
107
108	0	boxWidth = Math.round(
109		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
110		* od.getWidth() / alwidth);
111	0	boxHeight = Math.round(
112		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
113		* od.getSequencesHeight() / alheight);
114		}
115
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
116	0	@AfterClass(alwaysRun = true)...
117		public void cleanUp()
118		{
119	0	al = null;
120		}
121
122		/**
123		* Test that the OverviewDimensions constructor sets width and height
124		* correctly
125		*/
		0% Uncovered Elements: 51 (51) Complexity: 1 Complexity Density: 0.02 4-
126	0	@Test(groups = { "Functional" })...
127		public void testConstructor()
128		{
129	0	SequenceI seqa = new Sequence("Seq1", "ABC");
130	0	SequenceI seqb = new Sequence("Seq2", "ABC");
131	0	SequenceI seqc = new Sequence("Seq3", "ABC");
132	0	SequenceI seqd = new Sequence("Seq4", "ABC");
133	0	SequenceI seqe = new Sequence("Seq5",
134		"ABCABCABCABCABCABCABCABCBACBACBACBAC");
135
136	0	int defaultGraphHeight = 20;
137	0	int maxWidth = 400;
138	0	int minWidth = 120;
139	0	int maxSeqHeight = 300;
140	0	int minSeqHeight = 40;
141
142		// test for alignment with width > height
143	0	SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
144	0	Alignment al1 = new Alignment(seqs1);
145	0	ViewportRanges props = new ViewportRanges(al1);
146
147	0	OverviewDimensions od = new OverviewDimensionsHideHidden(props, true);
148	0	int scaledHeight = 267;
149	0	assertEquals(od.getGraphHeight(), defaultGraphHeight);
150	0	assertEquals(od.getSequencesHeight(), scaledHeight);
151	0	assertEquals(od.getWidth(), maxWidth);
152	0	assertEquals(od.getHeight(), scaledHeight + defaultGraphHeight);
153
154		// test for alignment with width < height
155	0	SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
156	0	Alignment al2 = new Alignment(seqs2);
157	0	props = new ViewportRanges(al2);
158
159	0	od = new OverviewDimensionsHideHidden(props, true);
160	0	int scaledWidth = 300;
161	0	assertEquals(od.getGraphHeight(), defaultGraphHeight);
162	0	assertEquals(od.getSequencesHeight(), maxSeqHeight);
163	0	assertEquals(od.getWidth(), scaledWidth);
164	0	assertEquals(od.getHeight(), scaledWidth + defaultGraphHeight);
165
166		// test for alignment with width > height and sequence height scaled below
167		// min value
168	0	SequenceI[] seqs3 = new SequenceI[] { seqe };
169	0	Alignment al3 = new Alignment(seqs3);
170	0	props = new ViewportRanges(al3);
171
172	0	od = new OverviewDimensionsHideHidden(props, true);
173	0	assertEquals(od.getGraphHeight(), defaultGraphHeight);
174	0	assertEquals(od.getSequencesHeight(), minSeqHeight);
175	0	assertEquals(od.getWidth(), maxWidth);
176	0	assertEquals(od.getHeight(), minSeqHeight + defaultGraphHeight);
177
178		// test for alignment with width < height and width scaled below min value
179	0	SequenceI[] seqs4 = new SequenceI[] { seqa, seqb, seqc, seqd, seqa,
180		seqb, seqc, seqd, seqa, seqb, seqc, seqd, seqa, seqb, seqc, seqd };
181	0	Alignment al4 = new Alignment(seqs4);
182	0	props = new ViewportRanges(al4);
183
184	0	od = new OverviewDimensionsHideHidden(props, true);
185	0	assertEquals(od.getGraphHeight(), defaultGraphHeight);
186	0	assertEquals(od.getSequencesHeight(), maxSeqHeight);
187	0	assertEquals(od.getWidth(), minWidth);
188	0	assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);
189
190	0	Alignment al5 = new Alignment(seqs4);
191	0	props = new ViewportRanges(al5);
192
193	0	od = new OverviewDimensionsHideHidden(props, false);
194	0	assertEquals(od.getGraphHeight(), 0);
195	0	assertEquals(od.getSequencesHeight(), maxSeqHeight);
196	0	assertEquals(od.getWidth(), minWidth);
197	0	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		*/
		0% Uncovered Elements: 55 (55) Complexity: 1 Complexity Density: 0.02 4-
205	0	@Test(groups = { "Functional" })...
206		public void testSetBoxFromMouseClick()
207		{
208	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
209	0	assertEquals(od.getBoxX(), 0);
210	0	assertEquals(od.getBoxY(), 0);
211	0	assertEquals(od.getBoxWidth(), boxWidth);
212	0	assertEquals(vpranges.getStartRes(), 0);
213	0	assertEquals(vpranges.getStartSeq(), 0);
214
215		// negative boxX value reset to 0
216	0	mouseClick(od, -5, 10);
217	0	assertEquals(od.getBoxX(), 0);
218	0	assertEquals(od.getBoxWidth(), boxWidth);
219	0	assertEquals(od.getBoxHeight(), boxHeight);
220	0	assertEquals(vpranges.getStartSeq() + vpranges.getViewportHeight() / 2,
221		Math.round((float) 10 * alheight / od.getSequencesHeight()));
222	0	assertEquals(vpranges.getStartRes(), 0);
223
224		// negative boxY value reset to 0
225	0	mouseClick(od, 6, -2);
226	0	assertEquals(od.getBoxY(), 0);
227	0	assertEquals(od.getBoxWidth(), boxWidth);
228	0	assertEquals(od.getBoxHeight(), boxHeight);
229	0	assertEquals(vpranges.getStartRes(), 0);
230	0	assertEquals(vpranges.getStartSeq(), 0);
231
232		// overly large boxX value reset to width-boxWidth
233	0	mouseClick(od, 101, 6);
234	0	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
235	0	assertEquals(od.getBoxY(), 1);
236	0	assertEquals(od.getBoxWidth(), boxWidth);
237	0	assertEquals(od.getBoxHeight(), boxHeight);
238	0	assertEquals(vpranges.getStartRes(),
239		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
240	0	assertEquals(vpranges.getStartSeq(), Math.round(
241		(float) od.getBoxY() * alheight / od.getSequencesHeight()));
242
243		// overly large boxY value reset to sequenceHeight - boxHeight
244	0	mouseClick(od, 10, 520);
245	0	assertEquals(od.getBoxX(), 0);
246	0	assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
247	0	assertEquals(od.getBoxWidth(), boxWidth);
248	0	assertEquals(od.getBoxHeight(), boxHeight);
249	0	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	0	assertEquals(vpranges.getStartSeq(), Math.round(
256		(float) od.getBoxY() * alheight / od.getSequencesHeight()) - 1);
257
258		// click past end of alignment, as above
259	0	mouseClick(od, 3000, 5);
260	0	assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
261	0	assertEquals(od.getBoxWidth(), boxWidth);
262	0	assertEquals(od.getBoxHeight(), boxHeight);
263	0	assertEquals(vpranges.getStartRes(),
264		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
265	0	assertEquals(vpranges.getStartSeq(), Math.round(
266		(float) od.getBoxY() * alheight / od.getSequencesHeight()));
267
268		// move viewport so startRes non-zero and then mouseclick
269	0	moveViewportH(20);
270
271		// click at viewport position
272	0	int oldboxx = od.getBoxX();
273	0	int oldboxy = od.getBoxY();
274	0	mouseClick(od, od.getBoxX() + od.getBoxWidth() / 2 + 6,
275		od.getBoxY() + od.getBoxHeight() / 2 + 3);
276	0	assertEquals(od.getBoxX(), oldboxx + 6);
277	0	assertEquals(od.getBoxWidth(), boxWidth);
278	0	assertEquals(od.getBoxHeight(), boxHeight);
279	0	assertEquals(vpranges.getStartRes(),
280		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
281	0	assertEquals(od.getBoxY(), oldboxy + 3);
282	0	assertEquals(vpranges.getStartSeq(), Math.round(
283		(float) od.getBoxY() * alheight / od.getSequencesHeight()));
284
285		// click at top corner
286	0	mouseClick(od, 0, 0);
287	0	assertEquals(od.getBoxX(), 0);
288	0	assertEquals(vpranges.getStartRes(), 0);
289	0	assertEquals(od.getBoxY(), 0);
290	0	assertEquals(vpranges.getStartSeq(), 0);
291	0	assertEquals(od.getBoxWidth(), boxWidth);
292	0	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		*/
		0% Uncovered Elements: 20 (20) Complexity: 1 Complexity Density: 0.05 4-
299	0	@Test(groups = { "Functional" })...
300		public void testFromMouseWithHiddenColsAtStart()
301		{
302	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
303	0	assertEquals(od.getBoxX(), 0);
304	0	assertEquals(od.getBoxY(), 0);
305	0	assertEquals(od.getBoxWidth(), boxWidth);
306	0	assertEquals(vpranges.getStartRes(), 0);
307	0	assertEquals(vpranges.getStartSeq(), 0);
308
309		// hide cols at start and check updated box position is correct
310	0	int lastHiddenCol = 30;
311	0	hiddenCols.hideColumns(0, lastHiddenCol);
312
313	0	testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
314
315		// click to right of hidden columns, box moves to click point
316	0	testBoxIsAtClickPoint(41 + boxWidth / 2, boxHeight / 2);
317	0	assertEquals(vpranges.getStartSeq(), 0);
318	0	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	0	int xpos = 100 + boxWidth / 2;
326	0	mouseClick(od, xpos, boxHeight / 2);
327	0	assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
328	0	assertEquals(od.getBoxY(), 0);
329	0	assertEquals(od.getBoxWidth(), boxWidth);
330	0	assertEquals(od.getBoxHeight(), boxHeight);
331	0	assertEquals(vpranges.getStartRes(),
332		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
333	0	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		*/
		0% Uncovered Elements: 51 (51) Complexity: 1 Complexity Density: 0.02 4-
340	0	@Test(groups = { "Functional" })...
341		public void testFromMouseWithHiddenColsInMiddle()
342		{
343	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
344	0	testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
345	0	assertEquals(od.getBoxX(), 0);
346	0	assertEquals(od.getBoxY(), 0);
347	0	assertEquals(od.getBoxWidth(), boxWidth);
348	0	assertEquals(vpranges.getStartRes(), 0);
349	0	assertEquals(vpranges.getStartSeq(), 0);
350
351		// hide columns 63-73, no change to box position or dimensions
352	0	int firstHidden = 63;
353	0	int lastHidden = 73;
354	0	hiddenCols.hideColumns(firstHidden, lastHidden);
355
356	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
357	0	testBoxIsAtClickPoint(boxWidth / 2, boxHeight / 2);
358	0	assertEquals(od.getBoxX(), 0);
359	0	assertEquals(od.getBoxY(), 0);
360	0	assertEquals(od.getBoxWidth(), boxWidth);
361	0	assertEquals(vpranges.getStartRes(), 0);
362	0	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	0	int xpos = 54 - boxWidth / 2; // 54 is position in overview approx halfway
367		// between cols 60 and 70
368	0	mouseClick(od, xpos, boxHeight / 2);
369	0	testBoxIsAtClickPoint(xpos, boxHeight / 2);
370	0	assertEquals(vpranges.getStartRes(), 1 + // rounding
371		Math.round((xpos - boxWidth / 2) * alwidth / od.getWidth()));
372	0	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	0	xpos = 33;
377	0	mouseClick(od, xpos, boxHeight / 2);
378	0	testBoxIsAtClickPoint(xpos, boxHeight / 2);
379	0	assertEquals(vpranges.getStartRes(), Math.round(
380		(float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
381	0	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	0	xpos = Math.round((float) 50 * od.getWidth() / alwidth) + boxWidth / 2;
386	0	mouseClick(od, xpos, boxHeight / 2);
387	0	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
388	0	assertEquals(od.getBoxY(), 0);
389	0	assertEquals(od.getBoxWidth(), boxWidth);
390	0	assertEquals(od.getBoxHeight(), boxHeight);
391	0	assertEquals(vpranges.getStartRes(), 50);
392	0	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	0	xpos = Math.round((float) 75 * od.getWidth() / alwidth) + boxWidth / 2;
398	0	mouseClick(od, xpos, boxHeight / 2);
399	0	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
400	0	assertEquals(od.getBoxY(), 0);
401	0	assertEquals(od.getBoxWidth(), boxWidth);
402	0	assertEquals(od.getBoxHeight(), boxHeight);
403	0	assertEquals(vpranges.getStartSeq(), 0);
404	0	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	0	xpos = 3000;
409	0	mouseClick(od, xpos, boxHeight / 2);
410	0	assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
411	0	assertEquals(od.getBoxY(), 0);
412	0	assertEquals(od.getBoxWidth(), boxWidth);
413	0	assertEquals(od.getBoxHeight(), boxHeight);
414	0	assertEquals(vpranges.getStartRes(),
415		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
416	0	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		*/
		0% Uncovered Elements: 33 (33) Complexity: 1 Complexity Density: 0.03 4-
424	0	@Test(groups = { "Functional" })...
425		public void testFromMouseWithHiddenColsAtEnd()
426		{
427	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
428	0	assertEquals(od.getBoxX(), 0);
429	0	assertEquals(od.getBoxY(), 0);
430	0	assertEquals(od.getBoxWidth(), boxWidth);
431	0	assertEquals(vpranges.getStartRes(), 0);
432	0	assertEquals(vpranges.getStartSeq(), 0);
433
434		// hide columns 140-164, no change to box position or dimensions
435	0	int firstHidden = 140;
436	0	int lastHidden = 164;
437	0	hiddenCols.hideColumns(firstHidden, lastHidden);
438	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
439	0	assertEquals(od.getBoxX(), 0);
440	0	assertEquals(od.getBoxY(), 0);
441	0	assertEquals(od.getBoxWidth(), boxWidth);
442	0	assertEquals(vpranges.getStartRes(), 0);
443	0	assertEquals(vpranges.getStartSeq(), 0);
444
445		// click to left of hidden cols, without overlapping
446		// boxX, scrollCol and width as normal
447	0	int xpos = 30;
448	0	int ypos = 6;
449	0	testBoxIsAtClickPoint(xpos, ypos);
450	0	assertEquals(vpranges.getStartSeq(), Math.round(
451		(float) (ypos - boxHeight / 2) * alheight / od.getHeight()));
452	0	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	0	xpos = Math.round((float) 144 * od.getWidth() / alwidth) - boxWidth;
458	0	mouseClick(od, xpos, boxHeight / 2);
459	0	testBoxIsAtClickPoint(xpos, boxHeight / 2);
460	0	assertEquals(vpranges.getStartRes(), Math.round(
461		(float) (xpos - boxWidth / 2) * alwidth / od.getWidth()));
462	0	assertEquals(vpranges.getStartSeq(), 0);
463
464		// click off end of alignment
465		// boxX and scrollCol adjusted backwards, width normal
466	0	xpos = 3000;
467	0	mouseClick(od, xpos, 0);
468	0	assertEquals(od.getBoxX(), Math.round(od.getWidth()) - boxWidth);
469	0	assertEquals(od.getBoxY(), 0);
470	0	assertEquals(od.getBoxWidth(), boxWidth);
471	0	assertEquals(od.getBoxHeight(), boxHeight);
472	0	assertEquals(vpranges.getStartRes(),
473		Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
474	0	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		*/
		0% Uncovered Elements: 20 (20) Complexity: 1 Complexity Density: 0.05 4-
481	0	@Test(groups = { "Functional" })...
482		public void testSetBoxFromViewport()
483		{
484		// move viewport to start of alignment
485	0	moveViewport(0, 0);
486	0	assertEquals(od.getBoxX(), 0);
487	0	assertEquals(od.getBoxY(), 0);
488	0	assertEquals(od.getBoxWidth(), boxWidth);
489	0	assertEquals(od.getBoxHeight(), boxHeight);
490
491		// move viewport to right
492	0	moveViewportH(70);
493	0	assertEquals(od.getBoxX(),
494		Math.round((float) 70 * od.getWidth() / alwidth));
495	0	assertEquals(od.getBoxY(), 0);
496	0	assertEquals(od.getBoxWidth(), boxWidth);
497	0	assertEquals(od.getBoxHeight(), boxHeight);
498
499		// move viewport down
500	0	moveViewportV(100);
501	0	assertEquals(od.getBoxX(),
502		Math.round((float) 70 * od.getWidth() / alwidth));
503	0	assertEquals(od.getBoxY(),
504		Math.round(100 * od.getSequencesHeight() / alheight));
505	0	assertEquals(od.getBoxWidth(), boxWidth);
506	0	assertEquals(od.getBoxHeight(), boxHeight);
507
508		// move viewport to bottom right
509	0	moveViewport(98, 508);
510	0	assertEquals(od.getBoxX(),
511		Math.round((float) 98 * od.getWidth() / alwidth));
512	0	assertEquals(od.getBoxY(),
513		Math.round((float) 508 * od.getSequencesHeight() / alheight));
514	0	assertEquals(od.getBoxWidth(), boxWidth);
515	0	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		*/
		0% Uncovered Elements: 13 (13) Complexity: 1 Complexity Density: 0.08 4-
522	0	@Test(groups = { "Functional" })...
523		public void testSetBoxFromViewportHiddenColsAtStart()
524		{
525	0	int firstHidden = 0;
526	0	int lastHidden = 20;
527	0	hiddenCols.hideColumns(firstHidden, lastHidden);
528
529		// move viewport to start of alignment
530	0	moveViewport(0, 0);
531	0	assertEquals(od.getBoxX(), 0);
532	0	assertEquals(od.getBoxY(), 0);
533	0	assertEquals(od.getBoxWidth(), boxWidth);
534	0	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	0	moveViewport(98 - lastHidden - 1, 0);
539	0	assertEquals(od.getBoxX(), Math.round(
540		(float) (98 - lastHidden - 1) * od.getWidth() / alwidth));
541	0	assertEquals(od.getBoxY(), 0);
542	0	assertEquals(od.getBoxWidth(), boxWidth);
543	0	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		*/
		0% Uncovered Elements: 23 (23) Complexity: 1 Complexity Density: 0.04 4-
550	0	@Test(groups = { "Functional" })...
551		public void testSetBoxFromViewportHiddenColsInMiddle()
552		{
553	0	int firstHidden = 68;
554	0	int lastHidden = 78;
555	0	hiddenCols.hideColumns(firstHidden, lastHidden);
556
557		// move viewport before hidden columns
558	0	moveViewport(3, 0);
559
560	0	assertEquals(od.getBoxX(),
561		Math.round((float) 3 * od.getWidth() / alwidth));
562	0	assertEquals(od.getBoxY(), 0);
563	0	assertEquals(od.getBoxWidth(), boxWidth);
564	0	assertEquals(od.getBoxHeight(), boxHeight);
565
566		// move viewport to left of hidden columns with overlap
567	0	moveViewport(10, 0);
568	0	assertEquals(od.getBoxX(),
569		Math.round((float) 10 * od.getWidth() / alwidth));
570	0	assertEquals(od.getBoxY(), 0);
571	0	assertEquals(od.getBoxWidth(), boxWidth);
572	0	assertEquals(od.getBoxHeight(), boxHeight);
573
574		// move viewport to straddle hidden columns
575	0	moveViewport(63, 0);
576	0	assertEquals(od.getBoxX(),
577		Math.round((float) 63 * od.getWidth() / alwidth));
578	0	assertEquals(od.getBoxY(), 0);
579	0	assertEquals(od.getBoxWidth(), boxWidth);
580	0	assertEquals(od.getBoxHeight(), boxHeight);
581
582		// move viewport to right of hidden columns, no overlap
583	0	moveViewport(80 - (lastHidden - firstHidden + 1), 0);
584	0	assertEquals(od.getBoxX(),
585		Math.round((float) (80 - (lastHidden - firstHidden + 1))
586		* od.getWidth() / alwidth));
587	0	assertEquals(od.getBoxY(), 0);
588	0	assertEquals(od.getBoxWidth(), boxWidth);
589	0	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		*/
		0% Uncovered Elements: 13 (13) Complexity: 1 Complexity Density: 0.08 4-
597	0	@Test(groups = { "Functional" })...
598		public void testSetBoxFromViewportHiddenColsAtEnd()
599		{
600	0	int firstHidden = 152;
601	0	int lastHidden = 164;
602	0	hiddenCols.hideColumns(firstHidden, lastHidden);
603
604		// move viewport before hidden columns
605	0	moveViewport(3, 0);
606	0	assertEquals(od.getBoxX(),
607		Math.round((float) 3 * od.getWidth() / alwidth));
608	0	assertEquals(od.getBoxY(), 0);
609	0	assertEquals(od.getBoxWidth(), boxWidth);
610	0	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	0	moveViewport(firstHidden - viewWidth, 0);
616	0	assertEquals(od.getBoxX(), Math.round(
617		(float) (firstHidden - viewWidth) * od.getWidth() / alwidth));
618	0	assertEquals(od.getBoxY(), 0);
619	0	assertEquals(od.getBoxWidth(), boxWidth);
620	0	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		*/
		0% Uncovered Elements: 17 (17) Complexity: 1 Complexity Density: 0.06 4-
627	0	@Test(groups = { "Functional" })...
628		public void testSetBoxFromViewportHiddenRowsAtStart()
629		{
630	0	int firstHidden = 0;
631	0	int lastHidden = 20;
632	0	hideSequences(firstHidden, lastHidden);
633
634		// calculate with visible values
635	0	alheight = vpranges.getVisibleAlignmentHeight();
636	0	alwidth = vpranges.getVisibleAlignmentWidth();
637
638	0	boxWidth = Math.round(
639		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
640		* od.getWidth() / alwidth);
641	0	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	0	moveViewport(0, 0);
648	0	assertEquals(od.getBoxX(), 0);
649	0	assertEquals(od.getBoxY(), 0);
650	0	assertEquals(od.getBoxWidth(), boxWidth);
651	0	assertEquals(od.getBoxHeight(), boxHeight);
652
653		// move viewport to end of alignment
654	0	moveViewport(0, 525 - viewHeight - lastHidden - 1);
655	0	assertEquals(od.getBoxX(), 0);
656	0	assertEquals(od.getBoxY(),
657		Math.round((float) (525 - viewHeight - lastHidden - 1)
658		* od.getSequencesHeight() / alheight));
659	0	assertEquals(od.getBoxWidth(), boxWidth);
660	0	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		*/
		0% Uncovered Elements: 17 (17) Complexity: 1 Complexity Density: 0.06 4-
667	0	@Test(groups = { "Functional" })...
668		public void testSetBoxFromViewportHiddenRowsInMiddle()
669		{
670	0	int firstHidden = 200;
671	0	int lastHidden = 210;
672	0	hideSequences(firstHidden, lastHidden);
673
674		// calculate with visible values
675	0	alheight = vpranges.getVisibleAlignmentHeight();
676	0	alwidth = vpranges.getVisibleAlignmentWidth();
677
678	0	boxWidth = Math.round(
679		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
680		* od.getWidth() / alwidth);
681	0	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	0	moveViewport(0, 0);
688	0	assertEquals(od.getBoxX(), 0);
689	0	assertEquals(od.getBoxY(), 0);
690	0	assertEquals(od.getBoxWidth(), boxWidth);
691	0	assertEquals(od.getBoxHeight(), boxHeight);
692
693		// move viewport to straddle hidden rows
694	0	moveViewport(0, 198);
695	0	assertEquals(od.getBoxX(), 0);
696	0	assertEquals(od.getBoxY(),
697		Math.round((float) 198 * od.getSequencesHeight() / alheight));
698	0	assertEquals(od.getBoxWidth(), boxWidth);
699	0	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		*/
		0% Uncovered Elements: 17 (17) Complexity: 1 Complexity Density: 0.06 4-
706	0	@Test(groups = { "Functional" })...
707		public void testSetBoxFromViewportHiddenRowsAtEnd()
708		{
709	0	int firstHidden = 500;
710	0	int lastHidden = 524;
711	0	hideSequences(firstHidden, lastHidden);
712
713		// calculate with visible values
714	0	alheight = vpranges.getVisibleAlignmentHeight();
715	0	alwidth = vpranges.getVisibleAlignmentWidth();
716
717	0	boxWidth = Math.round(
718		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
719		* od.getWidth() / alwidth);
720	0	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	0	moveViewport(0, 0);
727	0	assertEquals(od.getBoxX(), 0);
728	0	assertEquals(od.getBoxY(), 0);
729	0	assertEquals(od.getBoxWidth(), boxWidth);
730	0	assertEquals(od.getBoxHeight(), boxHeight);
731
732		// move viewport to end of alignment
733		// viewport sits above hidden rows and does not include them
734	0	moveViewport(0, firstHidden - viewHeight - 1);
735	0	assertEquals(od.getBoxX(), 0);
736	0	assertEquals(od.getBoxY(),
737		Math.round((float) (firstHidden - viewHeight - 1)
738		* od.getSequencesHeight() / alheight));
739	0	assertEquals(od.getBoxWidth(), boxWidth);
740	0	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		*/
		0% Uncovered Elements: 23 (23) Complexity: 1 Complexity Density: 0.04 4-
748	0	@Test(groups = { "Functional" })...
749		public void testFromMouseWithHiddenRowsAtStart()
750		{
751	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
752	0	assertEquals(od.getBoxX(), 0);
753	0	assertEquals(od.getBoxY(), 0);
754	0	assertEquals(od.getBoxHeight(), boxHeight);
755	0	assertEquals(od.getBoxWidth(), boxWidth);
756	0	assertEquals(vpranges.getStartRes(), 0);
757	0	assertEquals(vpranges.getStartSeq(), 0);
758
759		// hide rows at start and check updated box position is correct
760	0	int lastHiddenRow = 30;
761	0	hideSequences(0, lastHiddenRow);
762
763		// calculate with visible values
764	0	alheight = vpranges.getVisibleAlignmentHeight();
765	0	alwidth = vpranges.getVisibleAlignmentWidth();
766
767	0	boxWidth = Math.round(
768		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
769		* od.getWidth() / alwidth);
770	0	boxHeight = Math.round(
771		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
772		* od.getSequencesHeight() / alheight);
773
774	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
775	0	assertEquals(od.getBoxX(), 0);
776	0	assertEquals(od.getBoxY(), 0);
777	0	assertEquals(od.getBoxWidth(), boxWidth);
778	0	assertEquals(od.getBoxHeight(), boxHeight);
779
780		// click below hidden rows
781	0	mouseClick(od, 0, 151 + boxHeight / 2);
782	0	assertEquals(od.getBoxX(), 0);
783	0	assertEquals(od.getBoxY(), 151);
784	0	assertEquals(od.getBoxWidth(), boxWidth);
785	0	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		*/
		0% Uncovered Elements: 31 (31) Complexity: 1 Complexity Density: 0.03 4-
792	0	@Test(groups = { "Functional" })...
793		public void testFromMouseWithHiddenRowsInMiddle()
794		{
795	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
796
797	0	assertEquals(od.getBoxX(), 0);
798	0	assertEquals(od.getBoxY(), 0);
799	0	assertEquals(od.getBoxWidth(), boxWidth);
800	0	assertEquals(od.getBoxHeight(), boxHeight);
801	0	assertEquals(vpranges.getStartRes(), 0);
802	0	assertEquals(vpranges.getStartSeq(), 0);
803
804		// hide rows in middle and check updated box position is correct
805		// no changes
806	0	int firstHiddenRow = 50;
807	0	int lastHiddenRow = 54;
808	0	hideSequences(firstHiddenRow, lastHiddenRow);
809
810		// calculate with visible values
811	0	alheight = vpranges.getVisibleAlignmentHeight();
812	0	alwidth = vpranges.getVisibleAlignmentWidth();
813
814	0	boxWidth = Math.round(
815		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
816		* od.getWidth() / alwidth);
817	0	boxHeight = Math.round(
818		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
819		* od.getSequencesHeight() / alheight);
820
821	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
822
823	0	assertEquals(od.getBoxX(), 0);
824	0	assertEquals(od.getBoxY(), 0);
825	0	assertEquals(od.getBoxWidth(), boxWidth);
826	0	assertEquals(od.getBoxHeight(), boxHeight);
827
828		// click above hidden rows, so that box overlaps
829	0	int ypos = 35 + viewHeight / 2; // row value in residues
830	0	mouseClick(od, 0,
831		Math.round((float) ypos * od.getSequencesHeight() / alheight));
832	0	assertEquals(od.getBoxX(), 0);
833	0	assertEquals(od.getBoxY(),
834		Math.round((float) 35 * od.getSequencesHeight() / alheight));
835	0	assertEquals(od.getBoxWidth(), boxWidth);
836	0	assertEquals(od.getBoxHeight(), boxHeight);
837
838		// click so that box straddles hidden rows
839	0	ypos = 45 + viewHeight / 2; // row value in residues
840	0	mouseClick(od, 0,
841		Math.round((float) ypos * od.getSequencesHeight() / alheight));
842	0	assertEquals(od.getBoxX(), 0);
843	0	assertEquals(od.getBoxY(),
844		Math.round((float) 45 * od.getSequencesHeight() / alheight));
845	0	assertEquals(od.getBoxWidth(), boxWidth);
846	0	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		*/
		0% Uncovered Elements: 31 (31) Complexity: 1 Complexity Density: 0.03 4-
853	0	@Test(groups = { "Functional" })...
854		public void testFromMouseWithHiddenRowsAtEnd()
855		{
856	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
857	0	assertEquals(od.getBoxX(), 0);
858	0	assertEquals(od.getBoxY(), 0);
859	0	assertEquals(od.getBoxWidth(), boxWidth);
860	0	assertEquals(od.getBoxHeight(), boxHeight);
861	0	assertEquals(vpranges.getStartRes(), 0);
862	0	assertEquals(vpranges.getStartSeq(), 0);
863
864		// hide rows at end and check updated box position is correct
865		// no changes
866	0	int firstHidden = 500;
867	0	int lastHidden = 524;
868	0	hideSequences(firstHidden, lastHidden);
869
870		// calculate with visible values
871	0	alheight = vpranges.getVisibleAlignmentHeight();
872	0	alwidth = vpranges.getVisibleAlignmentWidth();
873
874	0	boxWidth = Math.round(
875		(float) (vpranges.getEndRes() - vpranges.getStartRes() + 1)
876		* od.getWidth() / alwidth);
877	0	boxHeight = Math.round(
878		(float) (vpranges.getEndSeq() - vpranges.getStartSeq() + 1)
879		* od.getSequencesHeight() / alheight);
880
881	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
882	0	assertEquals(od.getBoxX(), 0);
883	0	assertEquals(od.getBoxY(), 0);
884	0	assertEquals(od.getBoxWidth(), boxWidth);
885	0	assertEquals(od.getBoxHeight(), boxHeight);
886
887		// click above hidden rows
888	0	int ypos = 41 + viewHeight / 2; // row 41
889	0	mouseClick(od, 0,
890		Math.round((float) ypos * od.getSequencesHeight() / alheight));
891	0	assertEquals(od.getBoxX(), 0);
892	0	assertEquals(od.getBoxY(),
893		Math.round((float) 41 * od.getSequencesHeight() / alheight));
894	0	assertEquals(od.getBoxWidth(), boxWidth);
895	0	assertEquals(od.getBoxHeight(), boxHeight);
896
897		// click above hidden rows so box overlaps
898		// boxY, boxHeight remains same
899	0	ypos = 497 + viewHeight / 2; // row 497
900	0	mouseClick(od, 0,
901		Math.round((float) ypos * od.getSequencesHeight() / alheight));
902	0	assertEquals(od.getBoxX(), 0);
903	0	assertEquals(od.getBoxY(), Math
904		.round((float) firstHidden * od.getSequencesHeight() / alheight)
905		- boxHeight);
906	0	assertEquals(od.getBoxWidth(), boxWidth);
907	0	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		*/
		0% Uncovered Elements: 20 (20) Complexity: 1 Complexity Density: 0.05 4-
913	0	@Test(groups = { "Functional" })...
914		public void testPositionInBox()
915		{
916	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
917
918	0	assertFalse(od.isPositionInBox(0, 0));
919	0	assertTrue(od.isPositionInBox(10, 9));
920	0	assertFalse(od.isPositionInBox(0, 9));
921	0	assertFalse(od.isPositionInBox(9, 0));
922	0	assertFalse(od.isPositionInBox(75, 20));
923
924		// hide columns in the box area
925		// makes absolutely no difference
926	0	hiddenCols.hideColumns(1, 4);
927	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
928	0	assertFalse(od.isPositionInBox(0, 0));
929	0	assertTrue(od.isPositionInBox(10, 9));
930	0	assertFalse(od.isPositionInBox(0, 9));
931	0	assertFalse(od.isPositionInBox(9, 0));
932	0	assertFalse(od.isPositionInBox(75, 20));
933
934		// hide sequences in box area
935		// makes absolutely no difference
936	0	hideSequences(1, 3);
937	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
938	0	assertFalse(od.isPositionInBox(0, 0));
939	0	assertTrue(od.isPositionInBox(10, 9));
940	0	assertFalse(od.isPositionInBox(0, 9));
941	0	assertFalse(od.isPositionInBox(9, 0));
942	0	assertFalse(od.isPositionInBox(75, 20));
943		}
944
945		/**
946		* Test the dragging functionality
947		*/
		0% Uncovered Elements: 20 (20) Complexity: 1 Complexity Density: 0.05 4-
948	0	@Test(groups = { "Functional" })...
949		public void testDragging()
950		{
951	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
952	0	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
953	0	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	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
959
960		// corner moves 16 (20-4) right and 6 (22-16) up
961	0	assertEquals(od.getBoxX(), 16);
962	0	assertEquals(od.getBoxY(), 6);
963
964		// hide columns - makes no difference
965	0	hiddenCols.hideColumns(1, 4);
966	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
967	0	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
968	0	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
969	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
970
971		// corner moves 16 (20-4) right and 6 (22-16) up
972	0	assertEquals(od.getBoxX(), 16);
973	0	assertEquals(od.getBoxY(), 6);
974
975		// hide sequences in box area
976		// makes absolutely no difference
977	0	hideSequences(1, 3);
978	0	od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols);
979	0	od.setDragPoint(4, 16, al.getHiddenSequences(), hiddenCols);
980	0	od.adjustViewportFromMouse(20, 22, al.getHiddenSequences(), hiddenCols);
981	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
982
983		// corner moves 16 (20-4) right and 6 (22-16) up
984	0	assertEquals(od.getBoxX(), 16);
985	0	assertEquals(od.getBoxY(), 6);
986		}
987
988		/*
989		* Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
990		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
991	0	private void moveViewportH(int startRes)...
992		{
993	0	vpranges.setViewportStartAndWidth(startRes, viewWidth);
994	0	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		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
1000	0	private void moveViewportV(int startSeq)...
1001		{
1002	0	vpranges.setViewportStartAndHeight(startSeq, viewHeight);
1003	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1004		}
1005
1006		/*
1007		* Move viewport horizontally and vertically.
1008		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
1009	0	private void moveViewport(int startRes, int startSeq)...
1010		{
1011	0	vpranges.setViewportStartAndWidth(startRes, viewWidth);
1012	0	vpranges.setViewportStartAndHeight(startSeq, viewHeight);
1013	0	od.setBoxPosition(al.getHiddenSequences(), hiddenCols);
1014		}
1015
1016		/*
1017		* Mouse click as position x,y in overview window
1018		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
1019	0	private void mouseClick(OverviewDimensions od, int x, int y)...
1020		{
1021	0	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	0	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		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
1033	0	private void testBoxIsAtClickPoint(int xpos, int ypos)...
1034		{
1035	0	mouseClick(od, xpos, ypos);
1036	0	assertEquals(od.getBoxX() + od.getBoxWidth() / 2, xpos);
1037	0	assertEquals(od.getBoxY() + od.getBoxHeight() / 2, ypos);
1038	0	assertEquals(od.getBoxWidth(), boxWidth);
1039	0	assertEquals(od.getBoxHeight(), boxHeight);
1040
1041		}
1042
1043		/*
1044		* Hide sequences between start and end
1045		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
1046	0	private void hideSequences(int start, int end)...
1047		{
1048	0	SequenceI[] allseqs = al.getSequencesArray();
1049	0	SequenceGroup theseSeqs = new SequenceGroup();
1050
1051	0	for (int i = start; i <= end; i++)
1052		{
1053	0	theseSeqs.addSequence(allseqs[i], false);
1054	0	al.getHiddenSequences().hideSequence(allseqs[i]);
1055		}
1056
1057	0	hiddenRepSequences.put(allseqs[start], theseSeqs);
1058		}
1059		}