Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewDimensionsShowHidden	31	59	18	0.2261904822.6%	Show methods

Class OverviewDimensionsShowHidden

Class OverviewDimensionsShowHidden	Line # 31	Total Statements 59	Complexity 18	TOTAL Coverage 0.2261904822.6%
OverviewDimensionsShowHidden(ViewportRanges,boolean)   OverviewDimensionsShowHidden(ViewportRanges,boolean)	4949	3.03	1.01	1.0 1.0100%
updateViewportFromMouse(int,int,HiddenSequences,HiddenColumns) : void   updateViewportFromMouse(int,int,HiddenSequences,HiddenColumns) : void	7171	9.09	1.01	0.0 0.00%
adjustViewportFromMouse(int,int,HiddenSequences,HiddenColumns) : void   adjustViewportFromMouse(int,int,HiddenSequences,HiddenColumns) : void	9494	6.06	1.01	0.0 0.00%
updateViewportFromTopLeft(int,int,HiddenSequences,HiddenColumns) : void   updateViewportFromTopLeft(int,int,HiddenSequences,HiddenColumns) : void	118118	21.021	8.08	0.0 0.00%
setBoxPosition(HiddenSequences,HiddenColumns) : void   setBoxPosition(HiddenSequences,HiddenColumns) : void	200200	5.05	1.01	1.0 1.0100%
getColumns(AlignmentI) : AlignmentColsCollectionI   getColumns(AlignmentI) : AlignmentColsCollectionI	216216	1.01	1.01	1.0 1.0100%
getRows(AlignmentI) : AlignmentRowsCollectionI   getRows(AlignmentI) : AlignmentRowsCollectionI	223223	1.01	1.01	1.0 1.0100%
resetAlignmentDims() : void   resetAlignmentDims() : void	230230	4.04	1.01	1.0 1.0100%
getLeftXFromCentreX(int,HiddenColumns) : int   getLeftXFromCentreX(int,HiddenColumns) : int	244244	2.02	1.01	0.0 0.00%
getTopYFromCentreY(int,HiddenSequences) : int   getTopYFromCentreY(int,HiddenSequences) : int	256256	2.02	1.01	0.0 0.00%
setDragPoint(int,int,HiddenSequences,HiddenColumns) : void   setDragPoint(int,int,HiddenSequences,HiddenColumns) : void	263263	5.05	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.22619048	jalview.gui.AlignmentPanelTest.testSetOverviewTitlejalview.gui.AlignmentPanelTest.testSetOverviewTitle	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 jalview.api.AlignmentColsCollectionI;
24		import jalview.api.AlignmentRowsCollectionI;
25		import jalview.datamodel.AlignmentI;
26		import jalview.datamodel.AllColsCollection;
27		import jalview.datamodel.AllRowsCollection;
28		import jalview.datamodel.HiddenColumns;
29		import jalview.datamodel.HiddenSequences;
30
		22.6% Uncovered Elements: 65 (84) Complexity: 18 Complexity Density: 0.31
31		public class OverviewDimensionsShowHidden extends OverviewDimensions
32		{
33		private ViewportRanges ranges;
34
35		private int xdiff; // when dragging, difference in alignment units between
36		// start residue and original mouse click position
37
38		private int ydiff; // when dragging, difference in alignment units between
39		// start sequence and original mouse click position
40
41		/**
42		* Create an OverviewDimensions object
43		*
44		* @param ranges
45		* positional properties of the viewport
46		* @param showAnnotationPanel
47		* true if the annotation panel is to be shown, false otherwise
48		*/
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
49	2	public OverviewDimensionsShowHidden(ViewportRanges vpranges,...
50		boolean showAnnotationPanel)
51		{
52	2	super(vpranges, showAnnotationPanel);
53	2	ranges = vpranges;
54	2	resetAlignmentDims();
55		}
56
57		/**
58		* Check box dimensions and scroll positions and correct if necessary
59		*
60		* @param mousex
61		* x position in overview panel
62		* @param mousey
63		* y position in overview panel
64		* @param hiddenSeqs
65		* hidden sequences
66		* @param hiddenCols
67		* hidden columns
68		* @param ranges
69		* viewport position properties
70		*/
		0% Uncovered Elements: 9 (9) Complexity: 1 Complexity Density: 0.11
71	0	@Override...
72		public void updateViewportFromMouse(int mousex, int mousey,
73		HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
74		{
75	0	resetAlignmentDims();
76
77		// convert mousex and mousey to alignment units as well as
78		// translating to top left corner of viewport - this is an absolute position
79	0	int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
80	0	int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
81
82		// convert to visible positions
83	0	int visXAsRes = hiddenCols.absoluteToVisibleColumn(xAsRes);
84	0	yAsSeq = hiddenSeqs.adjustForHiddenSeqs(
85		hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq));
86	0	yAsSeq = Math.max(yAsSeq, 0); // -1 if before first visible sequence
87	0	int visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(yAsSeq);
88	0	visYAsSeq = Math.max(visYAsSeq, 0); // -1 if before first visible sequence
89
90		// update viewport accordingly
91	0	updateViewportFromTopLeft(visXAsRes, visYAsSeq, hiddenSeqs, hiddenCols);
92		}
93
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
94	0	@Override...
95		public void adjustViewportFromMouse(int mousex, int mousey,
96		HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
97		{
98	0	resetAlignmentDims();
99
100		// calculate translation in pixel terms:
101		// get mouse location in viewport coords, add translation in viewport
102		// coords,
103		// convert back to pixel coords
104	0	int vpx = Math.round((float) mousex * alwidth / width);
105	0	int visXAsRes = hiddenCols.absoluteToVisibleColumn(vpx) + xdiff;
106
107	0	int vpy = Math.round(mousey * heightRatio);
108	0	int visYAsRes = hiddenSeqs.findIndexWithoutHiddenSeqs(vpy) + ydiff;
109
110		// update viewport accordingly
111	0	updateViewportFromTopLeft(visXAsRes, visYAsRes, hiddenSeqs, hiddenCols);
112		}
113
114		/**
115		* {@inheritDoc} Callers should have already called resetAlignmentDims to
116		* refresh alwidth, alheight and width/height ratios
117		*/
		0% Uncovered Elements: 35 (35) Complexity: 8 Complexity Density: 0.38
118	0	@Override...
119		protected void updateViewportFromTopLeft(int leftx, int topy,
120		HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
121		{
122	0	int visXAsRes = leftx;
123	0	int visYAsSeq = topy;
124
125	0	if (visXAsRes < 0)
126		{
127	0	visXAsRes = 0;
128		}
129
130	0	if (visYAsSeq < 0)
131		{
132	0	visYAsSeq = 0;
133		}
134
135	0	if (ranges.isWrappedMode())
136		{
137	0	visYAsSeq = 0; // sorry, no vertical scroll when wrapped
138		}
139
140		// Determine where scrollCol should be, given visXAsRes
141
142		// get viewport width in residues
143	0	int vpwidth = ranges.getViewportWidth();
144
145		// check in case we went off the edge of the alignment
146	0	int visAlignWidth = hiddenCols.absoluteToVisibleColumn(alwidth - 1);
147	0	if (visXAsRes + vpwidth - 1 > visAlignWidth)
148		{
149		// went past the end of the alignment, adjust backwards
150
151		// if last position was before the end of the alignment, need to update
152	0	if (ranges.getEndRes() < visAlignWidth)
153		{
154	0	visXAsRes = hiddenCols.absoluteToVisibleColumn(hiddenCols
155		.offsetByVisibleColumns(-(vpwidth - 1), alwidth - 1));
156		}
157		else
158		{
159	0	visXAsRes = ranges.getStartRes();
160		}
161		}
162
163		// Determine where scrollRow should be, given visYAsSeq
164
165		// get viewport height in sequences
166	0	int vpheight = ranges.getViewportHeight();
167
168		// check in case we went off the edge of the alignment
169	0	int visAlignHeight = hiddenSeqs.findIndexWithoutHiddenSeqs(alheight);
170
171	0	if (visYAsSeq + vpheight - 1 > visAlignHeight)
172		{
173		// went past the end of the alignment, adjust backwards
174	0	if (ranges.getEndSeq() < visAlignHeight)
175		{
176	0	visYAsSeq = hiddenSeqs.findIndexWithoutHiddenSeqs(
177		hiddenSeqs.subtractVisibleRows(vpheight - 1, alheight - 1));
178		}
179		else
180		{
181	0	visYAsSeq = ranges.getStartSeq();
182		}
183		}
184
185		// update viewport
186	0	ranges.setStartResAndSeq(visXAsRes, visYAsSeq);
187		}
188
189		/**
190		* Update the overview panel box when the associated alignment panel is
191		* changed
192		*
193		* @param hiddenSeqs
194		* hidden sequences
195		* @param hiddenCols
196		* hidden columns
197		* @param ranges
198		* viewport position properties
199		*/
		100% Uncovered Elements: 0 (5) Complexity: 1 Complexity Density: 0.2
200	6	@Override...
201		public void setBoxPosition(HiddenSequences hiddenSeqs,
202		HiddenColumns hiddenCols)
203		{
204		// work with absolute values of startRes and endRes
205	6	int startRes = hiddenCols.visibleToAbsoluteColumn(ranges.getStartRes());
206	6	int endRes = hiddenCols.visibleToAbsoluteColumn(ranges.getEndRes());
207
208		// work with absolute values of startSeq and endSeq
209	6	int startSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getStartSeq());
210	6	int endSeq = hiddenSeqs.adjustForHiddenSeqs(ranges.getEndSeq());
211
212	6	setBoxPosition(startRes, startSeq, endRes - startRes + 1,
213		endSeq - startSeq + 1);
214		}
215
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
216	10	@Override...
217		public AlignmentColsCollectionI getColumns(AlignmentI al)
218		{
219	10	return new AllColsCollection(0, ranges.getAbsoluteAlignmentWidth() - 1,
220		al);
221		}
222
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
223	5	@Override...
224		public AlignmentRowsCollectionI getRows(AlignmentI al)
225		{
226	5	return new AllRowsCollection(0, ranges.getAbsoluteAlignmentHeight() - 1,
227		al);
228		}
229
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
230	18	@Override...
231		protected void resetAlignmentDims()
232		{
233	18	alwidth = ranges.getAbsoluteAlignmentWidth();
234	18	alheight = ranges.getAbsoluteAlignmentHeight();
235
236	18	widthRatio = (float) alwidth / width;
237	18	heightRatio = (float) alheight / sequencesHeight;
238		}
239
240		/**
241		* {@inheritDoc} Callers should have already called resetAlignmentDims to
242		* refresh widthRatio
243		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
244	0	@Override...
245		protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
246		{
247	0	int vpx = Math.round((float) mousex * alwidth / width);
248	0	return hidden.offsetByVisibleColumns(-ranges.getViewportWidth() / 2,
249		vpx);
250		}
251
252		/**
253		* {@inheritDoc} Callers should have already called resetAlignmentDims to
254		* refresh heightRatio
255		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
256	0	@Override...
257		protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
258		{
259	0	int vpy = Math.round(mousey * heightRatio);
260	0	return hidden.subtractVisibleRows(ranges.getViewportHeight() / 2, vpy);
261		}
262
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
263	0	@Override...
264		public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
265		HiddenColumns hiddenCols)
266		{
267	0	resetAlignmentDims();
268
269		// get alignment position of x and box (can get directly from vpranges) and
270		// calculate difference between the positions
271	0	int vpx = Math.round(x * widthRatio);
272	0	int vpy = Math.round(y * heightRatio);
273
274	0	xdiff = ranges.getStartRes() - hiddenCols.absoluteToVisibleColumn(vpx);
275	0	ydiff = ranges.getStartSeq()
276		- hiddenSeqs.findIndexWithoutHiddenSeqs(vpy);
277		}
278
279		}