Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewDimensionsHideHidden	31	46	18	0.211267621.1%	Show methods

Class OverviewDimensionsHideHidden

Class OverviewDimensionsHideHidden	Line # 31	Total Statements 46	Complexity 18	TOTAL Coverage 0.211267621.1%
OverviewDimensionsHideHidden(ViewportRanges,boolean)   OverviewDimensionsHideHidden(ViewportRanges,boolean)	4141	3.03	1.01	1.0 1.0100%
updateViewportFromMouse(int,int,HiddenSequences,HiddenColumns) : void   updateViewportFromMouse(int,int,HiddenSequences,HiddenColumns) : void	4949	4.04	1.01	0.0 0.00%
adjustViewportFromMouse(int,int,HiddenSequences,HiddenColumns) : void   adjustViewportFromMouse(int,int,HiddenSequences,HiddenColumns) : void	6262	4.04	1.01	0.0 0.00%
updateViewportFromTopLeft(int,int,HiddenSequences,HiddenColumns) : void   updateViewportFromTopLeft(int,int,HiddenSequences,HiddenColumns) : void	8383	19.019	8.08	0.0 0.00%
setBoxPosition(HiddenSequences,HiddenColumns) : void   setBoxPosition(HiddenSequences,HiddenColumns) : void	145145	1.01	1.01	1.0 1.0100%
getColumns(AlignmentI) : AlignmentColsCollectionI   getColumns(AlignmentI) : AlignmentColsCollectionI	153153	1.01	1.01	1.0 1.0100%
getRows(AlignmentI) : AlignmentRowsCollectionI   getRows(AlignmentI) : AlignmentRowsCollectionI	160160	1.01	1.01	1.0 1.0100%
resetAlignmentDims() : void   resetAlignmentDims() : void	167167	4.04	1.01	1.0 1.0100%
getLeftXFromCentreX(int,HiddenColumns) : int   getLeftXFromCentreX(int,HiddenColumns) : int	181181	2.02	1.01	0.0 0.00%
getTopYFromCentreY(int,HiddenSequences) : int   getTopYFromCentreY(int,HiddenSequences) : int	192192	2.02	1.01	0.0 0.00%
setDragPoint(int,int,HiddenSequences,HiddenColumns) : void   setDragPoint(int,int,HiddenSequences,HiddenColumns) : void	199199	5.05	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.2112676	jalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverviewjalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverview	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.HiddenColumns;
27		import jalview.datamodel.HiddenSequences;
28		import jalview.datamodel.VisibleColsCollection;
29		import jalview.datamodel.VisibleRowsCollection;
30
		21.1% Uncovered Elements: 56 (71) Complexity: 18 Complexity Density: 0.39
31		public class OverviewDimensionsHideHidden 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
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
41	2	public OverviewDimensionsHideHidden(ViewportRanges vpranges,...
42		boolean showAnnotationPanel)
43		{
44	2	super(vpranges, showAnnotationPanel);
45	2	ranges = vpranges;
46	2	resetAlignmentDims();
47		}
48
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
49	0	@Override...
50		public void updateViewportFromMouse(int mousex, int mousey,
51		HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
52		{
53	0	resetAlignmentDims();
54
55	0	int xAsRes = getLeftXFromCentreX(mousex, hiddenCols);
56	0	int yAsSeq = getTopYFromCentreY(mousey, hiddenSeqs);
57
58	0	updateViewportFromTopLeft(xAsRes, yAsSeq, hiddenSeqs, hiddenCols);
59
60		}
61
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
62	0	@Override...
63		public void adjustViewportFromMouse(int mousex, int mousey,
64		HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
65		{
66	0	resetAlignmentDims();
67
68		// calculate translation in pixel terms:
69		// get mouse location in viewport coords, add translation in viewport
70		// coords, and update viewport as usual
71	0	int vpx = Math.round(mousex * widthRatio);
72	0	int vpy = Math.round(mousey * heightRatio);
73
74	0	updateViewportFromTopLeft(vpx + xdiff, vpy + ydiff, hiddenSeqs,
75		hiddenCols);
76
77		}
78
79		/**
80		* {@inheritDoc} Callers should have already called resetAlignmentDims to
81		* refresh alwidth, alheight and width/height ratios
82		*/
		0% Uncovered Elements: 33 (33) Complexity: 8 Complexity Density: 0.42
83	0	@Override...
84		protected void updateViewportFromTopLeft(int leftx, int topy,
85		HiddenSequences hiddenSeqs, HiddenColumns hiddenCols)
86		{
87	0	int xAsRes = leftx;
88	0	int yAsSeq = topy;
89
90	0	if (xAsRes < 0)
91		{
92	0	xAsRes = 0;
93		}
94
95	0	if (yAsSeq < 0)
96		{
97	0	yAsSeq = 0;
98		}
99
100	0	if (ranges.isWrappedMode())
101		{
102	0	yAsSeq = 0; // sorry, no vertical scroll when wrapped
103		}
104
105		// get viewport width in residues
106	0	int vpwidth = ranges.getViewportWidth();
107
108	0	if (xAsRes + vpwidth > alwidth)
109		{
110		// went past the end of the alignment, adjust backwards
111
112		// if last position was before the end of the alignment, need to update
113	0	if (ranges.getStartRes() < alwidth)
114		{
115	0	xAsRes = alwidth - vpwidth;
116		}
117		else
118		{
119	0	xAsRes = ranges.getStartRes();
120		}
121		}
122
123		// Determine where scrollRow should be, given visYAsSeq
124
125		// get viewport height in sequences
126		// add 1 because height includes both endSeq and startSeq
127	0	int vpheight = ranges.getViewportHeight();
128
129	0	if (yAsSeq + vpheight > alheight)
130		{
131		// went past the end of the alignment, adjust backwards
132	0	if (ranges.getEndSeq() < alheight)
133		{
134	0	yAsSeq = alheight - vpheight;
135		}
136		else
137		{
138	0	yAsSeq = ranges.getStartSeq();
139		}
140		}
141
142	0	ranges.setStartResAndSeq(xAsRes, yAsSeq);
143		}
144
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
145	9	@Override...
146		public void setBoxPosition(HiddenSequences hiddenSeqs,
147		HiddenColumns hiddenCols)
148		{
149	9	setBoxPosition(ranges.getStartRes(), ranges.getStartSeq(),
150		ranges.getViewportWidth(), ranges.getViewportHeight());
151		}
152
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
153	22	@Override...
154		public AlignmentColsCollectionI getColumns(AlignmentI al)
155		{
156	22	return new VisibleColsCollection(0,
157		ranges.getAbsoluteAlignmentWidth() - 1, al.getHiddenColumns());
158		}
159
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
160	11	@Override...
161		public AlignmentRowsCollectionI getRows(AlignmentI al)
162		{
163	11	return new VisibleRowsCollection(0,
164		ranges.getAbsoluteAlignmentHeight() - 1, al);
165		}
166
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
167	33	@Override...
168		protected void resetAlignmentDims()
169		{
170	33	alwidth = ranges.getVisibleAlignmentWidth();
171	33	alheight = ranges.getVisibleAlignmentHeight();
172
173	33	widthRatio = (float) alwidth / width;
174	33	heightRatio = (float) alheight / sequencesHeight;
175		}
176
177		/**
178		* {@inheritDoc} Callers should have already called resetAlignmentDims to
179		* refresh widthRatio
180		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
181	0	@Override...
182		protected int getLeftXFromCentreX(int mousex, HiddenColumns hidden)
183		{
184	0	int vpx = Math.round(mousex * widthRatio);
185	0	return vpx - ranges.getViewportWidth() / 2;
186		}
187
188		/**
189		* {@inheritDoc} Callers should have already called resetAlignmentDims to
190		* refresh heightRatio
191		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
192	0	@Override...
193		protected int getTopYFromCentreY(int mousey, HiddenSequences hidden)
194		{
195	0	int vpy = Math.round(mousey * heightRatio);
196	0	return vpy - ranges.getViewportHeight() / 2;
197		}
198
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
199	0	@Override...
200		public void setDragPoint(int x, int y, HiddenSequences hiddenSeqs,
201		HiddenColumns hiddenCols)
202		{
203	0	resetAlignmentDims();
204
205		// get alignment position of x and box (can get directly from vpranges) and
206		// calculate difference between the positions
207	0	int vpx = Math.round(x * widthRatio);
208	0	int vpy = Math.round(y * heightRatio);
209
210	0	xdiff = ranges.getStartRes() - vpx;
211	0	ydiff = ranges.getStartSeq() - vpy;
212		}
213
214		}