Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewDimensions	31	37	22	0.00%	Show methods

Class OverviewDimensions

Class OverviewDimensions	Line # 31	Total Statements 37	Complexity 22	TOTAL Coverage 0.00%
OverviewDimensions(ViewportRanges,boolean)   OverviewDimensions(ViewportRanges,boolean)	7373	12.012	5.05	0.0 0.00%
drawBox(Graphics) : void   drawBox(Graphics) : void	115115	2.02	1.01	0.0 0.00%
getBoxX() : int   getBoxX() : int	121121	1.01	1.01	0.0 0.00%
getBoxY() : int   getBoxY() : int	126126	1.01	1.01	0.0 0.00%
getBoxWidth() : int   getBoxWidth() : int	131131	1.01	1.01	0.0 0.00%
getBoxHeight() : int   getBoxHeight() : int	136136	1.01	1.01	0.0 0.00%
getWidth() : int   getWidth() : int	141141	1.01	1.01	0.0 0.00%
getHeight() : int   getHeight() : int	146146	1.01	1.01	0.0 0.00%
getSequencesHeight() : int   getSequencesHeight() : int	151151	1.01	1.01	0.0 0.00%
getGraphHeight() : int   getGraphHeight() : int	156156	1.01	1.01	0.0 0.00%
getPixelsPerCol() : float   getPixelsPerCol() : float	161161	2.02	1.01	0.0 0.00%
getPixelsPerSeq() : float   getPixelsPerSeq() : float	167167	2.02	1.01	0.0 0.00%
setWidth(int) : void   setWidth(int) : void	173173	2.02	2.02	0.0 0.00%
setHeight(int) : void   setHeight(int) : void	179179	2.02	2.02	0.0 0.00%
setBoxPosition(int,int,int,int) : void   setBoxPosition(int,int,int,int) : void	275275	6.06	1.01	0.0 0.00%
isPositionInBox(int,int) : boolean   isPositionInBox(int,int) : boolean	301301	1.01	1.01	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 java.awt.Graphics;
24
25		import jalview.api.AlignmentColsCollectionI;
26		import jalview.api.AlignmentRowsCollectionI;
27		import jalview.datamodel.AlignmentI;
28		import jalview.datamodel.HiddenColumns;
29		import jalview.datamodel.HiddenSequences;
30
		0% Uncovered Elements: 65 (65) Complexity: 22 Complexity Density: 0.59
31		public abstract class OverviewDimensions
32		{
33		protected static final int MAX_WIDTH = 400;
34
35		protected static final int MIN_WIDTH = 120;
36
37		protected static final int MIN_SEQ_HEIGHT = 40;
38
39		protected static final int MAX_SEQ_HEIGHT = 300;
40
41		private static final int DEFAULT_GRAPH_HEIGHT = 20;
42
43		protected int width;
44
45		protected int sequencesHeight;
46
47		protected int graphHeight = DEFAULT_GRAPH_HEIGHT;
48
49		protected int boxX = -1;
50
51		protected int boxY = -1;
52
53		protected int boxWidth = -1;
54
55		protected int boxHeight = -1;
56
57		protected int alwidth;
58
59		protected int alheight;
60
61		protected float widthRatio;
62
63		protected float heightRatio;
64
65		/**
66		* Create an OverviewDimensions object
67		*
68		* @param ranges
69		* positional properties of the viewport
70		* @param showAnnotationPanel
71		* true if the annotation panel is to be shown, false otherwise
72		*/
		0% Uncovered Elements: 20 (20) Complexity: 5 Complexity Density: 0.42
73	0	public OverviewDimensions(ViewportRanges ranges,...
74		boolean showAnnotationPanel)
75		{
76		// scale the initial size of overviewpanel to shape of alignment
77	0	float initialScale = (float) ranges.getAbsoluteAlignmentWidth()
78		/ (float) ranges.getAbsoluteAlignmentHeight();
79
80	0	if (!showAnnotationPanel)
81		{
82	0	graphHeight = 0;
83		}
84
85	0	if (ranges.getAbsoluteAlignmentWidth() > ranges
86		.getAbsoluteAlignmentHeight())
87		{
88		// wider
89	0	width = MAX_WIDTH;
90	0	sequencesHeight = Math.round(MAX_WIDTH / initialScale);
91	0	if (sequencesHeight < MIN_SEQ_HEIGHT)
92		{
93	0	sequencesHeight = MIN_SEQ_HEIGHT;
94		}
95		}
96		else
97		{
98		// taller
99	0	width = Math.round(MAX_WIDTH * initialScale);
100	0	sequencesHeight = MAX_SEQ_HEIGHT;
101
102	0	if (width < MIN_WIDTH)
103		{
104	0	width = MIN_WIDTH;
105		}
106		}
107		}
108
109		/**
110		* Draw the overview panel's viewport box on a graphics object
111		*
112		* @param g
113		* the graphics object to draw on
114		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
115	0	public void drawBox(Graphics g)...
116		{
117	0	g.drawRect(boxX, boxY, boxWidth, boxHeight);
118	0	g.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
119		}
120
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
121	0	public int getBoxX()...
122		{
123	0	return boxX;
124		}
125
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
126	0	public int getBoxY()...
127		{
128	0	return boxY;
129		}
130
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
131	0	public int getBoxWidth()...
132		{
133	0	return boxWidth;
134		}
135
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
136	0	public int getBoxHeight()...
137		{
138	0	return boxHeight;
139		}
140
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
141	0	public int getWidth()...
142		{
143	0	return width;
144		}
145
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
146	0	public int getHeight()...
147		{
148	0	return sequencesHeight + graphHeight;
149		}
150
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
151	0	public int getSequencesHeight()...
152		{
153	0	return sequencesHeight;
154		}
155
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
156	0	public int getGraphHeight()...
157		{
158	0	return graphHeight;
159		}
160
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
161	0	public float getPixelsPerCol()...
162		{
163	0	resetAlignmentDims();
164	0	return 1 / widthRatio;
165		}
166
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
167	0	public float getPixelsPerSeq()...
168		{
169	0	resetAlignmentDims();
170	0	return 1 / heightRatio;
171		}
172
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
173	0	public void setWidth(int w)...
174		{
175	0	width = w < 1 ? 1 : w;
176	0	widthRatio = (float) alwidth / width;
177		}
178
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
179	0	public void setHeight(int h)...
180		{
181	0	sequencesHeight = (h < 1 ? 1 : h) - graphHeight;
182	0	heightRatio = (float) alheight / sequencesHeight;
183		}
184
185		/**
186		* Update the viewport location from a mouse click in the overview panel
187		*
188		* @param mousex
189		* x location of mouse
190		* @param mousey
191		* y location of mouse
192		* @param hiddenSeqs
193		* the alignment's hidden sequences
194		* @param hiddenCols
195		* the alignment's hidden columns
196		*/
197		public abstract void updateViewportFromMouse(int mousex, int mousey,
198		HiddenSequences hiddenSeqs, HiddenColumns hiddenCols);
199
200		/**
201		* Update the viewport location from a mouse drag within the overview's box
202		*
203		* @param mousex
204		* x location of mouse
205		* @param mousey
206		* y location of mouse
207		* @param hiddenSeqs
208		* the alignment's hidden sequences
209		* @param hiddenCols
210		* the alignment's hidden columns
211		*/
212		public abstract void adjustViewportFromMouse(int mousex, int mousey,
213		HiddenSequences hiddenSeqs, HiddenColumns hiddenCols);
214
215		/**
216		* Initialise dragging from the mouse - must be called on initial mouse click
217		* before using adjustViewportFromMouse in drag operations
218		*
219		* @param mousex
220		* x location of mouse
221		* @param mousey
222		* y location of mouse
223		* @param hiddenSeqs
224		* the alignment's hidden sequences
225		* @param hiddenCols
226		* the alignment's hidden columns
227		*/
228		public abstract void setDragPoint(int x, int y,
229		HiddenSequences hiddenSeqs, HiddenColumns hiddenCols);
230
231		/*
232		* Move the viewport so that the top left corner of the overview's box
233		* is at the mouse position (leftx, topy)
234		*/
235		protected abstract void updateViewportFromTopLeft(int leftx, int topy,
236		HiddenSequences hiddenSeqs, HiddenColumns hiddenCols);
237
238		/**
239		* Set the overview panel's box position to match the viewport
240		*
241		* @param hiddenSeqs
242		* the alignment's hidden sequences
243		* @param hiddenCols
244		* the alignment's hidden columns
245		*/
246		public abstract void setBoxPosition(HiddenSequences hiddenSeqs,
247		HiddenColumns hiddenCols);
248
249		/**
250		* Get the collection of columns used by this overview dimensions object
251		*
252		* @param hiddenCols
253		* the alignment's hidden columns
254		* @return a column collection
255		*/
256		public abstract AlignmentColsCollectionI getColumns(AlignmentI al);
257
258		/**
259		* Get the collection of rows used by this overview dimensions object
260		*
261		* @param al
262		* the alignment
263		* @return a row collection
264		*/
265		public abstract AlignmentRowsCollectionI getRows(AlignmentI al);
266
267		/**
268		* Updates overview dimensions to account for current alignment dimensions
269		*/
270		protected abstract void resetAlignmentDims();
271
272		/*
273		* Given the box coordinates in residues and sequences, set the box dimensions in the overview window
274		*/
		0% Uncovered Elements: 6 (6) Complexity: 1 Complexity Density: 0.17
275	0	protected void setBoxPosition(int startRes, int startSeq, int vpwidth,...
276		int vpheight)
277		{
278	0	resetAlignmentDims();
279
280		// boxX, boxY is the x,y location equivalent to startRes, startSeq
281	0	int xPos = Math.min(startRes, alwidth - vpwidth + 1);
282	0	boxX = Math.round(xPos / widthRatio);
283	0	boxY = Math.round(startSeq / heightRatio);
284
285		// boxWidth is the width in residues translated to pixels
286	0	boxWidth = Math.round(vpwidth / widthRatio);
287
288		// boxHeight is the height in sequences translated to pixels
289	0	boxHeight = Math.round(vpheight / heightRatio);
290		}
291
292		/**
293		* Answers if a mouse position is in the overview's red box
294		*
295		* @param x
296		* mouse x position
297		* @param y
298		* mouse y position
299		* @return true if (x,y) is inside the box
300		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
301	0	public boolean isPositionInBox(int x, int y)...
302		{
303	0	return (x > boxX && y > boxY && x < boxX + boxWidth
304		&& y < boxY + boxHeight);
305		}
306
307		/*
308		* Given the centre x position, calculate the box's left x position
309		*/
310		protected abstract int getLeftXFromCentreX(int mousex,
311		HiddenColumns hidden);
312
313		/*
314		* Given the centre y position, calculate the box's top y position
315		*/
316		protected abstract int getTopYFromCentreY(int mousey,
317		HiddenSequences hidden);
318
319		}