Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FeatureColourFinder	39	28	14	0.00%	Show methods

Class FeatureColourFinder

Class FeatureColourFinder	Line # 39	Total Statements 28	Complexity 14	TOTAL Coverage 0.00%
FeatureColourFinder(FeatureRenderer)   FeatureColourFinder(FeatureRenderer)	5757	2.02	1.01	0.0 0.00%
findFeatureColour(Color,SequenceI,int) : Color   findFeatureColour(Color,SequenceI,int) : Color	8282	13.013	6.06	0.0 0.00%
noFeaturesDisplayed() : boolean   noFeaturesDisplayed() : boolean	124124	13.013	7.07	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.renderer.seqfeatures;
22
23		import jalview.api.AlignViewportI;
24		import jalview.api.FeatureRenderer;
25		import jalview.api.FeaturesDisplayedI;
26		import jalview.datamodel.SequenceI;
27		import jalview.viewmodel.seqfeatures.FeatureRendererModel;
28
29		import java.awt.Color;
30		import java.awt.Graphics;
31		import java.awt.image.BufferedImage;
32
33		/**
34		* A helper class to find feature colour using an associated FeatureRenderer
35		*
36		* @author gmcarstairs
37		*
38		*/
		0% Uncovered Elements: 51 (51) Complexity: 14 Complexity Density: 0.5
39		public class FeatureColourFinder
40		{
41		/*
42		* the class we delegate feature finding to
43		*/
44		private FeatureRenderer featureRenderer;
45
46		/*
47		* a 1-pixel image on which features can be drawn, for the case where
48		* transparency allows 'see-through' of multiple feature colours
49		*/
50		private BufferedImage offscreenImage;
51
52		/**
53		* Constructor
54		*
55		* @param fr
56		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
57	0	public FeatureColourFinder(FeatureRenderer fr)...
58		{
59	0	featureRenderer = fr;
60	0	offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
61		}
62
63		/**
64		* Answers the feature colour to show for the given sequence and column
65		* position. This delegates to the FeatureRenderer to find the colour, which
66		* will depend on feature location, visibility, ordering, colour scheme, and
67		* whether or not transparency is applied. For feature rendering with
68		* transparency, this class provides a dummy 'offscreen' graphics context
69		* where multiple feature colours can be overlaid and the combined colour read
70		* back.
71		* <p>
72		* This method is not thread-safe when transparency is applied, since a shared
73		* BufferedImage would be used by all threads to hold the composite colour at
74		* a position. Each thread should use a separate instance of this class.
75		*
76		* @param defaultColour
77		* @param seq
78		* @param column
79		* alignment column position (0..)
80		* @return
81		*/
		0% Uncovered Elements: 23 (23) Complexity: 6 Complexity Density: 0.46
82	0	public Color findFeatureColour(Color defaultColour, SequenceI seq,...
83		int column)
84		{
85	0	if (noFeaturesDisplayed())
86		{
87	0	return defaultColour;
88		}
89
90	0	Graphics g = null;
91
92		/*
93		* if transparency applies, provide a notional 1x1 graphics context
94		* that has been primed with the default colour
95		*/
96	0	if (featureRenderer.getTransparency() != 1f)
97		{
98	0	g = offscreenImage.getGraphics();
99	0	if (defaultColour != null)
100		{
101	0	offscreenImage.setRGB(0, 0, defaultColour.getRGB());
102		}
103		}
104
105	0	Color c = featureRenderer.findFeatureColour(seq, column + 1, g);
106	0	if (c == null)
107		{
108	0	return defaultColour;
109		}
110
111	0	if (g != null)
112		{
113	0	c = new Color(offscreenImage.getRGB(0, 0));
114		}
115	0	return c;
116		}
117
118		/**
119		* Answers true if feature display is turned off, or there are no features
120		* configured to be visible
121		*
122		* @return
123		*/
		0% Uncovered Elements: 23 (23) Complexity: 7 Complexity Density: 0.54
124	0	boolean noFeaturesDisplayed()...
125		{
126	0	if (featureRenderer == null)
127		{
128	0	return true;
129		}
130	0	AlignViewportI av = featureRenderer.getViewport();
131	0	if (av.isShowComplementFeatures())
132		{
133	0	return false;
134		}
135	0	if (!av.isShowSequenceFeatures())
136		{
137	0	return true;
138		}
139
140	0	if (!((FeatureRendererModel) featureRenderer).hasRenderOrder())
141		{
142	0	return true;
143		}
144
145	0	FeaturesDisplayedI displayed = featureRenderer.getFeaturesDisplayed();
146	0	if (displayed == null || displayed.getVisibleFeatureCount() == 0)
147		{
148	0	return true;
149		}
150
151	0	return false;
152		}
153		}