Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
OverviewResColourFinder	29	24	11	8	0.794871879.5%	Show methods

Class OverviewResColourFinder

Class OverviewResColourFinder	Line # 29	Total Statements 24	Complexity 11	Uncovered Elements 8	TOTAL Coverage 0.794871879.5%
OverviewResColourFinder()   OverviewResColourFinder()	4949	1.01	1.01	0.00	1.0 1.0100%
OverviewResColourFinder(boolean,Color,Color)   OverviewResColourFinder(boolean,Color,Color)	6464	7.07	2.02	4.04	0.5555556 0.555555655.6%
getBoxColour(ResidueShaderI,SequenceI,int) : Color   getBoxColour(ResidueShaderI,SequenceI,int) : Color	8181	9.09	5.05	0.00	1.0 1.0100%
getResidueBoxColour(boolean,ResidueShaderI,SequenceGroup[],SequenceI,int) : Color   getResidueBoxColour(boolean,ResidueShaderI,SequenceGroup[],SequenceI,int) : Color	114114	6.06	2.02	2.02	0.75 0.7575%
getHiddenColour() : Color   getHiddenColour() : Color	139139	1.01	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.6666667	jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_zappojalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_zappo	1PASS
	0.6666667	jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_userdefjalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_userdef	1PASS
	0.64102566	jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_nonejalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_none	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.renderer;
22
23		import jalview.datamodel.SequenceGroup;
24		import jalview.datamodel.SequenceI;
25		import jalview.util.Comparison;
26
27		import java.awt.Color;
28
		79.5% Uncovered Elements: 8 (39) Complexity: 11 Complexity Density: 0.46
29		public class OverviewResColourFinder extends ResidueColourFinder
30		{
31		final Color GAP_COLOUR; // default colour to use at gaps
32
33		final Color RESIDUE_COLOUR; // default colour to use at residues
34
35		final Color HIDDEN_COLOUR; // colour for hidden regions
36
37		boolean useLegacy = false;
38
39		public static final Color OVERVIEW_DEFAULT_GAP = Color.lightGray;
40
41		public static final Color OVERVIEW_DEFAULT_LEGACY_GAP = Color.white;
42
43		public static final Color OVERVIEW_DEFAULT_HIDDEN = Color.darkGray
44		.darker();
45
46		/**
47		* Constructor without colour settings (used by applet)
48		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
49	3	public OverviewResColourFinder()...
50		{
51	3	this(false, OVERVIEW_DEFAULT_GAP, OVERVIEW_DEFAULT_HIDDEN);
52		}
53
54		/**
55		* Constructor with colour settings
56		*
57		* @param useLegacyColouring
58		* whether to use legacy gap colouring (white gaps, grey residues)
59		* @param gapCol
60		* gap colour if not legacy
61		* @param hiddenCol
62		* hidden region colour (transparency applied by rendering code)
63		*/
		55.6% Uncovered Elements: 4 (9) Complexity: 2 Complexity Density: 0.29
64	3	public OverviewResColourFinder(boolean useLegacyColouring, Color gapCol,...
65		Color hiddenCol)
66		{
67	3	if (useLegacyColouring)
68		{
69	0	GAP_COLOUR = Color.white;
70	0	RESIDUE_COLOUR = Color.lightGray;
71	0	HIDDEN_COLOUR = hiddenCol;
72		}
73		else
74		{
75	3	GAP_COLOUR = gapCol;
76	3	RESIDUE_COLOUR = Color.white;
77	3	HIDDEN_COLOUR = hiddenCol;
78		}
79		}
80
		100% Uncovered Elements: 0 (15) Complexity: 5 Complexity Density: 0.56
81	18	@Override...
82		public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
83		{
84	18	Color resBoxColour = RESIDUE_COLOUR;
85	18	char currentChar = seq.getCharAt(i);
86
87		// In the overview window, gaps are coloured grey, unless the colour scheme
88		// specifies a gap colour, in which case gaps honour the colour scheme
89		// settings
90	18	if (shader.getColourScheme() != null)
91		{
92	14	if (Comparison.isGap(currentChar)
93		&& (!shader.getColourScheme().hasGapColour()))
94		{
95	4	resBoxColour = GAP_COLOUR;
96		}
97		else
98		{
99	10	resBoxColour = shader.findColour(currentChar, i, seq);
100		}
101		}
102	4	else if (Comparison.isGap(currentChar))
103		{
104	2	resBoxColour = GAP_COLOUR;
105		}
106
107	18	return resBoxColour;
108		}
109
110		/**
111		* {@inheritDoc} In the overview, the showBoxes setting is ignored, as the
112		* overview displays the colours regardless.
113		*/
		75% Uncovered Elements: 2 (8) Complexity: 2 Complexity Density: 0.33
114	18	@Override...
115		protected Color getResidueBoxColour(boolean showBoxes,
116		ResidueShaderI shader,
117		SequenceGroup[] allGroups, SequenceI seq, int i)
118		{
119	18	ResidueShaderI currentShader;
120	18	SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
121		i);
122	18	if (currentSequenceGroup != null)
123		{
124	0	currentShader = currentSequenceGroup.getGroupColourScheme();
125		}
126		else
127		{
128	18	currentShader = shader;
129		}
130
131	18	return getBoxColour(currentShader, seq, i);
132		}
133
134		/**
135		* Supply hidden colour
136		*
137		* @return colour of hidden regions
138		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
139	0	protected Color getHiddenColour()...
140		{
141	0	return HIDDEN_COLOUR;
142		}
143		}