Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
OverviewResColourFinder	29	22	12	0.00%	Show methods

Class OverviewResColourFinder

Class OverviewResColourFinder	Line # 29	Total Statements 22	Complexity 12	TOTAL Coverage 0.00%
OverviewResColourFinder()   OverviewResColourFinder()	5454	1.01	1.01	0.0 0.00%
OverviewResColourFinder(Color,Color,Color)   OverviewResColourFinder(Color,Color,Color)	6767	3.03	1.01	0.0 0.00%
getBoxColour(ResidueShaderI,SequenceI,int) : Color   getBoxColour(ResidueShaderI,SequenceI,int) : Color	7474	9.09	5.05	0.0 0.00%
getResidueBoxColour(boolean,ResidueShaderI,SequenceGroup[],SequenceI,int) : Color   getResidueBoxColour(boolean,ResidueShaderI,SequenceGroup[],SequenceI,int) : Color	107107	6.06	2.02	0.0 0.00%
getHiddenColour() : Color   getHiddenColour() : Color	132132	1.01	1.01	0.0 0.00%
getGapColour() : Color   getGapColour() : Color	143143	1.01	1.01	0.0 0.00%
getResidueColour() : Color   getResidueColour() : Color	154154	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.renderer;
22
23		import java.awt.Color;
24
25		import jalview.datamodel.SequenceGroup;
26		import jalview.datamodel.SequenceI;
27		import jalview.util.Comparison;
28
		0% Uncovered Elements: 37 (37) Complexity: 12 Complexity Density: 0.55
29		public class OverviewResColourFinder extends ResidueColourFinder
30		{
31		/*
32		* colour for gaps (unless overridden by colour scheme)
33		* - as set in Preferences, _or_ read from a project file
34		*/
35		Color gapColour;
36
37		/*
38		* colour for residues if no colour scheme set (before feature colouring)
39		* - as set in Preferences, _or_ read from a project file
40		*/
41		Color residueColour;
42
43		/*
44		* colour for hidden regions
45		* - as set in Preferences, _or_ read from a project file
46		*/
47		Color hiddenColour;
48
49		/**
50		* Constructor without colour settings (used by applet)
51		*
52		* @deprecated
53		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
54	0	@Deprecated...
55		public OverviewResColourFinder()
56		{
57	0	this(Color.lightGray, Color.white, Color.darkGray.darker());
58		}
59
60		/**
61		* Constructor given default colours for gaps, residues and hidden regions
62		*
63		* @param gaps
64		* @param residues
65		* @param hidden
66		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
67	0	public OverviewResColourFinder(Color gaps, Color residues, Color hidden)...
68		{
69	0	gapColour = gaps;
70	0	residueColour = residues;
71	0	hiddenColour = hidden;
72		}
73
		0% Uncovered Elements: 15 (15) Complexity: 5 Complexity Density: 0.56
74	0	@Override...
75		public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
76		{
77	0	Color resBoxColour = residueColour;
78	0	char currentChar = seq.getCharAt(i);
79
80		// In the overview window, gaps are coloured grey, unless the colour scheme
81		// specifies a gap colour, in which case gaps honour the colour scheme
82		// settings
83	0	if (shader.getColourScheme() != null)
84		{
85	0	if (Comparison.isGap(currentChar)
86		&& (!shader.getColourScheme().hasGapColour()))
87		{
88	0	resBoxColour = gapColour;
89		}
90		else
91		{
92	0	resBoxColour = shader.findColour(currentChar, i, seq);
93		}
94		}
95	0	else if (Comparison.isGap(currentChar))
96		{
97	0	resBoxColour = gapColour;
98		}
99
100	0	return resBoxColour;
101		}
102
103		/**
104		* {@inheritDoc} In the overview, the showBoxes setting is ignored, as the
105		* overview displays the colours regardless.
106		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
107	0	@Override...
108		protected Color getResidueBoxColour(boolean showBoxes,
109		ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
110		int i)
111		{
112	0	ResidueShaderI currentShader;
113	0	SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
114		i);
115	0	if (currentSequenceGroup != null)
116		{
117	0	currentShader = currentSequenceGroup.getGroupColourScheme();
118		}
119		else
120		{
121	0	currentShader = shader;
122		}
123
124	0	return getBoxColour(currentShader, seq, i);
125		}
126
127		/**
128		* Returns the colour used for hidden regions
129		*
130		* @return
131		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
132	0	public Color getHiddenColour()...
133		{
134	0	return hiddenColour;
135		}
136
137		/**
138		* Returns the colour used for gaps, if not overridden by the alignment colour
139		* scheme
140		*
141		* @return
142		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
143	0	public Color getGapColour()...
144		{
145	0	return gapColour;
146		}
147
148		/**
149		* Returns the colour used for residues (before applying any feature
150		* colouring) if there is no alignment colour scheme
151		*
152		* @return
153		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
154	0	public Color getResidueColour()...
155		{
156	0	return residueColour;
157		}
158		}