Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ResidueColourFinder	29	21	14	0.00%	Show methods

Class ResidueColourFinder

Class ResidueColourFinder	Line # 29	Total Statements 21	Complexity 14	TOTAL Coverage 0.00%
ResidueColourFinder()   ResidueColourFinder()	3131	0.00	1.01	-1.0 -1.0 -
getResidueColour(boolean,ResidueShaderI,SequenceGroup[],SequenceI,int,FeatureColourFinder) : Color   getResidueColour(boolean,ResidueShaderI,SequenceGroup[],SequenceI,int,FeatureColourFinder) : Color	5252	4.04	2.02	0.0 0.00%
getResidueBoxColour(boolean,ResidueShaderI,SequenceGroup[],SequenceI,int) : Color   getResidueBoxColour(boolean,ResidueShaderI,SequenceGroup[],SequenceI,int) : Color	8383	7.07	4.04	0.0 0.00%
getCurrentSequenceGroup(SequenceGroup[],int) : SequenceGroup   getCurrentSequenceGroup(SequenceGroup[],int) : SequenceGroup	115115	6.06	5.05	0.0 0.00%
getBoxColour(ResidueShaderI,SequenceI,int) : Color   getBoxColour(ResidueShaderI,SequenceI,int) : Color	145145	4.04	2.02	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 jalview.datamodel.SequenceGroup;
24		import jalview.datamodel.SequenceI;
25		import jalview.renderer.seqfeatures.FeatureColourFinder;
26
27		import java.awt.Color;
28
		0% Uncovered Elements: 42 (42) Complexity: 14 Complexity Density: 0.67
29		public class ResidueColourFinder
30		{
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
31	0	public ResidueColourFinder()...
32		{
33		}
34
35		/**
36		* Get the colour of a residue in a sequence
37		*
38		* @param showBoxes
39		* true if the viewport's Show Boxes setting is true
40		* @param shader
41		* the viewport's colour scheme
42		* @param allGroups
43		* all the groups which seq participates in
44		* @param seq
45		* the sequence containing the residue
46		* @param position
47		* the position of the residue in the sequence
48		* @param finder
49		* FeatureColourFinder for the viewport
50		* @return colour of the residue
51		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
52	0	public Color getResidueColour(boolean showBoxes, ResidueShaderI shader,...
53		SequenceGroup[] allGroups, final SequenceI seq, int position,
54		FeatureColourFinder finder)
55		{
56	0	Color col = getResidueBoxColour(showBoxes, shader, allGroups, seq,
57		position);
58
59		// if there's a FeatureColourFinder we might override the residue colour
60		// here with feature colouring
61	0	if (finder != null)
62		{
63	0	col = finder.findFeatureColour(col, seq, position);
64		}
65	0	return col;
66		}
67
68		/**
69		* Get the residue colour without accounting for any features
70		*
71		* @param showBoxes
72		* true if the viewport's Show Boxes setting is true
73		* @param shader
74		* the viewport's colour scheme
75		* @param allGroups
76		* all the groups which seq participates in
77		* @param seq
78		* the sequence containing the residue
79		* @param i
80		* the position of the residue in the sequence
81		* @return
82		*/
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.57
83	0	protected Color getResidueBoxColour(boolean showBoxes,...
84		ResidueShaderI shader, SequenceGroup[] allGroups, SequenceI seq,
85		int i)
86		{
87	0	SequenceGroup currentSequenceGroup = getCurrentSequenceGroup(allGroups,
88		i);
89	0	if (currentSequenceGroup != null)
90		{
91	0	if (currentSequenceGroup.getDisplayBoxes())
92		{
93	0	return getBoxColour(currentSequenceGroup.getGroupColourScheme(),
94		seq, i);
95		}
96		}
97	0	else if (showBoxes)
98		{
99	0	return getBoxColour(shader, seq, i);
100		}
101
102	0	return Color.white;
103		}
104
105		/**
106		* Search all the groups for a sequence to find the one which a given res
107		* falls into
108		*
109		* @param allGroups
110		* all the groups a sequence participates in
111		* @param res
112		* the residue to search for
113		* @return a sequence group for res, or null if no sequence group applies
114		*/
		0% Uncovered Elements: 12 (12) Complexity: 5 Complexity Density: 0.83
115	0	public SequenceGroup getCurrentSequenceGroup(SequenceGroup[] allGroups,...
116		int res)
117		{
118	0	if (allGroups == null)
119		{
120	0	return null;
121		}
122
123	0	for (int i = 0; i < allGroups.length; i++)
124		{
125	0	if ((allGroups[i].getStartRes() <= res)
126		&& (allGroups[i].getEndRes() >= res))
127		{
128	0	return (allGroups[i]);
129		}
130		}
131
132	0	return null;
133		}
134
135		/**
136		* DOCUMENT ME!
137		*
138		* @param shader
139		* the viewport's colour scheme
140		* @param seq
141		* the sequence containing the residue
142		* @param i
143		* the position of the residue in the sequence
144		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
145	0	public Color getBoxColour(ResidueShaderI shader, SequenceI seq, int i)...
146		{
147	0	Color resBoxColour = Color.white;
148	0	if (shader.getColourScheme() != null)
149		{
150	0	resBoxColour = shader.findColour(seq.getCharAt(i), i, seq);
151		}
152	0	return resBoxColour;
153		}
154
155		}