Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
IdColourScheme	38	10	11	0.00%	Show methods

Class IdColourScheme

Class IdColourScheme	Line # 38	Total Statements 10	Complexity 11	TOTAL Coverage 0.00%
IdColourScheme()   IdColourScheme()	4242	0.00	1.01	-1.0 -1.0 -
IdColourScheme(AlignViewportI,AnnotatedCollectionI)   IdColourScheme(AlignViewportI,AnnotatedCollectionI)	4747	1.01	1.01	0.0 0.00%
getSchemeName() : String   getSchemeName() : String	5252	1.01	1.01	0.0 0.00%
getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI   getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI	6262	1.01	1.01	0.0 0.00%
alignmentChanged(AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : void   alignmentChanged(AnnotatedCollectionI,Map<SequenceI, SequenceCollectionI>) : void	6969	0.00	1.01	-1.0 -1.0 -
findColour(char,int,SequenceI,String,float) : Color   findColour(char,int,SequenceI,String,float) : Color	7575	4.04	3.03	0.0 0.00%
hasGapColour() : boolean   hasGapColour() : boolean	9191	1.01	1.01	0.0 0.00%
isApplicableTo(AnnotatedCollectionI) : boolean   isApplicableTo(AnnotatedCollectionI) : boolean	9797	1.01	1.01	0.0 0.00%
isSimple() : boolean   isSimple() : boolean	103103	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.schemes;
22
23		import jalview.api.AlignViewportI;
24		import jalview.datamodel.AnnotatedCollectionI;
25		import jalview.datamodel.SequenceCollectionI;
26		import jalview.datamodel.SequenceI;
27
28		import java.awt.Color;
29		import java.util.Map;
30
31		/**
32		* shade sequences using the colour shown in the ID panel. Useful to map
33		* sequence groupings onto residue data (eg tree subgroups visualised on
34		* structures or overview window)
35		*
36		* @author jprocter
37		*/
		0% Uncovered Elements: 23 (23) Complexity: 11 Complexity Density: 1.1
38		public class IdColourScheme implements ColourSchemeI
39		{
40		AlignViewportI view = null;
41
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
42	0	public IdColourScheme()...
43		{
44
45		}
46
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
47	0	public IdColourScheme(AlignViewportI view, AnnotatedCollectionI coll)...
48		{
49	0	this.view = view;
50		}
51
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
52	0	@Override...
53		public String getSchemeName()
54		{
55	0	return JalviewColourScheme.IdColour.toString();
56		}
57
58		/**
59		* Returns a new instance of this colour scheme with which the given data may
60		* be coloured
61		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	@Override...
63		public ColourSchemeI getInstance(AlignViewportI view,
64		AnnotatedCollectionI coll)
65		{
66	0	return new IdColourScheme(view, coll);
67		}
68
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
69	0	@Override...
70		public void alignmentChanged(AnnotatedCollectionI alignment,
71		Map<SequenceI, SequenceCollectionI> hiddenReps)
72		{
73		}
74
		0% Uncovered Elements: 8 (8) Complexity: 3 Complexity Density: 0.75
75	0	@Override...
76		public Color findColour(char symbol, int position, SequenceI seq,
77		String consensusResidue, float pid)
78		{
79		// rather than testing if coll is a sequence group, and if so looking at
80		// ((SequenceGroup)coll).idColour
81		// we always return the sequence ID colour, in case the user has customised
82		// the displayed Id colour by right-clicking an internal node in the tree.
83	0	if (view == null)
84		{
85	0	return Color.WHITE;
86		}
87	0	Color col = view.getSequenceColour(seq);
88	0	return Color.WHITE.equals(col) ? Color.WHITE : col.darker();
89		}
90
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
91	0	@Override...
92		public boolean hasGapColour()
93		{
94	0	return false;
95		}
96
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
97	0	@Override...
98		public boolean isApplicableTo(AnnotatedCollectionI ac)
99		{
100	0	return true;
101		}
102
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
103	0	@Override...
104		public boolean isSimple()
105		{
106	0	return false;
107		}
108		}