Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SeqDistanceContactMatrix	37	16	16	0.550%	Show methods

Class SeqDistanceContactMatrix

Class SeqDistanceContactMatrix	Line # 37	Total Statements 16	Complexity 16	TOTAL Coverage 0.550%
SeqDistanceContactMatrix(int)   SeqDistanceContactMatrix(int)	4545	1.01	1.01	1.0 1.0100%
getMin() : float   getMin() : float	5050	1.01	1.01	1.0 1.0100%
getMax() : float   getMax() : float	5656	1.01	1.01	1.0 1.0100%
getContactHeight() : int   getContactHeight() : int	8888	1.01	1.01	0.0 0.00%
getPosition() : int   getPosition() : int	9595	1.01	1.01	0.0 0.00%
getContactAt(int) : double   getContactAt(int) : double	101101	1.01	1.01	0.0 0.00%
getContactList(int) : ContactListI   getContactList(int) : ContactListI	6262	3.03	3.03	0.0 0.00%
getAnnotDescr() : String   getAnnotDescr() : String	109109	1.01	1.01	1.0 1.0100%
getAnnotLabel() : String   getAnnotLabel() : String	115115	1.01	1.01	1.0 1.0100%
getType() : String   getType() : String	121121	1.01	1.01	1.0 1.0100%
getWidth() : int   getWidth() : int	127127	1.01	1.01	0.0 0.00%
getHeight() : int   getHeight() : int	133133	1.01	1.01	0.0 0.00%
getElementAt(int,int) : double   getElementAt(int,int) : double	139139	1.01	1.01	1.0 1.0100%
newMappableContactMatrix(SequenceI,MapList) : SeqDistanceContactMatrix   newMappableContactMatrix(SequenceI,MapList) : SeqDistanceContactMatrix	145145	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.5	jalview.renderer.ContactGeometryTest.testContactGeometryjalview.renderer.ContactGeometryTest.testContactGeometry	1PASS
	0.375	jalview.renderer.ContactGeometryTest.testCoverageofRangejalview.renderer.ContactGeometryTest.testCoverageofRange	1PASS
	0.375	jalview.datamodel.SequenceTest.testCopyPasteStyleDerivesequence_withcontactMatrixAnnjalview.datamodel.SequenceTest.testCopyPasteStyleDerivesequence_withcontactMatrixAnn	1PASS
	0.375	jalview.gui.AlignViewportTest.testGetSelectionAsNewSequences_withContactMatricesjalview.gui.AlignViewportTest.testGetSelectionAsNewSequences_withContactMatrices	1PASS
	0.375	jalview.analysis.AlignmentUtilsTests.testAddReferenceContactMapjalview.analysis.AlignmentUtilsTests.testAddReferenceContactMap	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.datamodel;
22
23		import java.awt.Color;
24		import java.util.BitSet;
25		import java.util.HashMap;
26		import java.util.List;
27
28		import jalview.util.MapList;
29		import jalview.ws.datamodel.alphafold.MappableContactMatrix;
30
31		/**
32		* Dummy contact matrix based on sequence distance
33		*
34		* @author jprocter
35		*
36		*/
		50% Uncovered Elements: 16 (32) Complexity: 16 Complexity Density: 1
37		public class SeqDistanceContactMatrix
38		extends MappableContactMatrix<SeqDistanceContactMatrix>
39		implements ContactMatrixI
40		{
41		private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE";
42
43		private int width = 0;
44
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
45	63	public SeqDistanceContactMatrix(int width)...
46		{
47	63	this.width = width;
48		}
49
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
50	73	@Override...
51		public float getMin()
52		{
53	73	return 0f;
54		}
55
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
56	73	@Override...
57		public float getMax()
58		{
59	73	return width;
60		}
61
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
62	0	@Override...
63		public ContactListI getContactList(final int column)
64		{
65	0	if (column < 0 || column >= width)
66		{
67	0	return null;
68		}
69	0	return new ContactListImpl(new ContactListProviderI()
70		{
71
72		int p = column;
73
74		// @Override
75		// public Color getColorForScore(int column)
76		// {
77		// return jalview.util.ColorUtils.getGraduatedColour(Math.abs(column-p),
78		// 0, Color.white, width, Color.magenta);
79		// }
80		// @Override
81		// public Color getColorForRange(int from_column, int to_column)
82		// {
83		// return jalview.util.ColorUtils.getGraduatedColour(
84		// Math.abs(to_column + from_column - 2 * p) / 2, 0, Color.white, width,
85		// Color.magenta);
86		// }
87
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
88	0	@Override...
89		public int getContactHeight()
90		{
91	0	return width;
92
93		}
94
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
95	0	@Override...
96		public int getPosition()
97		{
98	0	return p;
99		}
100
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
101	0	@Override...
102		public double getContactAt(int column)
103		{
104	0	return Math.abs(column - p);
105		}
106		});
107		}
108
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
109	63	@Override...
110		public String getAnnotDescr()
111		{
112	63	return "Sequence distance matrix";
113		}
114
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
115	63	@Override...
116		public String getAnnotLabel()
117		{
118	63	return "Sequence Distance";
119		}
120
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
121	73	@Override...
122		public String getType()
123		{
124	73	return SEQUENCE_DISTANCE;
125		}
126
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
127	0	@Override...
128		public int getWidth()
129		{
130	0	return width;
131		}
132
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
133	0	@Override...
134		public int getHeight()
135		{
136	0	return width;
137		}
138
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
139	80	@Override...
140		public double getElementAt(int _column, int i)
141		{
142	80	return Math.abs(_column - i);
143		}
144
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
145	1	@Override...
146		protected SeqDistanceContactMatrix newMappableContactMatrix(
147		SequenceI newRefSeq, MapList newFromMapList)
148		{
149
150	1	return new SeqDistanceContactMatrix(width);
151		}
152		}