Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FloatContactMatrix	23	28	20	0.00%	Show methods

Class FloatContactMatrix

Class FloatContactMatrix	Line # 23	Total Statements 28	Complexity 20	TOTAL Coverage 0.00%
FloatContactMatrix(float[][])   FloatContactMatrix(float[][])	3333	10.010	3.03	0.0 0.00%
FloatContactMatrix(float[][],GroupSet)   FloatContactMatrix(float[][],GroupSet)	5555	2.02	1.01	0.0 0.00%
getPosition() : int   getPosition() : int	7575	1.01	1.01	0.0 0.00%
getContactHeight() : int   getContactHeight() : int	8181	1.01	1.01	0.0 0.00%
getContactAt(int) : double   getContactAt(int) : double	8787	3.03	3.03	0.0 0.00%
getContactList(int) : ContactListI   getContactList(int) : ContactListI	6565	3.03	3.03	0.0 0.00%
getElementAt(int,int) : double   getElementAt(int,int) : double	103103	1.01	1.01	0.0 0.00%
getMin() : float   getMin() : float	109109	1.01	1.01	0.0 0.00%
getMax() : float   getMax() : float	115115	1.01	1.01	0.0 0.00%
getAnnotDescr() : String   getAnnotDescr() : String	121121	1.01	1.01	0.0 0.00%
getAnnotLabel() : String   getAnnotLabel() : String	128128	1.01	1.01	0.0 0.00%
getType() : String   getType() : String	135135	1.01	1.01	0.0 0.00%
getWidth() : int   getWidth() : int	141141	1.01	1.01	0.0 0.00%
getHeight() : int   getHeight() : int	147147	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.datamodel;
22
		0% Uncovered Elements: 50 (50) Complexity: 20 Complexity Density: 0.71
23		public class FloatContactMatrix extends GroupSetHolder
24		implements ContactMatrixI
25		{
26
27		int maxrow = 0, maxcol = 0;
28
29		float[][] elements;
30
31		float maxscore;
32
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.3
33	0	public FloatContactMatrix(float[][] matrix)...
34		{
35	0	maxcol = 0;
36	0	for (float[] row : matrix)
37		{
38	0	if (row.length > maxcol)
39		{
40	0	maxcol = row.length;
41		}
42	0	maxscore = row[0];
43	0	for (float f : row)
44		{
45	0	if (maxscore < f)
46		{
47	0	maxscore = f;
48		}
49		}
50		}
51	0	maxrow = matrix.length;
52	0	elements = matrix;
53		}
54
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
55	0	public FloatContactMatrix(float[][] elements2, GroupSet grps2)...
56		{
57	0	this(elements2);
58	0	setGroupSet(grps2);
59		}
60
61		/**
62		* getContactList(column) @returns the vector of predicted alignment errors
63		* for reference position given by column
64		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
65	0	@Override...
66		public ContactListI getContactList(final int column)
67		{
68	0	if (column < 0 || column >= elements.length)
69		{
70	0	return null;
71		}
72
73	0	return new ContactListImpl(new ContactListProviderI()
74		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
75	0	@Override...
76		public int getPosition()
77		{
78	0	return column;
79		}
80
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
81	0	@Override...
82		public int getContactHeight()
83		{
84	0	return maxcol - 1;
85		}
86
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 1
87	0	@Override...
88		public double getContactAt(int mcolumn)
89		{
90	0	if (mcolumn < 0 || mcolumn >= elements[column].length)
91		{
92	0	return -1;
93		}
94	0	return elements[column][mcolumn];
95		}
96		});
97		}
98
99		/**
100		* getElementAt(column, i) @returns the predicted superposition error for the
101		* ith position when column is used as reference
102		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
103	0	@Override...
104		public double getElementAt(int _column, int i)
105		{
106	0	return elements[_column][i];
107		}
108
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
109	0	@Override...
110		public float getMin()
111		{
112	0	return 0;
113		}
114
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
115	0	@Override...
116		public float getMax()
117		{
118	0	return maxscore;
119		}
120
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
121	0	@Override...
122		public String getAnnotDescr()
123		{
124		// TODO Auto-generated method stub
125	0	return null;
126		}
127
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
128	0	@Override...
129		public String getAnnotLabel()
130		{
131		// TODO Auto-generated method stub
132	0	return null;
133		}
134
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
135	0	@Override...
136		public String getType()
137		{
138	0	return null;
139		}
140
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
141	0	@Override...
142		public int getWidth()
143		{
144	0	return maxcol;
145		}
146
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
147	0	@Override...
148		public int getHeight()
149		{
150	0	return maxrow;
151		}
152		}