Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HMMNode	8	26	23	0.00%	Show methods

Class HMMNode

Class HMMNode	Line # 8	Total Statements 26	Complexity 23	TOTAL Coverage 0.00%
HMMNode()   HMMNode()	3030	0.00	1.01	-1.0 -1.0 -
getMatchEmissions() : double[]   getMatchEmissions() : double[]	3434	1.01	1.01	0.0 0.00%
getMatchEmission(int) : double   getMatchEmission(int) : double	3939	1.01	1.01	0.0 0.00%
setMatchEmissions(double[]) : void   setMatchEmissions(double[]) : void	4444	1.01	1.01	0.0 0.00%
getInsertEmissions() : double[]   getInsertEmissions() : double[]	4949	1.01	1.01	0.0 0.00%
getInsertEmission(int) : double   getInsertEmission(int) : double	5454	1.01	1.01	0.0 0.00%
setInsertEmissions(double[]) : void   setInsertEmissions(double[]) : void	5959	1.01	1.01	0.0 0.00%
getStateTransitions() : double[]   getStateTransitions() : double[]	6464	1.01	1.01	0.0 0.00%
getStateTransition(int) : double   getStateTransition(int) : double	6969	1.01	1.01	0.0 0.00%
setStateTransitions(double[]) : void   setStateTransitions(double[]) : void	7474	1.01	1.01	0.0 0.00%
getResidueNumber() : int   getResidueNumber() : int	7979	1.01	1.01	0.0 0.00%
setResidueNumber(int) : void   setResidueNumber(int) : void	8383	1.01	1.01	0.0 0.00%
getConsensusResidue() : char   getConsensusResidue() : char	8888	1.01	1.01	0.0 0.00%
setConsensusResidue(char) : void   setConsensusResidue(char) : void	9292	1.01	1.01	0.0 0.00%
getReferenceAnnotation() : char   getReferenceAnnotation() : char	9797	1.01	1.01	0.0 0.00%
setReferenceAnnotation(char) : void   setReferenceAnnotation(char) : void	101101	1.01	1.01	0.0 0.00%
getMaskValue() : char   getMaskValue() : char	106106	1.01	1.01	0.0 0.00%
setMaskValue(char) : void   setMaskValue(char) : void	110110	1.01	1.01	0.0 0.00%
getConsensusStructure() : char   getConsensusStructure() : char	115115	1.01	1.01	0.0 0.00%
setConsensusStructure(char) : void   setConsensusStructure(char) : void	119119	1.01	1.01	0.0 0.00%
getMaxMatchEmissionIndex() : int   getMaxMatchEmissionIndex() : int	131131	7.07	3.03	0.0 0.00%

 

Contributing tests

Source view

1		package jalview.datamodel;
2
3		/**
4		* stores data for each node in the hmm model
5		* @author TZVanaalten
6		*
7		*/
		0% Uncovered Elements: 51 (51) Complexity: 23 Complexity Density: 0.88
8		public class HMMNode
9		{
10		//contains the match emissions for each symbol
11		double[] matchEmissions;
12
13		//contains the insert emissions for each symbol
14		double[] insertEmissions;
15
16		// contains the state transitions for each possible transition. These are mm,
17		// mi, md, im, ii, dm and dd in order
18		double[] stateTransitions;
19
20		//annotations
21		int residueNumber;
22		char consensusResidue;
23		char referenceAnnotation;
24		char maskValue;
25		char consensusStructure;
26
27		/**
28		* Constructor
29		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
30	0	public HMMNode()...
31		{
32		}
33
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
34	0	public double[] getMatchEmissions()...
35		{
36	0	return matchEmissions;
37		}
38
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
39	0	double getMatchEmission(int symbolIndex)...
40		{
41	0	return matchEmissions[symbolIndex];
42		}
43
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
44	0	public void setMatchEmissions(double[] matches)...
45		{
46	0	this.matchEmissions = matches;
47		}
48
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
49	0	public double[] getInsertEmissions()...
50		{
51	0	return insertEmissions;
52		}
53
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
54	0	double getInsertEmission(int symbolIndex)...
55		{
56	0	return insertEmissions[symbolIndex];
57		}
58
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	public void setInsertEmissions(double[] insertEmissionsL)...
60		{
61	0	this.insertEmissions = insertEmissionsL;
62		}
63
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
64	0	public double[] getStateTransitions()...
65		{
66	0	return stateTransitions;
67		}
68
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
69	0	double getStateTransition(int transition)...
70		{
71	0	return stateTransitions[transition];
72		}
73
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
74	0	public void setStateTransitions(double[] stateTransitionsM)...
75		{
76	0	this.stateTransitions = stateTransitionsM;
77		}
78
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
79	0	int getResidueNumber()...
80		{
81	0	return residueNumber;
82		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
83	0	public void setResidueNumber(int resNo)...
84		{
85	0	this.residueNumber = resNo;
86		}
87
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
88	0	char getConsensusResidue()...
89		{
90	0	return consensusResidue;
91		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
92	0	public void setConsensusResidue(char consensusResidue)...
93		{
94	0	this.consensusResidue = consensusResidue;
95		}
96
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
97	0	char getReferenceAnnotation()...
98		{
99	0	return referenceAnnotation;
100		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
101	0	public void setReferenceAnnotation(char referenceAnnotation)...
102		{
103	0	this.referenceAnnotation = referenceAnnotation;
104		}
105
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
106	0	char getMaskValue()...
107		{
108	0	return maskValue;
109		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	public void setMaskValue(char maskValue)...
111		{
112	0	this.maskValue = maskValue;
113		}
114
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
115	0	char getConsensusStructure()...
116		{
117	0	return consensusStructure;
118		}
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
119	0	public void setConsensusStructure(char consensusStructure)...
120		{
121	0	this.consensusStructure = consensusStructure;
122		}
123
124		/**
125		* Answers the symbol index of the symbol with the highest match emission
126		* probability (first symbol in case of a tie). Note this object stores
127		* probabilities, not the negative logarithms as in the HMM file.
128		*
129		* @return
130		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
131	0	int getMaxMatchEmissionIndex()...
132		{
133	0	int maxIndex = 0;
134	0	double max = 0D;
135
136	0	for (int i = 0; i < matchEmissions.length; i++)
137		{
138	0	if (matchEmissions[i] > max)
139		{
140	0	max = matchEmissions[i];
141	0	maxIndex = i;
142		}
143		}
144	0	return maxIndex;
145		}
146		}
147
148