Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HmmerLocalBackground	18	18	7	0.00%	Show methods

Class HmmerLocalBackground

Class HmmerLocalBackground	Line # 18	Total Statements 18	Complexity 7	TOTAL Coverage 0.00%
HmmerLocalBackground(AnnotatedCollectionI)   HmmerLocalBackground(AnnotatedCollectionI)	2727	2.02	1.01	0.0 0.00%
HmmerLocalBackground()   HmmerLocalBackground()	3636	0.00	1.01	-1.0 -1.0 -
getSchemeName() : String   getSchemeName() : String	4040	1.01	1.01	0.0 0.00%
countFrequencies(SequenceCollectionI) : void   countFrequencies(SequenceCollectionI) : void	5252	13.013	2.02	0.0 0.00%
getMaxInformationScore() : float   getMaxInformationScore() : float	8585	1.01	1.01	0.0 0.00%
newInstance(AnnotatedCollectionI) : HmmerColourScheme   newInstance(AnnotatedCollectionI) : HmmerColourScheme	9191	1.01	1.01	0.0 0.00%

 

Contributing tests

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1		package jalview.schemes;
2
3		import jalview.datamodel.AnnotatedCollectionI;
4		import jalview.datamodel.ResidueCount;
5		import jalview.datamodel.SequenceCollectionI;
6		import jalview.datamodel.SequenceI;
7
8		import java.util.HashMap;
9		import java.util.List;
10		import java.util.Map;
11
12		/**
13		* An HMM colour scheme that uses local (alignment or sub-group) background
14		* frequencies for residues
15		*
16		* @author tzvanaalten
17		*/
		0% Uncovered Elements: 26 (26) Complexity: 7 Complexity Density: 0.39
18		public class HmmerLocalBackground extends HmmerColourScheme
19		{
20		float logTotalCount;
21
22		/**
23		* Constructor given a sequence collection
24		*
25		* @param ac
26		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
27	0	public HmmerLocalBackground(AnnotatedCollectionI ac)...
28		{
29	0	super(ac.getHmmSequences());
30	0	countFrequencies(ac);
31		}
32
33		/**
34		* Default constructor (required by ColourSchemes.loadColourSchemes)
35		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
36	0	public HmmerLocalBackground()...
37		{
38		}
39
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
40	0	@Override...
41		public String getSchemeName()
42		{
43	0	return JalviewColourScheme.HMMERA.toString();
44		}
45
46		/**
47		* Counts and stores the relative frequency of every residue in the alignment
48		* (apart from any HMM consensus sequences)
49		*
50		* @param sc
51		*/
		0% Uncovered Elements: 15 (15) Complexity: 2 Complexity Density: 0.15
52	0	public void countFrequencies(SequenceCollectionI sc)...
53		{
54		// TODO or total counts in Consensus Profile (how do we get at it?)?
55	0	Map<Character, Float> freqs = new HashMap<>();
56
57		/*
58		* count symbols, excluding any HMM consensus sequences
59		*/
60	0	ResidueCount counts = new ResidueCount();
61	0	List<SequenceI> seqs = sc.getSequences();
62	0	for (SequenceI seq : seqs)
63		{
64	0	if (!seq.hasHMMProfile())
65		{
66	0	for (char c : seq.getSequence())
67		{
68	0	counts.add(c);
69		}
70		}
71		}
72	0	int total = counts.getTotalResidueCount(); // excludes gaps
73
74	0	for (char symbol : counts.getSymbolCounts().symbols)
75		{
76	0	double freq = counts.getCount(symbol) / (double) total;
77	0	freqs.put(symbol, (float) freq);
78		}
79
80	0	setFrequencies(freqs);
81
82	0	logTotalCount = (float) Math.log(total);
83		}
84
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
85	0	@Override...
86		float getMaxInformationScore()
87		{
88	0	return logTotalCount;
89		}
90
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
91	0	@Override...
92		protected HmmerColourScheme newInstance(AnnotatedCollectionI ac)
93		{
94	0	return new HmmerLocalBackground(ac);
95		}
96		}