Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
HmmerGlobalBackground	13	7	7	0.00%	Show methods

Class HmmerGlobalBackground

Class HmmerGlobalBackground	Line # 13	Total Statements 7	Complexity 7	TOTAL Coverage 0.00%
HmmerGlobalBackground(SequenceCollectionI)   HmmerGlobalBackground(SequenceCollectionI)	2727	3.03	2.02	0.0 0.00%
HmmerGlobalBackground()   HmmerGlobalBackground()	4040	0.00	1.01	-1.0 -1.0 -
getSchemeName() : String   getSchemeName() : String	4444	1.01	1.01	0.0 0.00%
newInstance(AnnotatedCollectionI) : HmmerColourScheme   newInstance(AnnotatedCollectionI) : HmmerColourScheme	5050	1.01	1.01	0.0 0.00%
getMaxInformationScore() : float   getMaxInformationScore() : float	5656	1.01	1.01	0.0 0.00%
getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI   getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI	6666	1.01	1.01	0.0 0.00%

 

Contributing tests

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1		package jalview.schemes;
2
3		import jalview.api.AlignViewportI;
4		import jalview.datamodel.AnnotatedCollectionI;
5		import jalview.datamodel.SequenceCollectionI;
6
7		/**
8		* An HMM colour scheme that uses global ('Uniprot') background frequencies for
9		* residues
10		*
11		* @author tzvanaalten
12		*/
		0% Uncovered Elements: 15 (15) Complexity: 7 Complexity Density: 1
13		public class HmmerGlobalBackground extends HmmerColourScheme
14		{
15		/*
16		* The highest possible log ratio is when match emission probability in
17		* the HMM model is 1, and background (for W) is 0.0109 giving
18		* log(1/0.0109) = log(91.743) = 4.519
19		*/
20		private static final float MAX_LOG_RATIO = 4.519f;
21
22		/**
23		* Constructor given a sequence collection
24		*
25		* @param ac
26		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
27	0	public HmmerGlobalBackground(SequenceCollectionI ac)...
28		{
29	0	super(ac.getHmmSequences());
30	0	String alphabetType = getHmm() == null
31		? ResidueProperties.ALPHABET_AMINO
32		: getHmm().getAlphabetType();
33	0	setFrequencies(
34		ResidueProperties.backgroundFrequencies.get(alphabetType));
35		}
36
37		/**
38		* Default constructor (required by ColourSchemes.loadColourSchemes)
39		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
40	0	public HmmerGlobalBackground()...
41		{
42		}
43
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
44	0	@Override...
45		public String getSchemeName()
46		{
47	0	return JalviewColourScheme.HMMERU.toString();
48		}
49
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
50	0	@Override...
51		protected HmmerColourScheme newInstance(AnnotatedCollectionI ac)
52		{
53	0	return new HmmerGlobalBackground(ac);
54		}
55
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
56	0	@Override...
57		float getMaxInformationScore()
58		{
59	0	return MAX_LOG_RATIO;
60		}
61
62		/**
63		* Answers a new colour scheme instance based on the HMM of the first sequence
64		* in alignment that has an HMM
65		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	@Override...
67		public ColourSchemeI getInstance(AlignViewportI viewport,
68		AnnotatedCollectionI ac)
69		{
70	0	return newInstance(ac);
71		}
72
73		}