Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
InformationThread	24	74	23	0.00%	Show methods

Class InformationThread

Class InformationThread	Line # 24	Total Statements 74	Complexity 23	TOTAL Coverage 0.00%
InformationThread(AlignViewportI,AlignmentViewPanel)   InformationThread(AlignViewportI,AlignmentViewPanel)	3434	1.01	1.01	0.0 0.00%
run() : void   run() : void	4444	14.014	6.06	0.0 0.00%
computeProfiles(AlignmentI) : void   computeProfiles(AlignmentI) : void	9090	13.013	3.03	0.0 0.00%
getSequences() : SequenceI[]   getSequences() : SequenceI[]	130130	1.01	1.01	0.0 0.00%
getGapAnnotation() : AlignmentAnnotation   getGapAnnotation() : AlignmentAnnotation	140140	1.01	1.01	0.0 0.00%
updateAnnotation() : void   updateAnnotation() : void	150150	16.016	3.03	0.0 0.00%
updateInformationAnnotation(SequenceI,ProfilesI,SequenceGroup,List<AlignmentAnnotation>) : float   updateInformationAnnotation(SequenceI,ProfilesI,SequenceGroup,List<AlignmentAnnotation>) : float	209209	7.07	3.03	0.0 0.00%
findOrCreateAnnotation(SequenceI,SequenceGroup) : AlignmentAnnotation   findOrCreateAnnotation(SequenceI,SequenceGroup) : AlignmentAnnotation	241241	21.021	5.05	0.0 0.00%

 

Contributing tests

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1		package jalview.workers;
2
3		import jalview.analysis.AAFrequency;
4		import jalview.api.AlignViewportI;
5		import jalview.api.AlignmentViewPanel;
6		import jalview.datamodel.AlignmentAnnotation;
7		import jalview.datamodel.AlignmentI;
8		import jalview.datamodel.Annotation;
9		import jalview.datamodel.HiddenMarkovModel;
10		import jalview.datamodel.ProfilesI;
11		import jalview.datamodel.SequenceGroup;
12		import jalview.datamodel.SequenceI;
13		import jalview.util.MessageManager;
14
15		import java.util.ArrayList;
16		import java.util.List;
17
18		/**
19		* This class calculates HMM Information Content annotations, based on any HMM
20		* consensus sequences and their HMM models. HMM consensus sequences may be
21		* present for the whole alignment, or subgroups of it.
22		*
23		*/
		0% Uncovered Elements: 108 (108) Complexity: 23 Complexity Density: 0.31
24		public class InformationThread extends AlignCalcWorker
25		{
26		public static final String HMM_CALC_ID = "HMM";
27
28		/**
29		* Constructor
30		*
31		* @param alignViewport
32		* @param alignPanel
33		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
34	0	public InformationThread(AlignViewportI alignViewport,...
35		AlignmentViewPanel alignPanel)
36		{
37	0	super(alignViewport, alignPanel);
38		}
39
40		/**
41		* Recomputes Information annotations for any HMM consensus sequences (for
42		* alignment and/or groups)
43		*/
		0% Uncovered Elements: 24 (24) Complexity: 6 Complexity Density: 0.43
44	0	@Override...
45		public void run()
46		{
47	0	if (alignViewport.getAlignment().getHmmSequences().isEmpty())
48		{
49	0	return;
50		}
51	0	if (alignViewport.isClosed())
52		{
53	0	abortAndDestroy();
54	0	return;
55		}
56
57	0	AlignmentI alignment = alignViewport.getAlignment();
58	0	int aWidth = alignment == null ? -1 : alignment.getWidth();
59	0	if (aWidth < 0)
60		{
61	0	return;
62		}
63
64		/*
65		* compute information profiles for any HMM consensus sequences
66		* for the alignment or sub-groups
67		*/
68	0	computeProfiles(alignment);
69
70		/*
71		* construct the corresponding annotations
72		*/
73	0	updateAnnotation();
74
75	0	if (ap != null)
76		{
77	0	ap.adjustAnnotationHeight();
78	0	ap.paintAlignment(true, true);
79		}
80		}
81
82		/**
83		* Computes HMM profiles for any HMM consensus sequences (for alignment or
84		* subgroups). Any alignment profile computed is stored on the viewport, any
85		* group profile computed is stored on the respective sequence group.
86		*
87		* @param alignment
88		* @see AlignViewportI#setHmmProfiles(ProfilesI)
89		*/
		0% Uncovered Elements: 17 (17) Complexity: 3 Complexity Density: 0.23
90	0	protected void computeProfiles(AlignmentI alignment)...
91		{
92	0	int width = alignment.getWidth();
93
94		/*
95		* alignment HMM profile
96		*/
97	0	List<SequenceI> seqs = alignment.getHmmSequences();
98	0	if (!seqs.isEmpty())
99		{
100	0	HiddenMarkovModel hmm = seqs.get(0).getHMM();
101	0	ProfilesI hmmProfiles = AAFrequency.calculateHMMProfiles(hmm, width,
102		0, width, alignViewport.isIgnoreBelowBackground(),
103		alignViewport.isInfoLetterHeight());
104	0	alignViewport.setHmmProfiles(hmmProfiles);
105		}
106
107		/*
108		* group HMM profiles
109		*/
110	0	List<SequenceGroup> groups = alignment.getGroups();
111	0	for (SequenceGroup group : groups)
112		{
113	0	seqs = group.getHmmSequences();
114	0	if (!seqs.isEmpty())
115		{
116	0	HiddenMarkovModel hmm = seqs.get(0).getHMM();
117	0	ProfilesI hmmProfiles = AAFrequency.calculateHMMProfiles(hmm, width,
118		0, width, group.isIgnoreBelowBackground(),
119		group.isUseInfoLetterHeight());
120	0	group.setHmmProfiles(hmmProfiles);
121		}
122		}
123		}
124
125		/**
126		* gets the sequences on the alignment on the viewport.
127		*
128		* @return
129		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
130	0	protected SequenceI[] getSequences()...
131		{
132	0	return alignViewport.getAlignment().getSequencesArray();
133		}
134
135		/**
136		* Get the Gap annotation for the alignment
137		*
138		* @return
139		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	protected AlignmentAnnotation getGapAnnotation()...
141		{
142	0	return alignViewport.getAlignmentGapAnnotation();
143		}
144
145		/**
146		* Computes Information Content annotation for any HMM consensus sequences
147		* (for alignment or groups), and updates (or adds) the annotation to the
148		* sequence and the alignment
149		*/
		0% Uncovered Elements: 20 (20) Complexity: 3 Complexity Density: 0.19
150	0	@Override...
151		public void updateAnnotation()
152		{
153	0	AlignmentI alignment = alignViewport.getAlignment();
154
155	0	float maxInformation = 0f;
156	0	List<AlignmentAnnotation> infos = new ArrayList<>();
157
158		/*
159		* annotation for alignment HMM consensus if present
160		*/
161	0	List<SequenceI> hmmSeqs = alignment.getHmmSequences();
162	0	if (!hmmSeqs.isEmpty())
163		{
164	0	ProfilesI profile = alignViewport.getHmmProfiles();
165	0	float m = updateInformationAnnotation(hmmSeqs.get(0), profile, null,
166		infos);
167	0	maxInformation = Math.max(maxInformation, m);
168		}
169
170		/*
171		* annotation for group HMM consensus if present
172		*/
173	0	for (SequenceGroup group : alignment.getGroups())
174		{
175	0	hmmSeqs = group.getHmmSequences();
176	0	if (!hmmSeqs.isEmpty())
177		{
178	0	ProfilesI profiles = group.getHmmProfiles();
179	0	float m = updateInformationAnnotation(hmmSeqs.get(0), profiles,
180		group, infos);
181	0	maxInformation = Math.max(maxInformation, m);
182		}
183		}
184
185		/*
186		* maxInformation holds the maximum value of information score;
187		* set this as graphMax in all annotations to scale them all the same
188		*/
189	0	for (AlignmentAnnotation ann : infos)
190		{
191	0	ann.graphMax = maxInformation;
192		}
193		}
194
195		/**
196		* Updates (and first constructs if necessary) an HMM Profile information
197		* content annotation for a sequence. The <code>group</code> argument is null
198		* for the whole alignment annotation, not null for a subgroup annotation. The
199		* updated annotation is added to the <code>infos</code> list. Answers the
200		* maximum information content value of any annotation (for use as a scaling
201		* factor for display).
202		*
203		* @param seq
204		* @param profile
205		* @param group
206		* @param infos
207		* @return
208		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.43
209	0	protected float updateInformationAnnotation(SequenceI seq,...
210		ProfilesI profile, SequenceGroup group,
211		List<AlignmentAnnotation> infos)
212		{
213	0	if (seq == null || profile == null)
214		{
215	0	return 0f;
216		}
217
218	0	AlignmentAnnotation ann = findOrCreateAnnotation(seq, group);
219
220	0	seq.addAlignmentAnnotation(ann);
221	0	infos.add(ann);
222
223	0	float max = AAFrequency.completeInformation(ann, profile,
224		profile.getStartColumn(), profile.getEndColumn() + 1);
225
226	0	return max;
227		}
228
229		/**
230		* A helper method that first searches for the HMM annotation that matches the
231		* group reference (null for the whole alignment annotation). If found, its
232		* sequence reference is updated to the given sequence (the recomputed HMM
233		* consensus sequence). If not found, it is created. This supports both
234		* creating the annotation the first time hmmbuild is run, and updating it if
235		* hmmbuild is re-run.
236		*
237		* @param seq
238		* @param group
239		* @return
240		*/
		0% Uncovered Elements: 27 (27) Complexity: 5 Complexity Density: 0.24
241	0	AlignmentAnnotation findOrCreateAnnotation(SequenceI seq,...
242		SequenceGroup group)
243		{
244		/*
245		* can't use Alignment.findOrCreateAnnotation here because we
246		* want to update, rather than match on, the sequence ref
247		*/
248	0	AlignmentAnnotation info = null;
249
250	0	AlignmentI alignment = alignViewport.getAlignment();
251	0	AlignmentAnnotation[] anns = alignment.getAlignmentAnnotation();
252	0	if (anns != null)
253		{
254	0	for (AlignmentAnnotation ann : anns)
255		{
256	0	if (HMM_CALC_ID.equals(ann.getCalcId()) && group == ann.groupRef)
257		{
258	0	info = ann;
259	0	info.setSequenceRef(seq);
260	0	info.label = seq.getName(); // in case group name changed!
261	0	break;
262		}
263		}
264		}
265
266	0	if (info == null)
267		{
268	0	int aWidth = alignment.getWidth();
269	0	String desc = MessageManager
270		.getString("label.information_description");
271	0	float graphMax = 6.52f; // todo where does this value derive from?
272	0	info = new AlignmentAnnotation(seq.getName(), desc,
273		new Annotation[aWidth], 0f, graphMax,
274		AlignmentAnnotation.BAR_GRAPH);
275	0	info.setCalcId(HMM_CALC_ID);
276	0	info.setSequenceRef(seq);
277	0	info.groupRef = group;
278	0	info.hasText = true;
279	0	alignment.addAnnotation(info);
280		}
281
282	0	return info;
283		}
284		}