Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
MappedFeatures	42	69	30	0.868421186.8%	Show methods

Class MappedFeatures

Class MappedFeatures	Line # 42	Total Statements 69	Complexity 30	TOTAL Coverage 0.868421186.8%
MappedFeatures(Mapping,SequenceI,int,char,List<SequenceFeature>)   MappedFeatures(Mapping,SequenceI,int,char,List<SequenceFeature>)	102102	16.016	4.04	1.0 1.0100%
findProteinVariants(SequenceFeature) : String   findProteinVariants(SequenceFeature) : String	151151	47.047	20.020	0.9350649 0.935064993.5%
getLinkedSequenceName() : String   getLinkedSequenceName() : String	274274	1.01	2.02	0.0 0.00%
getMappedPositions(int,int) : int[]   getMappedPositions(int,int) : int[]	296296	2.02	2.02	1.0 1.0100%
isFromCds() : boolean   isFromCds() : boolean	309309	3.03	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.7719298	jalview.datamodel.MappedFeaturesTest.testFindProteinVariantsjalview.datamodel.MappedFeaturesTest.testFindProteinVariants	1PASS
	0.7017544	jalview.io.SequenceAnnotationReportTest.testAppendFeature_virtualFeaturejalview.io.SequenceAnnotationReportTest.testAppendFeature_virtualFeature	1PASS
	0.1491228	jalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResiduejalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResidue	1PASS

 

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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
23		import java.util.Locale;
24
25		import java.util.HashSet;
26		import java.util.List;
27		import java.util.Set;
28
29		import jalview.io.gff.Gff3Helper;
30		import jalview.schemes.ResidueProperties;
31		import jalview.util.MapList;
32		import jalview.util.MappingUtils;
33		import jalview.util.StringUtils;
34
35		/**
36		* A data bean to hold a list of mapped sequence features (e.g. CDS features
37		* mapped from protein), and the mapping between the sequences. It also provides
38		* a method to derive peptide variants from codon variants.
39		*
40		* @author gmcarstairs
41		*/
		86.8% Uncovered Elements: 15 (114) Complexity: 30 Complexity Density: 0.43
42		public class MappedFeatures
43		{
44		/*
45		* VEP CSQ:HGVSp (if present) is a short-cut to the protein variant consequence
46		*/
47		private static final String HGV_SP = "HGVSp";
48
49		private static final String CSQ = "CSQ";
50
51		/*
52		* the sequence the mapped features are on
53		*/
54		private final SequenceI featureSequence;
55
56		/*
57		* the mapping between sequences;
58		* NB this could be in either sense (from or to featureSequence)
59		*/
60		private final Mapping mapping;
61
62		/*
63		* features on featureSequence that overlap the mapped positions
64		*/
65		public final List<SequenceFeature> features;
66
67		/*
68		* the residue position in the sequence mapped to
69		*/
70		private final int toPosition;
71
72		/*
73		* the residue at toPosition
74		*/
75		private final char toResidue;
76
77		/*
78		* if the mapping is 3:1 or 1:3 (peptide to CDS), this holds the
79		* mapped positions i.e. codon base positions in CDS; to
80		* support calculation of peptide variants from alleles
81		*/
82		private final int[] codonPos;
83
84		private final char[] baseCodon;
85
86		/**
87		* Constructor
88		*
89		* @param theMapping
90		* sequence mapping (which may be either to, or from, the sequence
91		* holding the linked features)
92		* @param featureSeq
93		* the sequence hosting the virtual features
94		* @param pos
95		* the residue position in the sequence mapped to
96		* @param res
97		* the residue character at position pos
98		* @param theFeatures
99		* list of mapped features found in the 'featureSeq' sequence at the
100		* mapped position(s)
101		*/
		100% Uncovered Elements: 0 (20) Complexity: 4 Complexity Density: 0.25
102	6	public MappedFeatures(Mapping theMapping, SequenceI featureSeq, int pos,...
103		char res, List<SequenceFeature> theFeatures)
104		{
105	6	mapping = theMapping;
106	6	featureSequence = featureSeq;
107	6	toPosition = pos;
108	6	toResidue = res;
109	6	features = theFeatures;
110
111		/*
112		* determine codon positions and canonical codon
113		* for a peptide-to-CDS mapping
114		*/
115	6	int[] codonIntervals = mapping.getMap().locateInFrom(toPosition,
116		toPosition);
117	6	int[] codonPositions = codonIntervals == null ? null
118		: MappingUtils.flattenRanges(codonIntervals);
119	6	if (codonPositions != null && codonPositions.length == 3)
120		{
121	5	codonPos = codonPositions;
122	5	baseCodon = new char[3];
123	5	int cdsStart = featureSequence.getStart();
124	5	baseCodon[0] = Character.toUpperCase(
125		featureSequence.getCharAt(codonPos[0] - cdsStart));
126	5	baseCodon[1] = Character.toUpperCase(
127		featureSequence.getCharAt(codonPos[1] - cdsStart));
128	5	baseCodon[2] = Character.toUpperCase(
129		featureSequence.getCharAt(codonPos[2] - cdsStart));
130		}
131		else
132		{
133	1	codonPos = null;
134	1	baseCodon = null;
135		}
136		}
137
138		/**
139		* Computes and returns comma-delimited HGVS notation peptide variants derived
140		* from codon allele variants. If no variants are found, answers an empty
141		* string. The peptide variant is either simply read from the "CSQ:HGVSp"
142		* attribute if present, else computed based on the "alleles" attribute if
143		* present. If neither attribute is found, no variant (empty string) is
144		* returned.
145		*
146		* @param sf
147		* a sequence feature (which must be one of those held in this
148		* object)
149		* @return
150		*/
		93.5% Uncovered Elements: 5 (77) Complexity: 20 Complexity Density: 0.43
151	12	public String findProteinVariants(SequenceFeature sf)...
152		{
153	12	if (!features.contains(sf) || baseCodon == null)
154		{
155	2	return "";
156		}
157
158		/*
159		* VCF data may already contain the protein consequence
160		*/
161	10	String hgvsp = sf.getValueAsString(CSQ, HGV_SP);
162	10	if (hgvsp != null)
163		{
164	3	int colonPos = hgvsp.lastIndexOf(':');
165	3	if (colonPos >= 0)
166		{
167	2	String var = hgvsp.substring(colonPos + 1);
168	2	if (var.contains("p.")) // sanity check
169		{
170	1	return var;
171		}
172		}
173		}
174
175		/*
176		* otherwise, compute codon and peptide variant
177		*/
178	9	int cdsPos = sf.getBegin();
179	9	if (cdsPos != sf.getEnd())
180		{
181		// not handling multi-locus variant features
182	0	return "";
183		}
184	9	if (cdsPos != codonPos[0] && cdsPos != codonPos[1]
185		&& cdsPos != codonPos[2])
186		{
187		// e.g. feature on intron within spliced codon!
188	0	return "";
189		}
190
191	9	String alls = (String) sf.getValue(Gff3Helper.ALLELES);
192	9	if (alls == null)
193		{
194	1	return "";
195		}
196
197	8	String from3 = StringUtils.toSentenceCase(
198		ResidueProperties.aa2Triplet.get(String.valueOf(toResidue)));
199
200		/*
201		* make a peptide variant for each SNP allele
202		* e.g. C,G,T gives variants G and T for base C
203		*/
204	8	Set<String> variantPeptides = new HashSet<>();
205	8	String[] alleles = alls.toUpperCase(Locale.ROOT).split(",");
206	8	StringBuilder vars = new StringBuilder();
207
208	8	for (String allele : alleles)
209		{
210	21	allele = allele.trim().toUpperCase(Locale.ROOT);
211	21	if (allele.length() > 1 || "-".equals(allele))
212		{
213	4	continue; // multi-locus variant
214		}
215	17	char[] variantCodon = new char[3];
216	17	variantCodon[0] = baseCodon[0];
217	17	variantCodon[1] = baseCodon[1];
218	17	variantCodon[2] = baseCodon[2];
219
220		/*
221		* poke variant base into canonical codon;
222		* ignore first 'allele' (canonical base)
223		*/
224	17	final int i = cdsPos == codonPos[0] ? 0
225	10	: (cdsPos == codonPos[1] ? 1 : 2);
226	17	variantCodon[i] = allele.toUpperCase(Locale.ROOT).charAt(0);
227	17	if (variantCodon[i] == baseCodon[i])
228		{
229	8	continue;
230		}
231	9	String codon = new String(variantCodon);
232	9	String peptide = ResidueProperties.codonTranslate(codon);
233	9	boolean synonymous = toResidue == peptide.charAt(0);
234	9	StringBuilder var = new StringBuilder();
235	9	if (synonymous)
236		{
237		/*
238		* synonymous variant notation e.g. c.1062C>A(p.=)
239		*/
240	3	var.append("c.").append(String.valueOf(cdsPos))
241		.append(String.valueOf(baseCodon[i])).append(">")
242		.append(String.valueOf(variantCodon[i])).append("(p.=)");
243		}
244		else
245		{
246		/*
247		* missense variant notation e.g. p.Arg355Met
248		*/
249	6	String to3 = ResidueProperties.STOP.equals(peptide) ? "Ter"
250		: StringUtils.toSentenceCase(
251		ResidueProperties.aa2Triplet.get(peptide));
252	6	var.append("p.").append(from3).append(String.valueOf(toPosition))
253		.append(to3);
254		}
255	9	if (!variantPeptides.contains(peptide)) // duplicate consequence
256		{
257	9	variantPeptides.add(peptide);
258	9	if (vars.length() > 0)
259		{
260	1	vars.append(",");
261		}
262	9	vars.append(var);
263		}
264		}
265
266	8	return vars.toString();
267		}
268
269		/**
270		* Answers the name of the linked sequence holding any mapped features
271		*
272		* @return
273		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
274	0	public String getLinkedSequenceName()...
275		{
276	0	return featureSequence == null ? null : featureSequence.getName();
277		}
278
279		/**
280		* Answers the mapped ranges (as one or more [start, end] positions) which
281		* correspond to the given [begin, end] range of the linked sequence.
282		*
283		* <pre>
284		* Example: MappedFeatures with CDS features mapped to peptide
285		* CDS/200-220 gtc aac TGa acGt att AAC tta
286		* mapped to PEP/6-7 WN by mapping [206, 207, 210, 210, 215, 217] to [6, 7]
287		* getMappedPositions(206, 206) should return [6, 6]
288		* getMappedPositions(200, 214) should return [6, 6]
289		* getMappedPositions(210, 215) should return [6, 7]
290		* </pre>
291		*
292		* @param begin
293		* @param end
294		* @return
295		*/
		100% Uncovered Elements: 0 (4) Complexity: 2 Complexity Density: 1
296	3	public int[] getMappedPositions(int begin, int end)...
297		{
298	3	MapList map = mapping.getMap();
299	3	return mapping.to == featureSequence ? map.getOverlapsInFrom(begin, end)
300		: map.getOverlapsInTo(begin, end);
301		}
302
303		/**
304		* Answers true if the linked features are on coding sequence, false if on
305		* peptide
306		*
307		* @return
308		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
309	0	public boolean isFromCds()...
310		{
311	0	if (mapping.getMap().getFromRatio() == 3)
312		{
313	0	return mapping.to != featureSequence;
314		}
315	0	return mapping.to == featureSequence;
316		}
317		}