Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
MappedFeatures	40	69	30	0.929824693%	Show methods

Class MappedFeatures

Class MappedFeatures	Line # 40	Total Statements 69	Complexity 30	TOTAL Coverage 0.929824693%
MappedFeatures(Mapping,SequenceI,int,char,List<SequenceFeature>)   MappedFeatures(Mapping,SequenceI,int,char,List<SequenceFeature>)	100100	16.016	4.04	1.0 1.0100%
findProteinVariants(SequenceFeature) : String   findProteinVariants(SequenceFeature) : String	148148	47.047	20.020	0.9350649 0.935064993.5%
getLinkedSequenceName() : String   getLinkedSequenceName() : String	272272	1.01	2.02	0.6666667 0.666666766.7%
getMappedPositions(int,int) : int[]   getMappedPositions(int,int) : int[]	294294	2.02	2.02	1.0 1.0100%
isFromCds() : boolean   isFromCds() : boolean	307307	3.03	2.02	0.6 0.660%

 

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
	0.68421054	jalview.datamodel.SequenceFeatureTest.testGetDetailsReport_virtualFeaturejalview.datamodel.SequenceFeatureTest.testGetDetailsReport_virtualFeature	1PASS
	0.1491228	jalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResiduejalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResidue	1PASS

 

Source view

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.HashSet;
24		import java.util.List;
25		import java.util.Set;
26
27		import jalview.io.gff.Gff3Helper;
28		import jalview.schemes.ResidueProperties;
29		import jalview.util.MapList;
30		import jalview.util.MappingUtils;
31		import jalview.util.StringUtils;
32
33		/**
34		* A data bean to hold a list of mapped sequence features (e.g. CDS features
35		* mapped from protein), and the mapping between the sequences. It also provides
36		* a method to derive peptide variants from codon variants.
37		*
38		* @author gmcarstairs
39		*/
		93% Uncovered Elements: 8 (114) Complexity: 30 Complexity Density: 0.43
40		public class MappedFeatures
41		{
42		/*
43		* VEP CSQ:HGVSp (if present) is a short-cut to the protein variant consequence
44		*/
45		private static final String HGV_SP = "HGVSp";
46
47		private static final String CSQ = "CSQ";
48
49		/*
50		* the sequence the mapped features are on
51		*/
52		private final SequenceI featureSequence;
53
54		/*
55		* the mapping between sequences;
56		* NB this could be in either sense (from or to featureSequence)
57		*/
58		private final Mapping mapping;
59
60		/*
61		* features on featureSequence that overlap the mapped positions
62		*/
63		public final List<SequenceFeature> features;
64
65		/*
66		* the residue position in the sequence mapped to
67		*/
68		private final int toPosition;
69
70		/*
71		* the residue at toPosition
72		*/
73		private final char toResidue;
74
75		/*
76		* if the mapping is 3:1 or 1:3 (peptide to CDS), this holds the
77		* mapped positions i.e. codon base positions in CDS; to
78		* support calculation of peptide variants from alleles
79		*/
80		private final int[] codonPos;
81
82		private final char[] baseCodon;
83
84		/**
85		* Constructor
86		*
87		* @param theMapping
88		* sequence mapping (which may be either to, or from, the sequence
89		* holding the linked features)
90		* @param featureSeq
91		* the sequence hosting the virtual features
92		* @param pos
93		* the residue position in the sequence mapped to
94		* @param res
95		* the residue character at position pos
96		* @param theFeatures
97		* list of mapped features found in the 'featureSeq' sequence at the
98		* mapped position(s)
99		*/
		100% Uncovered Elements: 0 (20) Complexity: 4 Complexity Density: 0.25
100	7	public MappedFeatures(Mapping theMapping, SequenceI featureSeq, int pos,...
101		char res, List<SequenceFeature> theFeatures)
102		{
103	7	mapping = theMapping;
104	7	featureSequence = featureSeq;
105	7	toPosition = pos;
106	7	toResidue = res;
107	7	features = theFeatures;
108
109		/*
110		* determine codon positions and canonical codon
111		* for a peptide-to-CDS mapping
112		*/
113	7	int[] codonIntervals = mapping.getMap().locateInFrom(toPosition, toPosition);
114	7	int[] codonPositions = codonIntervals == null ? null
115		: MappingUtils.flattenRanges(codonIntervals);
116	7	if (codonPositions != null && codonPositions.length == 3)
117		{
118	6	codonPos = codonPositions;
119	6	baseCodon = new char[3];
120	6	int cdsStart = featureSequence.getStart();
121	6	baseCodon[0] = Character
122		.toUpperCase(featureSequence.getCharAt(codonPos[0] - cdsStart));
123	6	baseCodon[1] = Character
124		.toUpperCase(featureSequence.getCharAt(codonPos[1] - cdsStart));
125	6	baseCodon[2] = Character
126		.toUpperCase(featureSequence.getCharAt(codonPos[2] - cdsStart));
127		}
128		else
129		{
130	1	codonPos = null;
131	1	baseCodon = null;
132		}
133		}
134
135		/**
136		* Computes and returns comma-delimited HGVS notation peptide variants derived
137		* from codon allele variants. If no variants are found, answers an empty
138		* string. The peptide variant is either simply read from the "CSQ:HGVSp"
139		* attribute if present, else computed based on the "alleles" attribute if
140		* present. If neither attribute is found, no variant (empty string) is
141		* returned.
142		*
143		* @param sf
144		* a sequence feature (which must be one of those held in this
145		* object)
146		* @return
147		*/
		93.5% Uncovered Elements: 5 (77) Complexity: 20 Complexity Density: 0.43
148	13	public String findProteinVariants(SequenceFeature sf)...
149		{
150	13	if (!features.contains(sf) || baseCodon == null)
151		{
152	2	return "";
153		}
154
155		/*
156		* VCF data may already contain the protein consequence
157		*/
158	11	String hgvsp = sf.getValueAsString(CSQ, HGV_SP);
159	11	if (hgvsp != null)
160		{
161	3	int colonPos = hgvsp.lastIndexOf(':');
162	3	if (colonPos >= 0)
163		{
164	2	String var = hgvsp.substring(colonPos + 1);
165	2	if (var.contains("p.")) // sanity check
166		{
167	1	return var;
168		}
169		}
170		}
171
172		/*
173		* otherwise, compute codon and peptide variant
174		*/
175	10	int cdsPos = sf.getBegin();
176	10	if (cdsPos != sf.getEnd())
177		{
178		// not handling multi-locus variant features
179	0	return "";
180		}
181	10	if (cdsPos != codonPos[0] && cdsPos != codonPos[1]
182		&& cdsPos != codonPos[2])
183		{
184		// e.g. feature on intron within spliced codon!
185	0	return "";
186		}
187
188	10	String alls = (String) sf.getValue(Gff3Helper.ALLELES);
189	10	if (alls == null)
190		{
191	1	return "";
192		}
193
194	9	String from3 = StringUtils.toSentenceCase(
195		ResidueProperties.aa2Triplet.get(String.valueOf(toResidue)));
196
197		/*
198		* make a peptide variant for each SNP allele
199		* e.g. C,G,T gives variants G and T for base C
200		*/
201	9	Set<String> variantPeptides = new HashSet<>();
202	9	String[] alleles = alls.toUpperCase().split(",");
203	9	StringBuilder vars = new StringBuilder();
204
205	9	for (String allele : alleles)
206		{
207	23	allele = allele.trim().toUpperCase();
208	23	if (allele.length() > 1 || "-".equals(allele))
209		{
210	4	continue; // multi-locus variant
211		}
212	19	char[] variantCodon = new char[3];
213	19	variantCodon[0] = baseCodon[0];
214	19	variantCodon[1] = baseCodon[1];
215	19	variantCodon[2] = baseCodon[2];
216
217		/*
218		* poke variant base into canonical codon;
219		* ignore first 'allele' (canonical base)
220		*/
221	19	final int i = cdsPos == codonPos[0] ? 0
222	12	: (cdsPos == codonPos[1] ? 1 : 2);
223	19	variantCodon[i] = allele.toUpperCase().charAt(0);
224	19	if (variantCodon[i] == baseCodon[i])
225		{
226	9	continue;
227		}
228	10	String codon = new String(variantCodon);
229	10	String peptide = ResidueProperties.codonTranslate(codon);
230	10	boolean synonymous = toResidue == peptide.charAt(0);
231	10	StringBuilder var = new StringBuilder();
232	10	if (synonymous)
233		{
234		/*
235		* synonymous variant notation e.g. c.1062C>A(p.=)
236		*/
237	3	var.append("c.").append(String.valueOf(cdsPos))
238		.append(String.valueOf(baseCodon[i])).append(">")
239		.append(String.valueOf(variantCodon[i]))
240		.append("(p.=)");
241		}
242		else
243		{
244		/*
245		* missense variant notation e.g. p.Arg355Met
246		*/
247	7	String to3 = ResidueProperties.STOP.equals(peptide) ? "Ter"
248		: StringUtils.toSentenceCase(
249		ResidueProperties.aa2Triplet.get(peptide));
250	7	var.append("p.").append(from3).append(String.valueOf(toPosition))
251		.append(to3);
252		}
253	10	if (!variantPeptides.contains(peptide)) // duplicate consequence
254		{
255	10	variantPeptides.add(peptide);
256	10	if (vars.length() > 0)
257		{
258	1	vars.append(",");
259		}
260	10	vars.append(var);
261		}
262		}
263
264	9	return vars.toString();
265		}
266
267		/**
268		* Answers the name of the linked sequence holding any mapped features
269		*
270		* @return
271		*/
		66.7% Uncovered Elements: 1 (3) Complexity: 2 Complexity Density: 2
272	1	public String getLinkedSequenceName()...
273		{
274	1	return featureSequence == null ? null : featureSequence.getName();
275		}
276
277		/**
278		* Answers the mapped ranges (as one or more [start, end] positions) which
279		* correspond to the given [begin, end] range of the linked sequence.
280		*
281		* <pre>
282		* Example: MappedFeatures with CDS features mapped to peptide
283		* CDS/200-220 gtc aac TGa acGt att AAC tta
284		* mapped to PEP/6-7 WN by mapping [206, 207, 210, 210, 215, 217] to [6, 7]
285		* getMappedPositions(206, 206) should return [6, 6]
286		* getMappedPositions(200, 214) should return [6, 6]
287		* getMappedPositions(210, 215) should return [6, 7]
288		* </pre>
289		*
290		* @param begin
291		* @param end
292		* @return
293		*/
		100% Uncovered Elements: 0 (4) Complexity: 2 Complexity Density: 1
294	8	public int[] getMappedPositions(int begin, int end)...
295		{
296	8	MapList map = mapping.getMap();
297	8	return mapping.to == featureSequence ? map.locateInFrom(begin, end)
298		: map.locateInTo(begin, end);
299		}
300
301		/**
302		* Answers true if the linked features are on coding sequence, false if on
303		* peptide
304		*
305		* @return
306		*/
		60% Uncovered Elements: 2 (5) Complexity: 2 Complexity Density: 0.67
307	2	public boolean isFromCds()...
308		{
309	2	if (mapping.getMap().getFromRatio() == 3)
310		{
311	2	return mapping.to != featureSequence;
312		}
313	0	return mapping.to == featureSequence;
314		}
315		}