Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
EmblEntry	55	232	94	81	0.77183177.2%	Show methods

Class EmblEntry

Class EmblEntry	Line # 55	Total Statements 232	Complexity 94	Uncovered Elements 81	TOTAL Coverage 0.77183177.2%
getAccession() : String   getAccession() : String	9696	1.01	1.01	0.00	1.0 1.0100%
setAccession(String) : void   setAccession(String) : void	105105	1.01	1.01	0.00	1.0 1.0100%
getDbRefs() : Vector<DBRefEntry>   getDbRefs() : Vector<DBRefEntry>	113113	1.01	1.01	0.00	1.0 1.0100%
setDbRefs(Vector<DBRefEntry>) : void   setDbRefs(Vector<DBRefEntry>) : void	122122	1.01	1.01	0.00	1.0 1.0100%
getFeatures() : Vector<EmblFeature>   getFeatures() : Vector<EmblFeature>	130130	1.01	1.01	0.00	1.0 1.0100%
setFeatures(Vector<EmblFeature>) : void   setFeatures(Vector<EmblFeature>) : void	139139	1.01	1.01	0.00	1.0 1.0100%
getKeywords() : Vector<String>   getKeywords() : Vector<String>	147147	1.01	1.01	0.00	1.0 1.0100%
setKeywords(Vector<String>) : void   setKeywords(Vector<String>) : void	156156	1.01	1.01	0.00	1.0 1.0100%
getSequence() : EmblSequence   getSequence() : EmblSequence	164164	1.01	1.01	0.00	1.0 1.0100%
setSequence(EmblSequence) : void   setSequence(EmblSequence) : void	173173	1.01	1.01	0.00	1.0 1.0100%
getSequence(String,List<SequenceI>) : SequenceI   getSequence(String,List<SequenceI>) : SequenceI	186186	22.022	5.05	28.028	0.0 0.00%
makeSequence(String) : SequenceI   makeSequence(String) : SequenceI	243243	5.05	2.02	3.03	0.5714286 0.571428657.1%
parseCodingFeature(EmblFeature,String,SequenceI,List<SequenceI>,SequenceIdMatcher) : void   parseCodingFeature(EmblFeature,String,SequenceI,List<SequenceI>,SequenceIdMatcher) : void	271271	119.0119	36.036	37.037	0.78612715 0.7861271578.6%
makeCdsFeature(String,String,int,int,String,Map<String, String>) : SequenceFeature   makeCdsFeature(String,String,int,int,String,Map<String, String>) : SequenceFeature	607607	12.012	3.03	2.02	0.875 0.87587.5%
getCdsRanges(EmblFeature) : int[]   getCdsRanges(EmblFeature) : int[]	637637	7.07	3.03	4.04	0.5555556 0.555555655.6%
listToArray(List<int[]>) : int[]   listToArray(List<int[]>) : int[]	664664	6.06	1.01	0.00	1.0 1.0100%
adjustForProteinLength(int,int[]) : int[]   adjustForProteinLength(int,int[]) : int[]	686686	27.027	10.010	6.06	0.85365856 0.8536585685.4%
getSequenceVersion() : String   getSequenceVersion() : String	753753	1.01	1.01	0.00	1.0 1.0100%
setSequenceVersion(String) : void   setSequenceVersion(String) : void	758758	1.01	1.01	0.00	1.0 1.0100%
getSequenceLength() : String   getSequenceLength() : String	763763	1.01	1.01	0.00	1.0 1.0100%
setSequenceLength(String) : void   setSequenceLength(String) : void	768768	1.01	1.01	0.00	1.0 1.0100%
getEntryVersion() : String   getEntryVersion() : String	773773	1.01	1.01	0.00	1.0 1.0100%
setEntryVersion(String) : void   setEntryVersion(String) : void	778778	1.01	1.01	0.00	1.0 1.0100%
getMoleculeType() : String   getMoleculeType() : String	783783	1.01	1.01	0.00	1.0 1.0100%
setMoleculeType(String) : void   setMoleculeType(String) : void	788788	1.01	1.01	0.00	1.0 1.0100%
getTopology() : String   getTopology() : String	793793	1.01	1.01	0.00	1.0 1.0100%
setTopology(String) : void   setTopology(String) : void	798798	1.01	1.01	0.00	1.0 1.0100%
getTaxonomicDivision() : String   getTaxonomicDivision() : String	803803	1.01	1.01	0.00	1.0 1.0100%
setTaxonomicDivision(String) : void   setTaxonomicDivision(String) : void	808808	1.01	1.01	0.00	1.0 1.0100%
getDescription() : String   getDescription() : String	813813	1.01	1.01	0.00	1.0 1.0100%
setDescription(String) : void   setDescription(String) : void	818818	1.01	1.01	0.00	1.0 1.0100%
getFirstPublicDate() : String   getFirstPublicDate() : String	823823	1.01	1.01	0.00	1.0 1.0100%
setFirstPublicDate(String) : void   setFirstPublicDate(String) : void	828828	1.01	1.01	0.00	1.0 1.0100%
getFirstPublicRelease() : String   getFirstPublicRelease() : String	833833	1.01	1.01	0.00	1.0 1.0100%
setFirstPublicRelease(String) : void   setFirstPublicRelease(String) : void	838838	1.01	1.01	0.00	1.0 1.0100%
getLastUpdatedDate() : String   getLastUpdatedDate() : String	843843	1.01	1.01	0.00	1.0 1.0100%
setLastUpdatedDate(String) : void   setLastUpdatedDate(String) : void	848848	1.01	1.01	0.00	1.0 1.0100%
getLastUpdatedRelease() : String   getLastUpdatedRelease() : String	853853	1.01	1.01	0.00	1.0 1.0100%
setLastUpdatedRelease(String) : void   setLastUpdatedRelease(String) : void	858858	1.01	1.01	0.00	1.0 1.0100%
getDataClass() : String   getDataClass() : String	863863	1.01	1.01	0.00	1.0 1.0100%
setDataClass(String) : void   setDataClass(String) : void	868868	1.01	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.69295776	jalview.datamodel.xdb.embl.EmblEntryTest.testParseCodingFeaturejalview.datamodel.xdb.embl.EmblEntryTest.testParseCodingFeature	1PASS
	0.1915493	jalview.datamodel.xdb.embl.EmblFileTest.testGetEmblFilejalview.datamodel.xdb.embl.EmblFileTest.testGetEmblFile	1PASS
	0.10140845	jalview.datamodel.xdb.embl.EmblEntryTest.testAdjustForProteinLengthjalview.datamodel.xdb.embl.EmblEntryTest.testAdjustForProteinLength	1PASS
	0.03661972	jalview.datamodel.xdb.embl.EmblEntryTest.testGetCdsRangesjalview.datamodel.xdb.embl.EmblEntryTest.testGetCdsRanges	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.xdb.embl;
22
23		import jalview.analysis.SequenceIdMatcher;
24		import jalview.bin.Cache;
25		import jalview.datamodel.DBRefEntry;
26		import jalview.datamodel.DBRefSource;
27		import jalview.datamodel.FeatureProperties;
28		import jalview.datamodel.Mapping;
29		import jalview.datamodel.Sequence;
30		import jalview.datamodel.SequenceFeature;
31		import jalview.datamodel.SequenceI;
32		import jalview.util.DBRefUtils;
33		import jalview.util.DnaUtils;
34		import jalview.util.MapList;
35		import jalview.util.MappingUtils;
36		import jalview.util.StringUtils;
37
38		import java.text.ParseException;
39		import java.util.Arrays;
40		import java.util.Hashtable;
41		import java.util.List;
42		import java.util.Map;
43		import java.util.Map.Entry;
44		import java.util.Vector;
45		import java.util.regex.Pattern;
46
47		/**
48		* Data model for one entry returned from an EMBL query, as marshalled by a
49		* Castor binding file
50		*
51		* For example: http://www.ebi.ac.uk/ena/data/view/J03321&display=xml
52		*
53		* @see embl_mapping.xml
54		*/
		77.2% Uncovered Elements: 81 (355) Complexity: 94 Complexity Density: 0.41
55		public class EmblEntry
56		{
57		private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
58
59		String accession;
60
61		String entryVersion;
62
63		String sequenceVersion;
64
65		String dataClass;
66
67		String moleculeType;
68
69		String topology;
70
71		String sequenceLength;
72
73		String taxonomicDivision;
74
75		String description;
76
77		String firstPublicDate;
78
79		String firstPublicRelease;
80
81		String lastUpdatedDate;
82
83		String lastUpdatedRelease;
84
85		Vector<String> keywords;
86
87		Vector<DBRefEntry> dbRefs;
88
89		Vector<EmblFeature> features;
90
91		EmblSequence sequence;
92
93		/**
94		* @return the accession
95		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
96	6	public String getAccession()...
97		{
98	6	return accession;
99		}
100
101		/**
102		* @param accession
103		* the accession to set
104		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
105	2	public void setAccession(String accession)...
106		{
107	2	this.accession = accession;
108		}
109
110		/**
111		* @return the dbRefs
112		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
113	14	public Vector<DBRefEntry> getDbRefs()...
114		{
115	14	return dbRefs;
116		}
117
118		/**
119		* @param dbRefs
120		* the dbRefs to set
121		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
122	2	public void setDbRefs(Vector<DBRefEntry> dbRefs)...
123		{
124	2	this.dbRefs = dbRefs;
125		}
126
127		/**
128		* @return the features
129		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
130	18	public Vector<EmblFeature> getFeatures()...
131		{
132	18	return features;
133		}
134
135		/**
136		* @param features
137		* the features to set
138		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
139	2	public void setFeatures(Vector<EmblFeature> features)...
140		{
141	2	this.features = features;
142		}
143
144		/**
145		* @return the keywords
146		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
147	9	public Vector<String> getKeywords()...
148		{
149	9	return keywords;
150		}
151
152		/**
153		* @param keywords
154		* the keywords to set
155		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
156	2	public void setKeywords(Vector<String> keywords)...
157		{
158	2	this.keywords = keywords;
159		}
160
161		/**
162		* @return the sequence
163		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
164	3	public EmblSequence getSequence()...
165		{
166	3	return sequence;
167		}
168
169		/**
170		* @param sequence
171		* the sequence to set
172		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
173	2	public void setSequence(EmblSequence sequence)...
174		{
175	2	this.sequence = sequence;
176		}
177
178		/**
179		* Recover annotated sequences from EMBL file
180		*
181		* @param sourceDb
182		* @param peptides
183		* a list of protein products found so far (to add to)
184		* @return dna dataset sequence with DBRefs and features
185		*/
		0% Uncovered Elements: 28 (28) Complexity: 5 Complexity Density: 0.23
186	0	public SequenceI getSequence(String sourceDb, List<SequenceI> peptides)...
187		{
188	0	SequenceI dna = makeSequence(sourceDb);
189	0	if (dna == null)
190		{
191	0	return null;
192		}
193	0	dna.setDescription(description);
194	0	DBRefEntry retrievedref = new DBRefEntry(sourceDb, getSequenceVersion(),
195		accession);
196	0	dna.addDBRef(retrievedref);
197		// add map to indicate the sequence is a valid coordinate frame for the
198		// dbref
199	0	retrievedref
200		.setMap(new Mapping(null, new int[]
201		{ 1, dna.getLength() }, new int[] { 1, dna.getLength() }, 1,
202		1));
203
204		/*
205		* transform EMBL Database refs to canonical form
206		*/
207	0	if (dbRefs != null)
208		{
209	0	for (DBRefEntry dbref : dbRefs)
210		{
211	0	dbref.setSource(DBRefUtils.getCanonicalName(dbref.getSource()));
212	0	dna.addDBRef(dbref);
213		}
214		}
215
216	0	SequenceIdMatcher matcher = new SequenceIdMatcher(peptides);
217	0	try
218		{
219	0	for (EmblFeature feature : features)
220		{
221	0	if (FeatureProperties.isCodingFeature(sourceDb, feature.getName()))
222		{
223	0	parseCodingFeature(feature, sourceDb, dna, peptides, matcher);
224		}
225		}
226		} catch (Exception e)
227		{
228	0	System.err.println("EMBL Record Features parsing error!");
229	0	System.err
230		.println("Please report the following to help@jalview.org :");
231	0	System.err.println("EMBL Record " + accession);
232	0	System.err.println("Resulted in exception: " + e.getMessage());
233	0	e.printStackTrace(System.err);
234		}
235
236	0	return dna;
237		}
238
239		/**
240		* @param sourceDb
241		* @return
242		*/
		57.1% Uncovered Elements: 3 (7) Complexity: 2 Complexity Density: 0.4
243	1	SequenceI makeSequence(String sourceDb)...
244		{
245	1	if (sequence == null)
246		{
247	0	System.err.println(
248		"No sequence was returned for ENA accession " + accession);
249	0	return null;
250		}
251	1	SequenceI dna = new Sequence(sourceDb + "|" + accession,
252		sequence.getSequence());
253	1	return dna;
254		}
255
256		/**
257		* Extracts coding region and product from a CDS feature and properly decorate
258		* it with annotations.
259		*
260		* @param feature
261		* coding feature
262		* @param sourceDb
263		* source database for the EMBLXML
264		* @param dna
265		* parent dna sequence for this record
266		* @param peptides
267		* list of protein product sequences for Embl entry
268		* @param matcher
269		* helper to match xrefs in already retrieved sequences
270		*/
		78.6% Uncovered Elements: 37 (173) Complexity: 36 Complexity Density: 0.3
271	3	void parseCodingFeature(EmblFeature feature, String sourceDb,...
272		SequenceI dna, List<SequenceI> peptides,
273		SequenceIdMatcher matcher)
274		{
275	3	boolean isEmblCdna = sourceDb.equals(DBRefSource.EMBLCDS);
276
277	3	int[] exons = getCdsRanges(feature);
278
279	3	String translation = null;
280	3	String proteinName = "";
281	3	String proteinId = null;
282	3	Map<String, String> vals = new Hashtable<>();
283
284		/*
285		* codon_start 1/2/3 in EMBL corresponds to phase 0/1/2 in CDS
286		* (phase is required for CDS features in GFF3 format)
287		*/
288	3	int codonStart = 1;
289
290		/*
291		* parse qualifiers, saving protein translation, protein id,
292		* codon start position, product (name), and 'other values'
293		*/
294	3	if (feature.getQualifiers() != null)
295		{
296	3	for (Qualifier q : feature.getQualifiers())
297		{
298	7	String qname = q.getName();
299	7	if (qname.equals("translation"))
300		{
301		// remove all spaces (precompiled String.replaceAll(" ", ""))
302	3	translation = SPACE_PATTERN.matcher(q.getValues()[0])
303		.replaceAll("");
304		}
305	4	else if (qname.equals("protein_id"))
306		{
307	3	proteinId = q.getValues()[0].trim();
308		}
309	1	else if (qname.equals("codon_start"))
310		{
311	0	try
312		{
313	0	codonStart = Integer.parseInt(q.getValues()[0].trim());
314		} catch (NumberFormatException e)
315		{
316	0	System.err.println("Invalid codon_start in XML for " + accession
317		+ ": " + e.getMessage());
318		}
319		}
320	1	else if (qname.equals("product"))
321		{
322		// sometimes name is returned e.g. for V00488
323	0	proteinName = q.getValues()[0].trim();
324		}
325		else
326		{
327		// throw anything else into the additional properties hash
328	1	String[] qvals = q.getValues();
329	1	if (qvals != null)
330		{
331	1	String commaSeparated = StringUtils.arrayToSeparatorList(qvals,
332		",");
333	1	vals.put(qname, commaSeparated);
334		}
335		}
336		}
337		}
338
339	3	DBRefEntry proteinToEmblProteinRef = null;
340	3	exons = MappingUtils.removeStartPositions(codonStart - 1, exons);
341
342	3	SequenceI product = null;
343	3	Mapping dnaToProteinMapping = null;
344	3	if (translation != null && proteinName != null && proteinId != null)
345		{
346	3	int translationLength = translation.length();
347
348		/*
349		* look for product in peptides list, if not found, add it
350		*/
351	3	product = matcher.findIdMatch(proteinId);
352	3	if (product == null)
353		{
354	3	product = new Sequence(proteinId, translation, 1,
355		translationLength);
356	3	product.setDescription(((proteinName.length() == 0)
357		? "Protein Product from " + sourceDb
358		: proteinName));
359	3	peptides.add(product);
360	3	matcher.add(product);
361		}
362
363		// we have everything - create the mapping and perhaps the protein
364		// sequence
365	3	if (exons == null || exons.length == 0)
366		{
367		/*
368		* workaround until we handle dna location for CDS sequence
369		* e.g. location="X53828.1:60..1058" correctly
370		*/
371	0	System.err.println(
372		"Implementation Notice: EMBLCDS records not properly supported yet - Making up the CDNA region of this sequence... may be incorrect ("
373		+ sourceDb + ":" + getAccession() + ")");
374	0	int dnaLength = dna.getLength();
375	0	if (translationLength * 3 == (1 - codonStart + dnaLength))
376		{
377	0	System.err.println(
378		"Not allowing for additional stop codon at end of cDNA fragment... !");
379		// this might occur for CDS sequences where no features are marked
380	0	exons = new int[] { dna.getStart() + (codonStart - 1),
381		dna.getEnd() };
382	0	dnaToProteinMapping = new Mapping(product, exons,
383		new int[]
384		{ 1, translationLength }, 3, 1);
385		}
386	0	if ((translationLength + 1) * 3 == (1 - codonStart + dnaLength))
387		{
388	0	System.err.println(
389		"Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
390	0	exons = new int[] { dna.getStart() + (codonStart - 1),
391		dna.getEnd() - 3 };
392	0	dnaToProteinMapping = new Mapping(product, exons,
393		new int[]
394		{ 1, translationLength }, 3, 1);
395		}
396		}
397		else
398		{
399		// Trim the exon mapping if necessary - the given product may only be a
400		// fragment of a larger protein. (EMBL:AY043181 is an example)
401
402	3	if (isEmblCdna)
403		{
404		// TODO: Add a DbRef back to the parent EMBL sequence with the exon
405		// map
406		// if given a dataset reference, search dataset for parent EMBL
407		// sequence if it exists and set its map
408		// make a new feature annotating the coding contig
409		}
410		else
411		{
412		// final product length truncation check
413	3	int[] cdsRanges = adjustForProteinLength(translationLength,
414		exons);
415	3	dnaToProteinMapping = new Mapping(product, cdsRanges,
416		new int[]
417		{ 1, translationLength }, 3, 1);
418	3	if (product != null)
419		{
420		/*
421		* make xref with mapping from protein to EMBL dna
422		*/
423	3	DBRefEntry proteinToEmblRef = new DBRefEntry(DBRefSource.EMBL,
424		getSequenceVersion(), proteinId,
425		new Mapping(dnaToProteinMapping.getMap().getInverse()));
426	3	product.addDBRef(proteinToEmblRef);
427
428		/*
429		* make xref from protein to EMBLCDS; we assume here that the
430		* CDS sequence version is same as dna sequence (?!)
431		*/
432	3	MapList proteinToCdsMapList = new MapList(
433		new int[]
434		{ 1, translationLength },
435		new int[]
436		{ 1 + (codonStart - 1),
437		(codonStart - 1) + 3 * translationLength },
438		1, 3);
439	3	DBRefEntry proteinToEmblCdsRef = new DBRefEntry(
440		DBRefSource.EMBLCDS, getSequenceVersion(), proteinId,
441		new Mapping(proteinToCdsMapList));
442	3	product.addDBRef(proteinToEmblCdsRef);
443
444		/*
445		* make 'direct' xref from protein to EMBLCDSPROTEIN
446		*/
447	3	proteinToEmblProteinRef = new DBRefEntry(proteinToEmblCdsRef);
448	3	proteinToEmblProteinRef.setSource(DBRefSource.EMBLCDSProduct);
449	3	proteinToEmblProteinRef.setMap(null);
450	3	product.addDBRef(proteinToEmblProteinRef);
451		}
452		}
453		}
454
455		/*
456		* add cds features to dna sequence
457		*/
458	3	String cds = feature.getName(); // "CDS"
459	7	for (int xint = 0; exons != null && xint < exons.length - 1; xint += 2)
460		{
461	4	int exonStart = exons[xint];
462	4	int exonEnd = exons[xint + 1];
463	4	int begin = Math.min(exonStart, exonEnd);
464	4	int end = Math.max(exonStart, exonEnd);
465	4	int exonNumber = xint / 2 + 1;
466	4	String desc = String.format("Exon %d for protein '%s' EMBLCDS:%s",
467		exonNumber, proteinName, proteinId);
468
469	4	SequenceFeature sf = makeCdsFeature(cds, desc, begin, end,
470		sourceDb, vals);
471
472	4	sf.setEnaLocation(feature.getLocation());
473	4	boolean forwardStrand = exonStart <= exonEnd;
474	4	sf.setStrand(forwardStrand ? "+" : "-");
475	4	sf.setPhase(String.valueOf(codonStart - 1));
476	4	sf.setValue(FeatureProperties.EXONPOS, exonNumber);
477	4	sf.setValue(FeatureProperties.EXONPRODUCT, proteinName);
478
479	4	dna.addSequenceFeature(sf);
480		}
481		}
482
483		/*
484		* add feature dbRefs to sequence, and mappings for Uniprot xrefs
485		*/
486	3	boolean hasUniprotDbref = false;
487	3	if (feature.dbRefs != null)
488		{
489	2	boolean mappingUsed = false;
490	2	for (DBRefEntry ref : feature.dbRefs)
491		{
492		/*
493		* ensure UniProtKB/Swiss-Prot converted to UNIPROT
494		*/
495	3	String source = DBRefUtils.getCanonicalName(ref.getSource());
496	3	ref.setSource(source);
497	3	DBRefEntry proteinDbRef = new DBRefEntry(ref.getSource(),
498		ref.getVersion(), ref.getAccessionId());
499	3	if (source.equals(DBRefSource.UNIPROT))
500		{
501	3	String proteinSeqName = DBRefSource.UNIPROT + "|"
502		+ ref.getAccessionId();
503	3	if (dnaToProteinMapping != null
504		&& dnaToProteinMapping.getTo() != null)
505		{
506	3	if (mappingUsed)
507		{
508		/*
509		* two or more Uniprot xrefs for the same CDS -
510		* each needs a distinct Mapping (as to a different sequence)
511		*/
512	1	dnaToProteinMapping = new Mapping(dnaToProteinMapping);
513		}
514	3	mappingUsed = true;
515
516		/*
517		* try to locate the protein mapped to (possibly by a
518		* previous CDS feature); if not found, construct it from
519		* the EMBL translation
520		*/
521	3	SequenceI proteinSeq = matcher.findIdMatch(proteinSeqName);
522	3	if (proteinSeq == null)
523		{
524	3	proteinSeq = new Sequence(proteinSeqName,
525		product.getSequenceAsString());
526	3	matcher.add(proteinSeq);
527	3	peptides.add(proteinSeq);
528		}
529	3	dnaToProteinMapping.setTo(proteinSeq);
530	3	dnaToProteinMapping.setMappedFromId(proteinId);
531	3	proteinSeq.addDBRef(proteinDbRef);
532	3	ref.setMap(dnaToProteinMapping);
533		}
534	3	hasUniprotDbref = true;
535		}
536	3	if (product != null)
537		{
538		/*
539		* copy feature dbref to our protein product
540		*/
541	3	DBRefEntry pref = proteinDbRef;
542	3	pref.setMap(null); // reference is direct
543	3	product.addDBRef(pref);
544		// Add converse mapping reference
545	3	if (dnaToProteinMapping != null)
546		{
547	3	Mapping pmap = new Mapping(dna,
548		dnaToProteinMapping.getMap().getInverse());
549	3	pref = new DBRefEntry(sourceDb, getSequenceVersion(),
550		this.getAccession());
551	3	pref.setMap(pmap);
552	3	if (dnaToProteinMapping.getTo() != null)
553		{
554	3	dnaToProteinMapping.getTo().addDBRef(pref);
555		}
556		}
557		}
558	3	dna.addDBRef(ref);
559		}
560		}
561
562		/*
563		* if we have a product (translation) but no explicit Uniprot dbref
564		* (example: EMBL AAFI02000057 protein_id EAL65544.1)
565		* then construct mappings to an assumed EMBLCDSPROTEIN accession
566		*/
567	3	if (!hasUniprotDbref && product != null)
568		{
569	1	if (proteinToEmblProteinRef == null)
570		{
571		// assuming CDSPROTEIN sequence version = dna version (?!)
572	0	proteinToEmblProteinRef = new DBRefEntry(DBRefSource.EMBLCDSProduct,
573		getSequenceVersion(), proteinId);
574		}
575	1	product.addDBRef(proteinToEmblProteinRef);
576
577	1	if (dnaToProteinMapping != null
578		&& dnaToProteinMapping.getTo() != null)
579		{
580	1	DBRefEntry dnaToEmblProteinRef = new DBRefEntry(
581		DBRefSource.EMBLCDSProduct, getSequenceVersion(),
582		proteinId);
583	1	dnaToEmblProteinRef.setMap(dnaToProteinMapping);
584	1	dnaToProteinMapping.setMappedFromId(proteinId);
585	1	dna.addDBRef(dnaToEmblProteinRef);
586		}
587		}
588		}
589
590		/**
591		* Helper method to construct a SequenceFeature for one cds range
592		*
593		* @param type
594		* feature type ("CDS")
595		* @param desc
596		* description
597		* @param begin
598		* start position
599		* @param end
600		* end position
601		* @param group
602		* feature group
603		* @param vals
604		* map of 'miscellaneous values' for feature
605		* @return
606		*/
		87.5% Uncovered Elements: 2 (16) Complexity: 3 Complexity Density: 0.25
607	4	protected SequenceFeature makeCdsFeature(String type, String desc,...
608		int begin, int end, String group, Map<String, String> vals)
609		{
610	4	SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
611	4	if (!vals.isEmpty())
612		{
613	1	StringBuilder sb = new StringBuilder();
614	1	boolean first = true;
615	1	for (Entry<String, String> val : vals.entrySet())
616		{
617	1	if (!first)
618		{
619	0	sb.append(";");
620		}
621	1	sb.append(val.getKey()).append("=").append(val.getValue());
622	1	first = false;
623	1	sf.setValue(val.getKey(), val.getValue());
624		}
625	1	sf.setAttributes(sb.toString());
626		}
627	4	return sf;
628		}
629
630		/**
631		* Returns the CDS positions as a single array of [start, end, start, end...]
632		* positions. If on the reverse strand, these will be in descending order.
633		*
634		* @param feature
635		* @return
636		*/
		55.6% Uncovered Elements: 4 (9) Complexity: 3 Complexity Density: 0.43
637	4	protected int[] getCdsRanges(EmblFeature feature)...
638		{
639	4	if (feature.location == null)
640		{
641	0	return new int[] {};
642		}
643
644	4	try
645		{
646	4	List<int[]> ranges = DnaUtils.parseLocation(feature.location);
647	4	return listToArray(ranges);
648		} catch (ParseException e)
649		{
650	0	Cache.log.warn(
651		String.format("Not parsing inexact CDS location %s in ENA %s",
652		feature.location, this.accession));
653	0	return new int[] {};
654		}
655		}
656
657		/**
658		* Converts a list of [start, end] ranges to a single array of [start, end,
659		* start, end ...]
660		*
661		* @param ranges
662		* @return
663		*/
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17
664	4	int[] listToArray(List<int[]> ranges)...
665		{
666	4	int[] result = new int[ranges.size() * 2];
667	4	int i = 0;
668	4	for (int[] range : ranges)
669		{
670	9	result[i++] = range[0];
671	9	result[i++] = range[1];
672		}
673	4	return result;
674		}
675
676		/**
677		* Truncates (if necessary) the exon intervals to match 3 times the length of
678		* the protein; also accepts 3 bases longer (for stop codon not included in
679		* protein)
680		*
681		* @param proteinLength
682		* @param exon
683		* an array of [start, end, start, end...] intervals
684		* @return the same array (if unchanged) or a truncated copy
685		*/
		85.4% Uncovered Elements: 6 (41) Complexity: 10 Complexity Density: 0.37
686	9	static int[] adjustForProteinLength(int proteinLength, int[] exon)...
687		{
688	9	if (proteinLength <= 0 || exon == null)
689		{
690	0	return exon;
691		}
692	9	int expectedCdsLength = proteinLength * 3;
693	9	int exonLength = MappingUtils.getLength(Arrays.asList(exon));
694
695		/*
696		* if exon length matches protein, or is shorter, or longer by the
697		* length of a stop codon (3 bases), then leave it unchanged
698		*/
699	9	if (expectedCdsLength >= exonLength
700		|| expectedCdsLength == exonLength - 3)
701		{
702	6	return exon;
703		}
704
705	3	int origxon[];
706	3	int sxpos = -1;
707	3	int endxon = 0;
708	3	origxon = new int[exon.length];
709	3	System.arraycopy(exon, 0, origxon, 0, exon.length);
710	3	int cdspos = 0;
711	7	for (int x = 0; x < exon.length; x += 2)
712		{
713	7	cdspos += Math.abs(exon[x + 1] - exon[x]) + 1;
714	7	if (expectedCdsLength <= cdspos)
715		{
716		// advanced beyond last codon.
717	3	sxpos = x;
718	3	if (expectedCdsLength != cdspos)
719		{
720		// System.err
721		// .println("Truncating final exon interval on region by "
722		// + (cdspos - cdslength));
723		}
724
725		/*
726		* shrink the final exon - reduce end position if forward
727		* strand, increase it if reverse
728		*/
729	3	if (exon[x + 1] >= exon[x])
730		{
731	3	endxon = exon[x + 1] - cdspos + expectedCdsLength;
732		}
733		else
734		{
735	0	endxon = exon[x + 1] + cdspos - expectedCdsLength;
736		}
737	3	break;
738		}
739		}
740
741	3	if (sxpos != -1)
742		{
743		// and trim the exon interval set if necessary
744	3	int[] nxon = new int[sxpos + 2];
745	3	System.arraycopy(exon, 0, nxon, 0, sxpos + 2);
746	3	nxon[sxpos + 1] = endxon; // update the end boundary for the new exon
747		// set
748	3	exon = nxon;
749		}
750	3	return exon;
751		}
752
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
753	13	public String getSequenceVersion()...
754		{
755	13	return sequenceVersion;
756		}
757
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
758	2	public void setSequenceVersion(String sequenceVersion)...
759		{
760	2	this.sequenceVersion = sequenceVersion;
761		}
762
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
763	3	public String getSequenceLength()...
764		{
765	3	return sequenceLength;
766		}
767
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
768	2	public void setSequenceLength(String sequenceLength)...
769		{
770	2	this.sequenceLength = sequenceLength;
771		}
772
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
773	3	public String getEntryVersion()...
774		{
775	3	return entryVersion;
776		}
777
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
778	2	public void setEntryVersion(String entryVersion)...
779		{
780	2	this.entryVersion = entryVersion;
781		}
782
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
783	3	public String getMoleculeType()...
784		{
785	3	return moleculeType;
786		}
787
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
788	2	public void setMoleculeType(String moleculeType)...
789		{
790	2	this.moleculeType = moleculeType;
791		}
792
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
793	3	public String getTopology()...
794		{
795	3	return topology;
796		}
797
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
798	2	public void setTopology(String topology)...
799		{
800	2	this.topology = topology;
801		}
802
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
803	3	public String getTaxonomicDivision()...
804		{
805	3	return taxonomicDivision;
806		}
807
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
808	2	public void setTaxonomicDivision(String taxonomicDivision)...
809		{
810	2	this.taxonomicDivision = taxonomicDivision;
811		}
812
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
813	3	public String getDescription()...
814		{
815	3	return description;
816		}
817
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
818	2	public void setDescription(String description)...
819		{
820	2	this.description = description;
821		}
822
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
823	4	public String getFirstPublicDate()...
824		{
825	4	return firstPublicDate;
826		}
827
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
828	2	public void setFirstPublicDate(String firstPublicDate)...
829		{
830	2	this.firstPublicDate = firstPublicDate;
831		}
832
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
833	4	public String getFirstPublicRelease()...
834		{
835	4	return firstPublicRelease;
836		}
837
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
838	2	public void setFirstPublicRelease(String firstPublicRelease)...
839		{
840	2	this.firstPublicRelease = firstPublicRelease;
841		}
842
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
843	3	public String getLastUpdatedDate()...
844		{
845	3	return lastUpdatedDate;
846		}
847
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
848	2	public void setLastUpdatedDate(String lastUpdatedDate)...
849		{
850	2	this.lastUpdatedDate = lastUpdatedDate;
851		}
852
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
853	3	public String getLastUpdatedRelease()...
854		{
855	3	return lastUpdatedRelease;
856		}
857
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
858	2	public void setLastUpdatedRelease(String lastUpdatedRelease)...
859		{
860	2	this.lastUpdatedRelease = lastUpdatedRelease;
861		}
862
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
863	3	public String getDataClass()...
864		{
865	3	return dataClass;
866		}
867
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
868	2	public void setDataClass(String dataClass)...
869		{
870	2	this.dataClass = dataClass;
871		}
872		}