Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
TDBeacons	69	135	53	0.00%	Show methods

Class TDBeacons

Class TDBeacons	Line # 69	Total Statements 135	Complexity 53	TOTAL Coverage 0.00%
TDBeacons()   TDBeacons()	8080	1.01	1.01	0.0 0.00%
getDomain() : String   getDomain() : String	8585	1.01	1.01	0.0 0.00%
getAccessionSeparator() : String   getAccessionSeparator() : String	9696	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	107107	1.01	1.01	0.0 0.00%
getDbSource() : String   getDbSource() : String	118118	1.01	1.01	0.0 0.00%
getDbVersion() : String   getDbVersion() : String	129129	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	140140	18.018	3.03	0.0 0.00%
uniprotEntryToSequence(Entry) : SequenceI   uniprotEntryToSequence(Entry) : SequenceI	184184	45.045	11.011	0.0 0.00%
getDescription(FeatureType) : String   getDescription(FeatureType) : String	307307	34.034	15.015	0.0 0.00%
getProperty(List<PropertyType>,String) : String   getProperty(List<PropertyType>,String) : String	400400	7.07	3.03	0.0 0.00%
getUniprotEntryDescription(Entry) : String   getUniprotEntryDescription(Entry) : String	423423	4.04	3.03	0.0 0.00%
getUniprotEntryId(Entry) : String   getUniprotEntryId(Entry) : String	443443	6.06	2.02	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	462462	1.01	3.03	0.0 0.00%
getTestQuery() : String   getTestQuery() : String	473473	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	479479	1.01	1.01	0.0 0.00%
getTier() : int   getTier() : int	485485	1.01	1.01	0.0 0.00%
getUniprotEntries(InputStream) : List<Entry>   getUniprotEntries(InputStream) : List<Entry>	499499	11.011	4.04	0.0 0.00%

 

Contributing tests

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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.ws.dbsources;
22
23		import java.io.InputStream;
24		import java.net.URL;
25		import java.net.URLConnection;
26		import java.util.ArrayList;
27		import java.util.List;
28		import java.util.Locale;
29		import java.util.Vector;
30
31		import javax.xml.bind.JAXBContext;
32		import javax.xml.bind.JAXBElement;
33		import javax.xml.bind.JAXBException;
34		import javax.xml.stream.FactoryConfigurationError;
35		import javax.xml.stream.XMLInputFactory;
36		import javax.xml.stream.XMLStreamException;
37		import javax.xml.stream.XMLStreamReader;
38
39		import com.stevesoft.pat.Regex;
40
41		import jalview.bin.Cache;
42		import jalview.datamodel.Alignment;
43		import jalview.datamodel.AlignmentI;
44		import jalview.datamodel.DBRefEntry;
45		import jalview.datamodel.DBRefSource;
46		import jalview.datamodel.PDBEntry;
47		import jalview.datamodel.Sequence;
48		import jalview.datamodel.SequenceFeature;
49		import jalview.datamodel.SequenceI;
50		import jalview.schemes.ResidueProperties;
51		import jalview.util.HttpUtils;
52		import jalview.util.StringUtils;
53		import jalview.ws.seqfetcher.DbSourceProxyImpl;
54		import jalview.xml.binding.uniprot.DbReferenceType;
55		import jalview.xml.binding.uniprot.Entry;
56		import jalview.xml.binding.uniprot.FeatureType;
57		import jalview.xml.binding.uniprot.LocationType;
58		import jalview.xml.binding.uniprot.PositionType;
59		import jalview.xml.binding.uniprot.PropertyType;
60
61		/**
62		* This class queries the Uniprot database for sequence data, unmarshals the
63		* returned XML, and converts it to Jalview Sequence records (including attached
64		* database references and sequence features)
65		*
66		* @author JimP
67		*
68		*/
		0% Uncovered Elements: 204 (204) Complexity: 53 Complexity Density: 0.39
69		public class TDBeacons extends DbSourceProxyImpl
70		{
71		private static final String DEFAULT_UNIPROT_DOMAIN = "https://www.uniprot.org";
72
73		private static final String BAR_DELIMITER = "|";
74
75		private static final String DEFAULT_THREEDBEACONS_DOMAIN = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/summary/";
76
77		/**
78		* Constructor
79		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
80	0	public TDBeacons()...
81		{
82	0	super();
83		}
84
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
85	0	private String getDomain()...
86		{
87	0	return Cache.getDefault("UNIPROT_DOMAIN", DEFAULT_UNIPROT_DOMAIN);
88		// return Cache.getDefault("3DB_DOMAIN", DEFAULT_THREEDBEACONS_DOMAIN );
89		}
90
91		/*
92		* (non-Javadoc)
93		*
94		* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
95		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
96	0	@Override...
97		public String getAccessionSeparator()
98		{
99	0	return null;
100		}
101
102		/*
103		* (non-Javadoc)
104		*
105		* @see jalview.ws.DbSourceProxy#getAccessionValidator()
106		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
107	0	@Override...
108		public Regex getAccessionValidator()
109		{
110	0	return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
111		}
112
113		/*
114		* (non-Javadoc)
115		*
116		* @see jalview.ws.DbSourceProxy#getDbSource()
117		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
118	0	@Override...
119		public String getDbSource()
120		{
121	0	return "3d-beacons";// DBRefSource.UNIPROT;
122		}
123
124		/*
125		* (non-Javadoc)
126		*
127		* @see jalview.ws.DbSourceProxy#getDbVersion()
128		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
129	0	@Override...
130		public String getDbVersion()
131		{
132	0	return "0"; // we really don't know what version we're on.
133		}
134
135		/*
136		* (non-Javadoc)
137		*
138		* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
139		*/
		0% Uncovered Elements: 20 (20) Complexity: 3 Complexity Density: 0.17
140	0	@Override...
141		public AlignmentI getSequenceRecords(String queries) throws Exception
142		{
143	0	startQuery();
144	0	try
145		{
146	0	queries = queries.toUpperCase(Locale.ROOT).replaceAll(
147		"(UNIPROT\\|?|UNIPROT_|UNIREF\\d+_|UNIREF\\d+\\|?)", "");
148	0	AlignmentI al = null;
149
150	0	String downloadstring = getDomain() + "/uniprot/" + queries + ".xml";
151		// String downloadstring = getDomain() + queries + ".json";
152
153	0	URL url = new URL(downloadstring);
154	0	URLConnection urlconn = HttpUtils.openConnection(url);
155	0	InputStream istr = urlconn.getInputStream();
156	0	List<Entry> entries = getUniprotEntries(istr);
157	0	if (entries != null)
158		{
159	0	List<SequenceI> seqs = new ArrayList<>();
160	0	for (Entry entry : entries)
161		{
162	0	seqs.add(uniprotEntryToSequence(entry));
163		}
164	0	al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
165		}
166
167	0	stopQuery();
168	0	return al;
169		} catch (Exception e)
170		{
171	0	throw (e);
172		} finally
173		{
174	0	stopQuery();
175		}
176		}
177
178		/**
179		* Converts an Entry object (bound from Uniprot XML) to a Jalview Sequence
180		*
181		* @param entry
182		* @return
183		*/
		0% Uncovered Elements: 61 (61) Complexity: 11 Complexity Density: 0.24
184	0	SequenceI uniprotEntryToSequence(Entry entry)...
185		{
186	0	String id = getUniprotEntryId(entry);
187		/*
188		* Sequence should not include any whitespace, but JAXB leaves these in
189		*/
190	0	String seqString = entry.getSequence().getValue().replaceAll("\\s*",
191		"");
192
193	0	SequenceI sequence = new Sequence(id, seqString);
194	0	sequence.setDescription(getUniprotEntryDescription(entry));
195
196		/*
197		* add a 'self' DBRefEntry for each accession
198		*/
199	0	final String dbVersion = getDbVersion();
200	0	List<DBRefEntry> dbRefs = new ArrayList<>();
201	0	for (String accessionId : entry.getAccession())
202		{
203	0	DBRefEntry dbRef = new DBRefEntry(DBRefSource.UNIPROT, dbVersion,
204		accessionId);
205	0	dbRefs.add(dbRef);
206		}
207
208		/*
209		* add a DBRefEntry for each dbReference element in the XML;
210		* also add a PDBEntry if type="PDB";
211		* also add an EMBLCDS dbref if protein sequence id is given
212		* also add an Ensembl dbref " " " " " "
213		*/
214	0	Vector<PDBEntry> pdbRefs = new Vector<>();
215	0	for (DbReferenceType dbref : entry.getDbReference())
216		{
217	0	String type = dbref.getType();
218	0	DBRefEntry dbr = new DBRefEntry(type,
219		DBRefSource.UNIPROT + ":" + dbVersion, dbref.getId());
220	0	dbRefs.add(dbr);
221	0	if ("PDB".equals(type))
222		{
223	0	pdbRefs.add(new PDBEntry(dbr));
224		}
225	0	if ("EMBL".equals(type))
226		{
227		/*
228		* e.g. Uniprot accession Q9BXM7 has
229		* <dbReference type="EMBL" id="M19359">
230		* <property type="protein sequence ID" value="AAA40981.1"/>
231		* <property type="molecule type" value="Genomic_DNA"/>
232		* </dbReference>
233		*/
234	0	String cdsId = getProperty(dbref.getProperty(),
235		"protein sequence ID");
236	0	if (cdsId != null && cdsId.trim().length() > 0)
237		{
238		// remove version
239	0	String[] vrs = cdsId.split("\\.");
240	0	String version = vrs.length > 1 ? vrs[1]
241		: DBRefSource.UNIPROT + ":" + dbVersion;
242	0	dbr = new DBRefEntry(DBRefSource.EMBLCDS, version, vrs[0]);
243	0	dbRefs.add(dbr);
244		}
245		}
246	0	if ("Ensembl".equals(type))
247		{
248		/*
249		* e.g. Uniprot accession Q9BXM7 has
250		* <dbReference type="Ensembl" id="ENST00000321556">
251		* <molecule id="Q9BXM7-1"/>
252		* <property type="protein sequence ID" value="ENSP00000364204"/>
253		* <property type="gene ID" value="ENSG00000158828"/>
254		* </dbReference>
255		*/
256	0	String cdsId = getProperty(dbref.getProperty(),
257		"protein sequence ID");
258	0	if (cdsId != null && cdsId.trim().length() > 0)
259		{
260	0	dbr = new DBRefEntry(DBRefSource.ENSEMBL,
261		DBRefSource.UNIPROT + ":" + dbVersion, cdsId.trim());
262	0	dbRefs.add(dbr);
263		}
264		}
265		}
266
267		/*
268		* create features; they have either begin and end, or position, in XML
269		*/
270	0	sequence.setPDBId(pdbRefs);
271	0	if (entry.getFeature() != null)
272		{
273	0	for (FeatureType uf : entry.getFeature())
274		{
275	0	LocationType location = uf.getLocation();
276	0	int start = 0;
277	0	int end = 0;
278	0	if (location.getPosition() != null)
279		{
280	0	start = location.getPosition().getPosition().intValue();
281	0	end = start;
282		}
283		else
284		{
285	0	start = location.getBegin().getPosition().intValue();
286	0	end = location.getEnd().getPosition().intValue();
287		}
288	0	SequenceFeature sf = new SequenceFeature(uf.getType(),
289		getDescription(uf), start, end, "Uniprot");
290	0	sf.setStatus(uf.getStatus());
291	0	sequence.addSequenceFeature(sf);
292		}
293		}
294	0	for (DBRefEntry dbr : dbRefs)
295		{
296	0	sequence.addDBRef(dbr);
297		}
298	0	return sequence;
299		}
300
301		/**
302		* A helper method that builds a sequence feature description
303		*
304		* @param feature
305		* @return
306		*/
		0% Uncovered Elements: 56 (56) Complexity: 15 Complexity Density: 0.44
307	0	static String getDescription(FeatureType feature)...
308		{
309	0	String orig = feature.getOriginal();
310	0	List<String> variants = feature.getVariation();
311	0	StringBuilder sb = new StringBuilder();
312
313		/*
314		* append variant in standard format if present
315		* e.g. p.Arg59Lys
316		* multiple variants are split over lines using <br>
317		*/
318	0	boolean asHtml = false;
319	0	if (orig != null && !orig.isEmpty() && variants != null
320		&& !variants.isEmpty())
321		{
322	0	int p = 0;
323	0	for (String var : variants)
324		{
325		// TODO proper HGVS nomenclature for delins structural variations
326		// http://varnomen.hgvs.org/recommendations/protein/variant/delins/
327		// for now we are pragmatic - any orig/variant sequence longer than
328		// three characters is shown with single-character notation rather than
329		// three-letter notation
330	0	sb.append("p.");
331	0	if (orig.length() < 4)
332		{
333	0	for (int c = 0, clen = orig.length(); c < clen; c++)
334		{
335	0	char origchar = orig.charAt(c);
336	0	String orig3 = ResidueProperties.aa2Triplet.get("" + origchar);
337	0	sb.append(orig3 == null ? origchar
338		: StringUtils.toSentenceCase(orig3));
339		}
340		}
341		else
342		{
343	0	sb.append(orig);
344		}
345
346	0	LocationType location = feature.getLocation();
347	0	PositionType start = location.getPosition() == null
348		? location.getBegin()
349		: location.getPosition();
350	0	sb.append(Integer.toString(start.getPosition().intValue()));
351
352	0	if (var.length() < 4)
353		{
354	0	for (int c = 0, clen = var.length(); c < clen; c++)
355		{
356	0	char varchar = var.charAt(c);
357	0	String var3 = ResidueProperties.aa2Triplet.get("" + varchar);
358
359	0	sb.append(var3 != null ? StringUtils.toSentenceCase(var3)
360		: "" + varchar);
361		}
362		}
363		else
364		{
365	0	sb.append(var);
366		}
367	0	if (++p != variants.size())
368		{
369	0	sb.append("<br/>&nbsp;&nbsp;");
370	0	asHtml = true;
371		}
372		else
373		{
374	0	sb.append(" ");
375		}
376		}
377		}
378	0	String description = feature.getDescription();
379	0	if (description != null)
380		{
381	0	sb.append(description);
382		}
383	0	if (asHtml)
384		{
385	0	sb.insert(0, "<html>");
386	0	sb.append("</html>");
387		}
388
389	0	return sb.toString();
390		}
391
392		/**
393		* A helper method that searches the list of properties for one with the given
394		* key, and if found returns the property value, else returns null
395		*
396		* @param properties
397		* @param key
398		* @return
399		*/
		0% Uncovered Elements: 11 (11) Complexity: 3 Complexity Density: 0.43
400	0	static String getProperty(List<PropertyType> properties, String key)...
401		{
402	0	String value = null;
403	0	if (properties != null)
404		{
405	0	for (PropertyType prop : properties)
406		{
407	0	if (key.equals(prop.getType()))
408		{
409	0	value = prop.getValue();
410	0	break;
411		}
412		}
413		}
414	0	return value;
415		}
416
417		/**
418		* Extracts xml element entry/protein/recommendedName/fullName
419		*
420		* @param entry
421		* @return
422		*/
		0% Uncovered Elements: 6 (6) Complexity: 3 Complexity Density: 0.75
423	0	static String getUniprotEntryDescription(Entry entry)...
424		{
425	0	String desc = "";
426	0	if (entry.getProtein() != null
427		&& entry.getProtein().getRecommendedName() != null)
428		{
429		// fullName is mandatory if recommendedName is present
430	0	desc = entry.getProtein().getRecommendedName().getFullName()
431		.getValue();
432		}
433	0	return desc;
434		}
435
436		/**
437		* Constructs a sequence id by concatenating all entry/name elements with '|'
438		* separator
439		*
440		* @param entry
441		* @return
442		*/
		0% Uncovered Elements: 8 (8) Complexity: 2 Complexity Density: 0.33
443	0	static String getUniprotEntryId(Entry entry)...
444		{
445	0	StringBuilder name = new StringBuilder(32);
446	0	for (String n : entry.getName())
447		{
448	0	if (name.length() > 0)
449		{
450	0	name.append(BAR_DELIMITER);
451		}
452	0	name.append(n);
453		}
454	0	return name.toString();
455		}
456
457		/*
458		* (non-Javadoc)
459		*
460		* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
461		*/
		0% Uncovered Elements: 3 (3) Complexity: 3 Complexity Density: 3
462	0	@Override...
463		public boolean isValidReference(String accession)
464		{
465		// TODO: make the following a standard validator
466	0	return (accession == null || accession.length() < 2) ? false
467		: getAccessionValidator().search(accession);
468		}
469
470		/**
471		* return LDHA_CHICK uniprot entry
472		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
473	0	@Override...
474		public String getTestQuery()
475		{
476	0	return "P00340";
477		}
478
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
479	0	@Override...
480		public String getDbName()
481		{
482	0	return "Uniprot"; // getDbSource();
483		}
484
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
485	0	@Override...
486		public int getTier()
487		{
488	0	return 0;
489		}
490
491		/**
492		* Reads the reply to the EBI Fetch Uniprot data query, unmarshals it to an
493		* Uniprot object, and returns the enclosed Entry objects, or null on any
494		* failure
495		*
496		* @param is
497		* @return
498		*/
		0% Uncovered Elements: 13 (13) Complexity: 4 Complexity Density: 0.36
499	0	public List<Entry> getUniprotEntries(InputStream is)...
500		{
501	0	List<Entry> entries = null;
502	0	try
503		{
504	0	JAXBContext jc = JAXBContext
505		.newInstance("jalview.xml.binding.uniprot");
506	0	XMLStreamReader streamReader = XMLInputFactory.newInstance()
507		.createXMLStreamReader(is);
508	0	javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
509	0	JAXBElement<jalview.xml.binding.uniprot.Uniprot> uniprotElement = um
510		.unmarshal(streamReader,
511		jalview.xml.binding.uniprot.Uniprot.class);
512	0	jalview.xml.binding.uniprot.Uniprot uniprot = uniprotElement
513		.getValue();
514
515	0	if (uniprot != null && !uniprot.getEntry().isEmpty())
516		{
517	0	entries = uniprot.getEntry();
518		}
519		} catch (JAXBException | XMLStreamException
520		| FactoryConfigurationError e)
521		{
522	0	e.printStackTrace();
523		}
524	0	return entries;
525		}
526		}