Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
DBRefEntry	31	70	70	0.00%	Show methods

Class DBRefEntry

Class DBRefEntry	Line # 31	Total Statements 70	Complexity 70	TOTAL Coverage 0.00%
DBRefEntry()   DBRefEntry()	5252	0.00	1.01	-1.0 -1.0 -
DBRefEntry(String,String,String)   DBRefEntry(String,String,String)	6666	1.01	1.01	0.0 0.00%
DBRefEntry(String,String,String,Mapping)   DBRefEntry(String,String,String,Mapping)	8080	1.01	1.01	0.0 0.00%
DBRefEntry(String,String,String,Mapping,boolean)   DBRefEntry(String,String,String,Mapping,boolean)	9898	5.05	1.01	0.0 0.00%
DBRefEntry(DBRefEntryI)   DBRefEntry(DBRefEntryI)	113113	1.01	5.05	0.0 0.00%
equals(Object) : boolean   equals(Object) : boolean	124124	2.02	1.01	0.0 0.00%
updateFrom(DBRefEntryI) : boolean   updateFrom(DBRefEntryI) : boolean	166166	24.024	27.027	0.0 0.00%
equalRef(DBRefEntryI) : boolean   equalRef(DBRefEntryI) : boolean	254254	5.05	3.03	0.0 0.00%
getSource() : String   getSource() : String	279279	1.01	1.01	0.0 0.00%
getSourceKey() : int   getSourceKey() : int	285285	1.01	2.02	0.0 0.00%
getVersion() : String   getVersion() : String	296296	1.01	1.01	0.0 0.00%
getAccessionId() : String   getAccessionId() : String	305305	1.01	1.01	0.0 0.00%
setAccessionId(String) : void   setAccessionId(String) : void	311311	1.01	1.01	0.0 0.00%
setSource(String) : void   setSource(String) : void	322322	1.01	1.01	0.0 0.00%
setVersion(String) : void   setVersion(String) : void	332332	2.02	2.02	0.0 0.00%
getMap() : Mapping   getMap() : Mapping	340340	1.01	1.01	0.0 0.00%
setMap(Mapping) : void   setMap(Mapping) : void	350350	1.01	1.01	0.0 0.00%
hasMap() : boolean   hasMap() : boolean	355355	1.01	1.01	0.0 0.00%
getSrcAccString() : String   getSrcAccString() : String	364364	1.01	3.03	0.0 0.00%
toString() : String   toString() : String	370370	1.01	1.01	0.0 0.00%
isPrimaryCandidate() : boolean   isPrimaryCandidate() : boolean	376376	15.015	10.010	0.0 0.00%
getCanonicalSourceName() : String   getCanonicalSourceName() : String	424424	1.01	2.02	0.0 0.00%
setCanonical(boolean) : void   setCanonical(boolean) : void	436436	1.01	1.01	0.0 0.00%
isCanonical() : boolean   isCanonical() : boolean	446446	1.01	1.01	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.datamodel;
22
23		import java.util.Locale;
24
25		import jalview.api.DBRefEntryI;
26		import jalview.util.DBRefUtils;
27		import jalview.util.MapList;
28
29		import java.util.List;
30
		0% Uncovered Elements: 146 (146) Complexity: 70 Complexity Density: 1
31		public class DBRefEntry implements DBRefEntryI
32		{
33		String source = "";
34
35		private String version = "";
36
37		private String ucversion;
38
39		private String accessionId = "";
40
41		int sourceKey = Integer.MIN_VALUE;
42
43		String canonicalSourceName;
44
45		boolean isCanonicalAccession = false;
46
47		/*
48		* maps from associated sequence to the database sequence's coordinate system
49		*/
50		Mapping map = null;
51
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
52	0	public DBRefEntry()...
53		{
54
55		}
56
57		/**
58		*
59		* @param source
60		* may not be null
61		* @param version
62		* may be null
63		* @param accessionId
64		* may be null
65		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	public DBRefEntry(String source, String version, String accessionId)...
67		{
68	0	this(source, version, accessionId, null, false);
69		}
70
71		/**
72		*
73		* @param source
74		* may not be null
75		* @param version
76		* may be null
77		* @param accessionId
78		* may be null
79		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
80	0	public DBRefEntry(String source, String version, String accessionId,...
81		Mapping map)
82		{
83	0	this(source, version, accessionId, map, false);
84		}
85
86		/**
87		*
88		* @param source
89		* canonical source (turned to uppercase; cannot be null)
90		* @param version
91		* (source dependent version string or null)
92		* @param accessionId
93		* (source dependent accession number string or null)
94		* @param map
95		* (mapping from local sequence numbering to source accession
96		* numbering or null)
97		*/
		0% Uncovered Elements: 5 (5) Complexity: 1 Complexity Density: 0.2
98	0	public DBRefEntry(String source, String version, String accessionId,...
99		Mapping map, boolean isCanonical)
100		{
101
102	0	this.source = source.toUpperCase(Locale.ROOT);
103	0	setVersion(version);
104	0	this.accessionId = accessionId;
105	0	this.map = map;
106	0	this.isCanonicalAccession = isCanonical;
107		}
108
109		/**
110		* Clone an entry, this time not allowing any null fields except map.
111		*
112		*/
		0% Uncovered Elements: 9 (9) Complexity: 5 Complexity Density: 5
113	0	public DBRefEntry(DBRefEntryI entry)...
114		{
115	0	this((entry.getSource() == null ? "" : new String(entry.getSource())),
116	0	(entry.getVersion() == null ? ""
117		: new String(entry.getVersion())),
118	0	(entry.getAccessionId() == null ? ""
119		: new String(entry.getAccessionId())),
120	0	(entry.getMap() == null ? null : new Mapping(entry.getMap())),
121		entry.isCanonical());
122		}
123
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
124	0	@Override...
125		public boolean equals(Object o)
126		{
127		// TODO should also override hashCode to ensure equal objects have equal
128		// hashcodes
129
130		// if (o == null || !(o instanceof DBRefEntry))
131		// {
132		// return false;
133		// }
134		// DBRefEntry entry = (DBRefEntry) o;
135		// if (entry == this)
136		// {
137		// return true;
138		// }
139	0	Mapping em;
140	0	return (o != null && o instanceof DBRefEntry && (o == this || equalRef(
141		(DBRefEntry) o)
142		&& (map == null) == ((em = ((DBRefEntry) o).map) == null)
143		&& (map == null || map.equals(em))));
144		//
145		// {
146		// return true;
147		// }
148		// return false;
149		}
150
151		/**
152		* Answers true if this object is either equivalent to, or can be 'improved'
153		* by, the given entry. Specifically, answers true if
154		* <ul>
155		* <li>source and accession are identical (ignoring case)</li>
156		* <li>version is identical (ignoring case), or this version is of the format
157		* "someSource:0", in which case the version for the other entry replaces
158		* it</li>
159		* <li>mappings are not compared but if this entry has no mapping, replace
160		* with that for the other entry</li>
161		* </ul>
162		*
163		* @param other
164		* @return
165		*/
		0% Uncovered Elements: 42 (42) Complexity: 27 Complexity Density: 1.12
166	0	@Override...
167		public boolean updateFrom(DBRefEntryI other)
168		{
169	0	if (other == null)
170		{
171	0	return false;
172		}
173	0	if (other == this)
174		{
175	0	return true;
176		}
177
178	0	boolean improved = false;
179		/*
180		* source must either match or be both null
181		*/
182	0	String otherSource = other.getSource();
183	0	if ((source == null && otherSource != null)
184		|| (source != null && otherSource == null)
185		|| (source != null && !source.equalsIgnoreCase(otherSource)))
186		{
187	0	return false;
188		}
189
190		/*
191		* accession id must either match or be both null
192		*/
193	0	String otherAccession = other.getAccessionId();
194	0	if ((accessionId == null && otherAccession != null)
195		|| (accessionId != null && otherAccession == null)
196		|| (accessionId != null
197		&& !accessionId.equalsIgnoreCase(otherAccession)))
198		{
199	0	return false;
200		}
201
202	0	if (!isCanonicalAccession && other.isCanonical())
203		{
204	0	isCanonicalAccession = true;
205	0	improved = true;
206		}
207		else
208		{
209	0	if (isCanonicalAccession && !other.isCanonical())
210		{
211		// other is not an authoritative source of canonical accessions
212	0	return false;
213		}
214		}
215		/*
216		* if my version is null, "0" or "source:0" then replace with other version,
217		* otherwise the versions have to match
218		*/
219	0	String otherVersion = other.getVersion();
220
221	0	if ((version == null || version.equals("0") || version.endsWith(":0"))
222		&& otherVersion != null)
223		{
224	0	setVersion(otherVersion);
225		}
226		else
227		{
228	0	if (version != null && (otherVersion == null
229		|| !version.equalsIgnoreCase(otherVersion)))
230		{
231		// FIXME: there may be a problem with old version strings not allowing
232		// updating of dbrefentries
233	0	return improved;
234		}
235		}
236
237		/*
238		* if I have no mapping, take that of the other dbref
239		* - providing it had a version and so do I
240		*/
241	0	if (map == null)
242		{
243	0	setMap(other.getMap());
244		}
245	0	return true;
246		}
247
248		/**
249		* test for similar DBRef attributes, except for the map object.
250		*
251		* @param entry
252		* @return true if source, accession and version are equal with those of entry
253		*/
		0% Uncovered Elements: 9 (9) Complexity: 3 Complexity Density: 0.6
254	0	@Override...
255		public boolean equalRef(DBRefEntryI entry)
256		{
257		// TODO is this method and equals() not needed?
258	0	if (entry == null)
259		{
260	0	return false;
261		}
262	0	if (entry == this)
263		{
264	0	return true;
265		}
266
267		// BH 2019.01.25/2019.02.04 source cannot/should not be null.
268		// for example, StructureChooser has dbRef.getSource().equalsIgnoreCase...
269
270	0	return (entry != null
271		&& (source != null && entry.getSource() != null
272		&& source.equalsIgnoreCase(entry.getSource()))
273		&& (accessionId != null && entry.getAccessionId() != null
274		&& accessionId.equalsIgnoreCase(entry.getAccessionId()))
275		&& (version != null && entry.getVersion() != null
276		&& version.equalsIgnoreCase(entry.getVersion())));
277		}
278
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
279	0	@Override...
280		public String getSource()
281		{
282	0	return source;
283		}
284
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
285	0	public int getSourceKey()...
286		{
287	0	return (sourceKey == Integer.MIN_VALUE
288		? (sourceKey = DBRefSource
289		.getSourceKey(getCanonicalSourceName()))
290		: sourceKey);
291		}
292
293		/**
294		* can be null
295		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
296	0	@Override...
297		public String getVersion()
298		{
299	0	return version;
300		}
301
302		/**
303		* can be null
304		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
305	0	@Override...
306		public String getAccessionId()
307		{
308	0	return accessionId;
309		}
310
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
311	0	@Override...
312		public void setAccessionId(String accessionId)
313		{
314	0	this.accessionId = accessionId;
315		// this.accessionId = (accessionId == null ? "" :
316		// accessionId).toUpperCase(Locale.ROOT);
317		}
318
319		/**
320		* CAUTION! allows setting source null or not uppercase!
321		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
322	0	@Override...
323		public void setSource(String source)
324		{
325	0	this.source = source;
326
327		// this.source = (source == null ? "" : source).toUpperCase(Locale.ROOT);
328		// this.canonicalSourceName = DBRefUtils.getCanonicalName(this.source);
329		// this.sourceKey = DBRefSource.getSourceKey(this.canonicalSourceName);
330		}
331
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
332	0	@Override...
333		public void setVersion(String version)
334		{
335	0	this.version = version;
336	0	this.ucversion = (version == null ? null
337		: version.toUpperCase(Locale.ROOT));
338		}
339
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
340	0	@Override...
341		public Mapping getMap()
342		{
343	0	return map;
344		}
345
346		/**
347		* @param map
348		* the map to set
349		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
350	0	public void setMap(Mapping map)...
351		{
352	0	this.map = map;
353		}
354
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
355	0	public boolean hasMap()...
356		{
357	0	return map != null;
358		}
359
360		/**
361		*
362		* @return source+":"+accessionId
363		*/
		0% Uncovered Elements: 5 (5) Complexity: 3 Complexity Density: 3
364	0	public String getSrcAccString()...
365		{
366	0	return ((source != null) ? source : "") + ":"
367	0	+ ((accessionId != null) ? accessionId : "");
368		}
369
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
370	0	@Override...
371		public String toString()
372		{
373	0	return getSrcAccString();
374		}
375
		0% Uncovered Elements: 27 (27) Complexity: 10 Complexity Density: 0.67
376	0	@Override...
377		public boolean isPrimaryCandidate()
378		{
379		/*
380		* if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference.
381		*/
382	0	if (map != null)
383		{
384	0	SequenceI mto = map.getTo();
385	0	if (mto != null)
386		{
387	0	return false;
388		}
389	0	MapList ml = map.getMap();
390	0	if (ml.getFromRatio() != ml.getToRatio() || ml.getFromRatio() != 1)
391		{
392	0	return false;
393		}
394		// check map is between identical single contiguous ranges
395	0	List<int[]> fromRanges, toRanges;
396	0	if ((fromRanges = ml.getFromRanges()).size() != 1
397		|| (toRanges = ml.getToRanges()).size() != 1)
398		{
399	0	return false;
400		}
401	0	if (fromRanges.get(0)[0] != toRanges.get(0)[0]
402		|| fromRanges.get(0)[1] != toRanges.get(0)[1])
403		{
404	0	return false;
405		}
406		}
407	0	if (version == null)
408		{
409		// no version string implies the reference has not been verified at all.
410	0	return false;
411		}
412
413	0	return DBRefSource.isPrimaryCandidate(ucversion);
414		}
415
416		/**
417		* stores the upper-case canonical name of the source for use in
418		* Sequence.getPrimaryDBRefs().
419		*
420		* @author Bob Hanson
421		*
422		* @return
423		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
424	0	public String getCanonicalSourceName()...
425		{
426	0	return (canonicalSourceName == null
427		? (canonicalSourceName = DBRefUtils
428		.getCanonicalName(this.source))
429		: canonicalSourceName);
430		}
431
432		/**
433		*
434		* @param canonical
435		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
436	0	public void setCanonical(boolean canonical)...
437		{
438	0	isCanonicalAccession = canonical;
439		}
440
441		/**
442		*
443		* @return true if this is the primary canonical accession for the database
444		* source
445		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
446	0	public boolean isCanonical()...
447		{
448		// TODO Auto-generated method stub
449	0	return isCanonicalAccession;
450		}
451		}