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Coverage Report

  1. Project Clover database Mon Sep 2 2024 17:57:51 BST
  2. Package jalview.datamodel

File DBRefEntry.java

 

Coverage histogram

../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

52
70
24
1
451
245
70
1
2.92
24
2.92

Classes

Class Line # Actions
DBRefEntry 31 70 70
0.952054895.2%
 

Contributing tests

This file is covered by 125 tests. .

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.Locale;
24   
25    import jalview.api.DBRefEntryI;
26    import jalview.util.DBRefUtils;
27    import jalview.util.MapList;
28   
29    import java.util.List;
30   
 
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   
 
52  384 toggle 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    */
 
66  3004 toggle public DBRefEntry(String source, String version, String accessionId)
67    {
68  3004 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    */
 
80  118 toggle public DBRefEntry(String source, String version, String accessionId,
81    Mapping map)
82    {
83  118 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    */
 
98  3215 toggle public DBRefEntry(String source, String version, String accessionId,
99    Mapping map, boolean isCanonical)
100    {
101   
102  3215 this.source = source.toUpperCase(Locale.ROOT);
103  3215 setVersion(version);
104  3215 this.accessionId = accessionId;
105  3215 this.map = map;
106  3215 this.isCanonicalAccession = isCanonical;
107    }
108   
109    /**
110    * Clone an entry, this time not allowing any null fields except map.
111    *
112    */
 
113  22 toggle public DBRefEntry(DBRefEntryI entry)
114    {
115  22 this((entry.getSource() == null ? "" : new String(entry.getSource())),
116  22 (entry.getVersion() == null ? ""
117    : new String(entry.getVersion())),
118  22 (entry.getAccessionId() == null ? ""
119    : new String(entry.getAccessionId())),
120  22 (entry.getMap() == null ? null : new Mapping(entry.getMap())),
121    entry.isCanonical());
122    }
123   
 
124  80 toggle @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  80 Mapping em;
140  80 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    */
 
166  68295 toggle @Override
167    public boolean updateFrom(DBRefEntryI other)
168    {
169  68295 if (other == null)
170    {
171  1 return false;
172    }
173  68294 if (other == this)
174    {
175  1 return true;
176    }
177   
178  68293 boolean improved = false;
179    /*
180    * source must either match or be both null
181    */
182  68293 String otherSource = other.getSource();
183  68293 if ((source == null && otherSource != null)
184    || (source != null && otherSource == null)
185    || (source != null && !source.equalsIgnoreCase(otherSource)))
186    {
187  56124 return false;
188    }
189   
190    /*
191    * accession id must either match or be both null
192    */
193  12169 String otherAccession = other.getAccessionId();
194  12169 if ((accessionId == null && otherAccession != null)
195    || (accessionId != null && otherAccession == null)
196    || (accessionId != null
197    && !accessionId.equalsIgnoreCase(otherAccession)))
198    {
199  12118 return false;
200    }
201   
202  51 if (!isCanonicalAccession && other.isCanonical())
203    {
204  2 isCanonicalAccession = true;
205  2 improved = true;
206    }
207    else
208    {
209  49 if (isCanonicalAccession && !other.isCanonical())
210    {
211    // other is not an authoritative source of canonical accessions
212  3 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  48 String otherVersion = other.getVersion();
220   
221  48 if ((version == null || version.equals("0") || version.endsWith(":0"))
222    && otherVersion != null)
223    {
224  13 setVersion(otherVersion);
225    }
226    else
227    {
228  35 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  4 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  44 if (map == null)
242    {
243  40 setMap(other.getMap());
244    }
245  44 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    */
 
254  82 toggle @Override
255    public boolean equalRef(DBRefEntryI entry)
256    {
257    // TODO is this method and equals() not needed?
258  82 if (entry == null)
259    {
260  1 return false;
261    }
262  81 if (entry == this)
263    {
264  1 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  80 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   
 
279  501052 toggle @Override
280    public String getSource()
281    {
282  501052 return source;
283    }
284   
 
285  325 toggle public int getSourceKey()
286    {
287  325 return (sourceKey == Integer.MIN_VALUE
288    ? (sourceKey = DBRefSource
289    .getSourceKey(getCanonicalSourceName()))
290    : sourceKey);
291    }
292   
293    /**
294    * can be null
295    */
 
296  484 toggle @Override
297    public String getVersion()
298    {
299  484 return version;
300    }
301   
302    /**
303    * can be null
304    */
 
305  49941 toggle @Override
306    public String getAccessionId()
307    {
308  49941 return accessionId;
309    }
310   
 
311  386 toggle @Override
312    public void setAccessionId(String accessionId)
313    {
314  386 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    */
 
322  309 toggle @Override
323    public void setSource(String source)
324    {
325  309 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   
 
332  3549 toggle @Override
333    public void setVersion(String version)
334    {
335  3549 this.version = version;
336  3549 this.ucversion = (version == null ? null
337    : version.toUpperCase(Locale.ROOT));
338    }
339   
 
340  2488 toggle @Override
341    public Mapping getMap()
342    {
343  2488 return map;
344    }
345   
346    /**
347    * @param map
348    * the map to set
349    */
 
350  207 toggle public void setMap(Mapping map)
351    {
352  207 this.map = map;
353    }
354   
 
355  641 toggle public boolean hasMap()
356    {
357  641 return map != null;
358    }
359   
360    /**
361    *
362    * @return source+":"+accessionId
363    */
 
364  7 toggle public String getSrcAccString()
365    {
366  7 return ((source != null) ? source : "") + ":"
367  7 + ((accessionId != null) ? accessionId : "");
368    }
369   
 
370  7 toggle @Override
371    public String toString()
372    {
373  7 return getSrcAccString();
374    }
375   
 
376  880 toggle @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  880 if (map != null)
383    {
384  51 SequenceI mto = map.getTo();
385  51 if (mto != null)
386    {
387  25 return false;
388    }
389  26 MapList ml = map.getMap();
390  26 if (ml.getFromRatio() != ml.getToRatio() || ml.getFromRatio() != 1)
391    {
392  4 return false;
393    }
394    // check map is between identical single contiguous ranges
395  22 List<int[]> fromRanges, toRanges;
396  ? if ((fromRanges = ml.getFromRanges()).size() != 1
397    || (toRanges = ml.getToRanges()).size() != 1)
398    {
399  13 return false;
400    }
401  9 if (fromRanges.get(0)[0] != toRanges.get(0)[0]
402    || fromRanges.get(0)[1] != toRanges.get(0)[1])
403    {
404  3 return false;
405    }
406    }
407  835 if (version == null)
408    {
409    // no version string implies the reference has not been verified at all.
410  1 return false;
411    }
412   
413  834 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    */
 
424  358 toggle public String getCanonicalSourceName()
425    {
426  358 return (canonicalSourceName == null
427    ? (canonicalSourceName = DBRefUtils
428    .getCanonicalName(this.source))
429    : canonicalSourceName);
430    }
431   
432    /**
433    *
434    * @param canonical
435    */
 
436  1104 toggle public void setCanonical(boolean canonical)
437    {
438  1104 isCanonicalAccession = canonical;
439    }
440   
441    /**
442    *
443    * @return true if this is the primary canonical accession for the database
444    * source
445    */
 
446  411 toggle public boolean isCanonical()
447    {
448    // TODO Auto-generated method stub
449  411 return isCanonicalAccession;
450    }
451    }
  • Report generated by OpenClover v 4.4.1 on Mon Sep 2 2024 18:05:00 BST using coverage data from Mon Sep 2 2024 18:04:45 BST.
  • OpenClover is free and open-source software.