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Coverage Report

  1. Project Clover database Wed Nov 6 2024 00:56:24 GMT
  2. Package jalview.ws.seqfetcher

File ASequenceFetcher.java

 

Coverage histogram

../../../img/srcFileCovDistChart2.png
54% of files have more coverage

Code metrics

64
149
12
1
460
331
50
0.34
12.42
12
4.17

Classes

Class Line # Actions
ASequenceFetcher 42 149 50
0.1955555519.6%
 

Contributing tests

This file is covered by 208 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.ws.seqfetcher;
22   
23    import jalview.api.FeatureSettingsModelI;
24    import jalview.bin.Console;
25    import jalview.datamodel.AlignmentI;
26    import jalview.datamodel.DBRefEntry;
27    import jalview.datamodel.SequenceI;
28    import jalview.util.DBRefUtils;
29    import jalview.util.MessageManager;
30   
31    import java.util.ArrayList;
32    import java.util.Collections;
33    import java.util.Comparator;
34    import java.util.Enumeration;
35    import java.util.HashSet;
36    import java.util.Hashtable;
37    import java.util.List;
38    import java.util.Map;
39    import java.util.Stack;
40    import java.util.Vector;
41   
 
42    public class ASequenceFetcher
43    {
44   
45    /*
46    * set of databases we can retrieve entries from
47    */
48    protected Hashtable<String, Map<String, DbSourceProxy>> fetchableDbs;
49   
50    /*
51    * comparator to sort by tier (0/1/2) and name
52    */
53    private Comparator<DbSourceProxy> proxyComparator;
54   
55    /**
56    * Constructor
57    */
 
58  16 toggle protected ASequenceFetcher()
59    {
60  16 super();
61   
62    /*
63    * comparator to sort proxies by tier and name
64    */
65  16 proxyComparator = new Comparator<DbSourceProxy>()
66    {
 
67  0 toggle @Override
68    public int compare(DbSourceProxy o1, DbSourceProxy o2)
69    {
70    /*
71    * Tier 0 precedes 1 precedes 2
72    */
73  0 int compared = Integer.compare(o1.getTier(), o2.getTier());
74  0 if (compared == 0)
75    {
76    // defend against NullPointer - should never happen
77  0 String o1Name = o1.getDbName();
78  0 String o2Name = o2.getDbName();
79  0 if (o1Name != null && o2Name != null)
80    {
81  0 compared = o1Name.compareToIgnoreCase(o2Name);
82    }
83    }
84  0 return compared;
85    }
86    };
87    }
88   
89    /**
90    * get array of supported Databases
91    *
92    * @return database source string for each database - only the latest version
93    * of a source db is bound to each source.
94    */
 
95  3360 toggle public String[] getSupportedDb()
96    {
97  3360 if (fetchableDbs == null)
98    {
99  0 return null;
100    }
101  3360 String[] sf = fetchableDbs.keySet()
102    .toArray(new String[fetchableDbs.size()]);
103  3360 return sf;
104    }
105   
 
106  0 toggle public boolean isFetchable(String source)
107    {
108  0 for (String db : fetchableDbs.keySet())
109    {
110  0 if (source.equalsIgnoreCase(db))
111    {
112  0 return true;
113    }
114    }
115  0 Console.warn("isFetchable doesn't know about '" + source + "'");
116  0 return false;
117    }
118   
119    /**
120    * Fetch sequences for the given cross-references
121    *
122    * @param refs
123    * @param dna
124    * if true, only fetch from nucleotide data sources, else peptide
125    * @return
126    */
 
127  0 toggle public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
128    {
129  0 Vector<SequenceI> rseqs = new Vector<>();
130  0 Hashtable<String, List<String>> queries = new Hashtable<>();
131  0 for (DBRefEntry ref : refs)
132    {
133  0 String canonical = DBRefUtils.getCanonicalName(ref.getSource());
134  0 if (!queries.containsKey(canonical))
135    {
136  0 queries.put(canonical, new ArrayList<String>());
137    }
138  0 List<String> qset = queries.get(canonical);
139  0 if (!qset.contains(ref.getAccessionId()))
140    {
141  0 qset.add(ref.getAccessionId());
142    }
143    }
144  0 Enumeration<String> e = queries.keys();
145  0 while (e.hasMoreElements())
146    {
147  0 List<String> query = null;
148  0 String db = null;
149  0 db = e.nextElement();
150  0 query = queries.get(db);
151  0 if (!isFetchable(db))
152    {
153  0 reportStdError(db, query, new Exception(
154    "Don't know how to fetch from this database :" + db));
155  0 continue;
156    }
157   
158  0 Stack<String> queriesLeft = new Stack<>();
159  0 queriesLeft.addAll(query);
160   
161  0 List<DbSourceProxy> proxies = getSourceProxy(db);
162  0 for (DbSourceProxy fetcher : proxies)
163    {
164  0 List<String> queriesMade = new ArrayList<>();
165  0 HashSet<String> queriesFound = new HashSet<>();
166  0 try
167    {
168  0 if (fetcher.isDnaCoding() != dna)
169    {
170  0 continue; // wrong sort of data
171    }
172  0 boolean doMultiple = fetcher.getMaximumQueryCount() > 1;
173  0 while (!queriesLeft.isEmpty())
174    {
175  0 StringBuffer qsb = new StringBuffer();
176  0 do
177    {
178  0 if (qsb.length() > 0)
179    {
180  0 qsb.append(fetcher.getAccessionSeparator());
181    }
182  0 String q = queriesLeft.pop();
183  0 queriesMade.add(q);
184  0 qsb.append(q);
185  0 } while (doMultiple && !queriesLeft.isEmpty());
186   
187  0 AlignmentI seqset = null;
188  0 try
189    {
190    // create a fetcher and go to it
191  0 seqset = fetcher.getSequenceRecords(qsb.toString());
192    } catch (Exception ex)
193    {
194  0 jalview.bin.Console.errPrintln(
195    "Failed to retrieve the following from " + db);
196  0 jalview.bin.Console.errPrintln(qsb);
197  0 ex.printStackTrace(System.err);
198    }
199    // TODO: Merge alignment together - perhaps
200  0 if (seqset != null)
201    {
202  0 SequenceI seqs[] = seqset.getSequencesArray();
203  0 if (seqs != null)
204    {
205  0 for (int is = 0; is < seqs.length; is++)
206    {
207  0 rseqs.addElement(seqs[is]);
208    // BH 2015.01.25 check about version/accessid being null here
209  0 List<DBRefEntry> frefs = DBRefUtils.searchRefs(
210    seqs[is].getDBRefs(),
211    new DBRefEntry(db, null, null),
212    DBRefUtils.SEARCH_MODE_FULL);
213  0 for (DBRefEntry dbr : frefs)
214    {
215  0 queriesFound.add(dbr.getAccessionId());
216  0 queriesMade.remove(dbr.getAccessionId());
217    }
218  0 seqs[is] = null;
219    }
220    }
221    else
222    {
223  0 if (fetcher.getRawRecords() != null)
224    {
225  0 jalview.bin.Console.outPrintln(
226    "# Retrieved from " + db + ":" + qsb.toString());
227  0 StringBuffer rrb = fetcher.getRawRecords();
228    /*
229    * for (int rr = 0; rr<rrb.length; rr++) {
230    */
231  0 String hdr;
232    // if (rr<qs.length)
233    // {
234  0 hdr = "# " + db + ":" + qsb.toString();
235    /*
236    * } else { hdr = "# part "+rr; }
237    */
238  0 jalview.bin.Console.outPrintln(hdr);
239  0 if (rrb != null)
240    {
241  0 jalview.bin.Console.outPrintln(rrb);
242    }
243  0 jalview.bin.Console.outPrintln("# end of " + hdr);
244    }
245   
246    }
247    }
248   
249    }
250    } catch (Exception ex)
251    {
252  0 reportStdError(db, queriesMade, ex);
253    }
254  0 if (queriesMade.size() > 0)
255    {
256  0 jalview.bin.Console.outPrintln("# Adding " + queriesMade.size()
257    + " ids back to queries list for searching again (" + db
258    + ")");
259  0 queriesLeft.addAll(queriesMade);
260    }
261    }
262    }
263   
264  0 SequenceI[] result = null;
265  0 if (rseqs.size() > 0)
266    {
267  0 result = new SequenceI[rseqs.size()];
268  0 int si = 0;
269  0 for (SequenceI s : rseqs)
270    {
271  0 result[si++] = s;
272  0 s.updatePDBIds();
273    }
274    }
275  0 return result;
276    }
277   
 
278  0 toggle public void reportStdError(String db, List<String> queriesMade,
279    Exception ex)
280    {
281   
282  0 jalview.bin.Console.errPrintln(
283    "Failed to retrieve the following references from " + db);
284  0 int n = 0;
285  0 for (String qv : queriesMade)
286    {
287  0 System.err.print(" " + qv + ";");
288  0 if (n++ > 10)
289    {
290  0 jalview.bin.Console.errPrintln();
291  0 n = 0;
292    }
293    }
294  0 jalview.bin.Console.errPrintln();
295  0 ex.printStackTrace();
296    }
297   
298    /**
299    * Returns a list of proxies for the given source
300    *
301    * @param db
302    * database source string TODO: add version string/wildcard for
303    * retrieval of specific DB source/version combinations.
304    * @return a list of DbSourceProxy for the db
305    */
 
306  43689 toggle public List<DbSourceProxy> getSourceProxy(String db)
307    {
308  43689 db = DBRefUtils.getCanonicalName(db);
309  43689 Map<String, DbSourceProxy> dblist = fetchableDbs.get(db);
310  43689 if (dblist == null)
311    {
312  1 return new ArrayList<>();
313    }
314   
315    /*
316    * sort so that primary sources precede secondary
317    */
318  43688 List<DbSourceProxy> dbs = new ArrayList<>(dblist.values());
319  43688 Collections.sort(dbs, proxyComparator);
320  43688 return dbs;
321    }
322   
323    /**
324    * constructs an instance of the proxy and registers it as a valid dbrefsource
325    *
326    * @param dbSourceProxy
327    * reference for class implementing
328    * jalview.ws.seqfetcher.DbSourceProxy
329    */
 
330  128 toggle protected void addDBRefSourceImpl(
331    Class<? extends DbSourceProxy> dbSourceProxy)
332    throws IllegalArgumentException
333    {
334  128 DbSourceProxy proxy = null;
335  128 try
336    {
337  128 DbSourceProxy proxyObj = dbSourceProxy.getConstructor().newInstance();
338  128 proxy = proxyObj;
339    } catch (IllegalArgumentException e)
340    {
341  0 throw e;
342    } catch (Exception e)
343    {
344    // Serious problems if this happens.
345  0 throw new Error(MessageManager
346    .getString("error.dbrefsource_implementation_exception"), e);
347    }
348  128 addDbRefSourceImpl(proxy);
349    }
350   
351    /**
352    * add the properly initialised DbSourceProxy object 'proxy' to the list of
353    * sequence fetchers
354    *
355    * @param proxy
356    */
 
357  128 toggle protected void addDbRefSourceImpl(DbSourceProxy proxy)
358    {
359  128 if (proxy != null)
360    {
361  128 if (fetchableDbs == null)
362    {
363  16 fetchableDbs = new Hashtable<>();
364    }
365  128 Map<String, DbSourceProxy> slist = fetchableDbs
366    .get(proxy.getDbSource());
367  128 if (slist == null)
368    {
369  128 fetchableDbs.put(proxy.getDbSource(), slist = new Hashtable<>());
370    }
371  128 slist.put(proxy.getDbName(), proxy);
372    }
373    }
374   
375    /**
376    * select sources which are implemented by instances of the given class
377    *
378    * @param class
379    * that implements DbSourceProxy
380    * @return null or vector of source names for fetchers
381    */
 
382  0 toggle public String[] getDbInstances(Class class1)
383    {
384  0 if (!DbSourceProxy.class.isAssignableFrom(class1))
385    {
386  0 throw new Error(MessageManager.formatMessage(
387    "error.implementation_error_dbinstance_must_implement_interface",
388    new String[]
389    { class1.toString() }));
390    }
391  0 if (fetchableDbs == null)
392    {
393  0 return null;
394    }
395  0 String[] sources = null;
396  0 Vector<String> src = new Vector<>();
397  0 Enumeration<String> dbs = fetchableDbs.keys();
398  0 while (dbs.hasMoreElements())
399    {
400  0 String dbn = dbs.nextElement();
401  0 for (DbSourceProxy dbp : fetchableDbs.get(dbn).values())
402    {
403  0 if (class1.isAssignableFrom(dbp.getClass()))
404    {
405  0 src.addElement(dbn);
406    }
407    }
408    }
409  0 if (src.size() > 0)
410    {
411  0 src.copyInto(sources = new String[src.size()]);
412    }
413  0 return sources;
414    }
415   
 
416  0 toggle public DbSourceProxy[] getDbSourceProxyInstances(Class class1)
417    {
418  0 List<DbSourceProxy> prlist = new ArrayList<>();
419  0 for (String fetchable : getSupportedDb())
420    {
421  0 for (DbSourceProxy pr : getSourceProxy(fetchable))
422    {
423  0 if (class1.isInstance(pr))
424    {
425  0 prlist.add(pr);
426    }
427    }
428    }
429  0 if (prlist.size() == 0)
430    {
431  0 return null;
432    }
433  0 return prlist.toArray(new DbSourceProxy[0]);
434    }
435   
436    /**
437    * Returns a preferred feature colouring scheme for the given source, or null
438    * if none is defined.
439    *
440    * @param source
441    * @return
442    */
 
443  4 toggle public FeatureSettingsModelI getFeatureColourScheme(String source)
444    {
445    /*
446    * return the first non-null colour scheme for any proxy for
447    * this database source
448    */
449  4 for (DbSourceProxy proxy : getSourceProxy(source))
450    {
451  4 FeatureSettingsModelI preferredColours = proxy
452    .getFeatureColourScheme();
453  4 if (preferredColours != null)
454    {
455  2 return preferredColours;
456    }
457    }
458  2 return null;
459    }
460    }
  • Report generated by OpenClover v 4.4.1 on Wed Nov 6 2024 01:03:43 GMT using coverage data from Wed Nov 6 2024 01:03:32 GMT.
  • OpenClover is free and open-source software.