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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.ws.seqfetcher

File ASequenceFetcher.java

 

Coverage histogram

../../../img/srcFileCovDistChart2.png
51% of files have more coverage

Code metrics

64
149
12
1
459
331
50
0.34
12.42
12
4.17

Classes

Class Line # Actions
ASequenceFetcher 42 149 50 189
0.1616%
 

Contributing tests

This file is covered by 80 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.Cache;
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  6 toggle protected ASequenceFetcher()
59    {
60  6 super();
61   
62    /*
63    * comparator to sort proxies by tier and name
64    */
65  6 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  1102 toggle public String[] getSupportedDb()
96    {
97  1102 if (fetchableDbs == null)
98    {
99  0 return null;
100    }
101  1102 String[] sf = fetchableDbs.keySet()
102    .toArray(new String[fetchableDbs.size()]);
103  1102 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 Cache.log.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 System.err.println(
195    "Failed to retrieve the following from " + db);
196  0 System.err.println(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  0 List<DBRefEntry> frefs = DBRefUtils.searchRefs(
209    seqs[is].getDBRefs(),
210    new DBRefEntry(db, null, null));
211  0 for (DBRefEntry dbr : frefs)
212    {
213  0 queriesFound.add(dbr.getAccessionId());
214  0 queriesMade.remove(dbr.getAccessionId());
215    }
216  0 seqs[is] = null;
217    }
218    }
219    else
220    {
221  0 if (fetcher.getRawRecords() != null)
222    {
223  0 System.out.println(
224    "# Retrieved from " + db + ":" + qsb.toString());
225  0 StringBuffer rrb = fetcher.getRawRecords();
226    /*
227    * for (int rr = 0; rr<rrb.length; rr++) {
228    */
229  0 String hdr;
230    // if (rr<qs.length)
231    // {
232  0 hdr = "# " + db + ":" + qsb.toString();
233    /*
234    * } else { hdr = "# part "+rr; }
235    */
236  0 System.out.println(hdr);
237  0 if (rrb != null)
238    {
239  0 System.out.println(rrb);
240    }
241  0 System.out.println("# end of " + hdr);
242    }
243   
244    }
245    }
246   
247    }
248    } catch (Exception ex)
249    {
250  0 reportStdError(db, queriesMade, ex);
251    }
252  0 if (queriesMade.size() > 0)
253    {
254  0 System.out.println("# Adding " + queriesMade.size()
255    + " ids back to queries list for searching again (" + db
256    + ")");
257  0 queriesLeft.addAll(queriesMade);
258    }
259    }
260    }
261   
262  0 SequenceI[] result = null;
263  0 if (rseqs.size() > 0)
264    {
265  0 result = new SequenceI[rseqs.size()];
266  0 int si = 0;
267  0 for (SequenceI s : rseqs)
268    {
269  0 result[si++] = s;
270  0 s.updatePDBIds();
271    }
272    }
273  0 return result;
274    }
275   
 
276  0 toggle public void reportStdError(String db, List<String> queriesMade,
277    Exception ex)
278    {
279   
280  0 System.err.println(
281    "Failed to retrieve the following references from " + db);
282  0 int n = 0;
283  0 for (String qv : queriesMade)
284    {
285  0 System.err.print(" " + qv + ";");
286  0 if (n++ > 10)
287    {
288  0 System.err.println();
289  0 n = 0;
290    }
291    }
292  0 System.err.println();
293  0 ex.printStackTrace();
294    }
295   
296    /**
297    * Returns a list of proxies for the given source
298    *
299    * @param db
300    * database source string TODO: add version string/wildcard for
301    * retrieval of specific DB source/version combinations.
302    * @return a list of DbSourceProxy for the db
303    */
 
304  19841 toggle public List<DbSourceProxy> getSourceProxy(String db)
305    {
306  19841 db = DBRefUtils.getCanonicalName(db);
307  19841 Map<String, DbSourceProxy> dblist = fetchableDbs.get(db);
308  19841 if (dblist == null)
309    {
310  1 return new ArrayList<>();
311    }
312   
313    /*
314    * sort so that primary sources precede secondary
315    */
316  19840 List<DbSourceProxy> dbs = new ArrayList<>(dblist.values());
317  19840 Collections.sort(dbs, proxyComparator);
318  19840 return dbs;
319    }
320   
321    /**
322    * constructs an instance of the proxy and registers it as a valid dbrefsource
323    *
324    * @param dbSourceProxy
325    * reference for class implementing
326    * jalview.ws.seqfetcher.DbSourceProxy
327    */
 
328  54 toggle protected void addDBRefSourceImpl(
329    Class<? extends DbSourceProxy> dbSourceProxy)
330    throws IllegalArgumentException
331    {
332  54 DbSourceProxy proxy = null;
333  54 try
334    {
335  54 DbSourceProxy proxyObj = dbSourceProxy.getConstructor().newInstance();
336  54 proxy = proxyObj;
337    } catch (IllegalArgumentException e)
338    {
339  0 throw e;
340    } catch (Exception e)
341    {
342    // Serious problems if this happens.
343  0 throw new Error(MessageManager
344    .getString("error.dbrefsource_implementation_exception"), e);
345    }
346  54 addDbRefSourceImpl(proxy);
347    }
348   
349    /**
350    * add the properly initialised DbSourceProxy object 'proxy' to the list of
351    * sequence fetchers
352    *
353    * @param proxy
354    */
 
355  54 toggle protected void addDbRefSourceImpl(DbSourceProxy proxy)
356    {
357  54 if (proxy != null)
358    {
359  54 if (fetchableDbs == null)
360    {
361  6 fetchableDbs = new Hashtable<>();
362    }
363  54 Map<String, DbSourceProxy> slist = fetchableDbs
364    .get(proxy.getDbSource());
365  54 if (slist == null)
366    {
367  54 fetchableDbs.put(proxy.getDbSource(),
368    slist = new Hashtable<>());
369    }
370  54 slist.put(proxy.getDbName(), proxy);
371    }
372    }
373   
374    /**
375    * select sources which are implemented by instances of the given class
376    *
377    * @param class
378    * that implements DbSourceProxy
379    * @return null or vector of source names for fetchers
380    */
 
381  0 toggle public String[] getDbInstances(Class class1)
382    {
383  0 if (!DbSourceProxy.class.isAssignableFrom(class1))
384    {
385  0 throw new Error(MessageManager.formatMessage(
386    "error.implementation_error_dbinstance_must_implement_interface",
387    new String[]
388    { class1.toString() }));
389    }
390  0 if (fetchableDbs == null)
391    {
392  0 return null;
393    }
394  0 String[] sources = null;
395  0 Vector<String> src = new Vector<>();
396  0 Enumeration<String> dbs = fetchableDbs.keys();
397  0 while (dbs.hasMoreElements())
398    {
399  0 String dbn = dbs.nextElement();
400  0 for (DbSourceProxy dbp : fetchableDbs.get(dbn).values())
401    {
402  0 if (class1.isAssignableFrom(dbp.getClass()))
403    {
404  0 src.addElement(dbn);
405    }
406    }
407    }
408  0 if (src.size() > 0)
409    {
410  0 src.copyInto(sources = new String[src.size()]);
411    }
412  0 return sources;
413    }
414   
 
415  0 toggle public DbSourceProxy[] getDbSourceProxyInstances(Class class1)
416    {
417  0 List<DbSourceProxy> prlist = new ArrayList<>();
418  0 for (String fetchable : getSupportedDb())
419    {
420  0 for (DbSourceProxy pr : getSourceProxy(fetchable))
421    {
422  0 if (class1.isInstance(pr))
423    {
424  0 prlist.add(pr);
425    }
426    }
427    }
428  0 if (prlist.size() == 0)
429    {
430  0 return null;
431    }
432  0 return prlist.toArray(new DbSourceProxy[0]);
433    }
434   
435    /**
436    * Returns a preferred feature colouring scheme for the given source, or null
437    * if none is defined.
438    *
439    * @param source
440    * @return
441    */
 
442  0 toggle public FeatureSettingsModelI getFeatureColourScheme(String source)
443    {
444    /*
445    * return the first non-null colour scheme for any proxy for
446    * this database source
447    */
448  0 for (DbSourceProxy proxy : getSourceProxy(source))
449    {
450  0 FeatureSettingsModelI preferredColours = proxy
451    .getFeatureColourScheme();
452  0 if (preferredColours != null)
453    {
454  0 return preferredColours;
455    }
456    }
457  0 return null;
458    }
459    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.