2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ws.seqfetcher;
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;
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;
39 import java.util.Map.Entry;
40 import java.util.Stack;
41 import java.util.Vector;
43 public class ASequenceFetcher
47 * set of databases we can retrieve entries from
49 protected Hashtable<String, Map<String, DbSourceProxyRoot>> fetchableDbs;
52 * comparator to sort by tier (0/1/2) and name
54 private Comparator<DbSourceProxy> proxyComparator;
59 protected ASequenceFetcher()
62 * comparator to sort proxies by tier and name
64 proxyComparator = new Comparator<DbSourceProxy>()
67 public int compare(DbSourceProxy o1, DbSourceProxy o2)
70 * Tier 0 precedes 1 precedes 2
72 int compared = Integer.compare(o1.getTier(), o2.getTier());
75 // defend against NullPointer - should never happen
76 String o1Name = o1.getDbName();
77 String o2Name = o2.getDbName();
78 if (o1Name != null && o2Name != null)
80 compared = o1Name.compareToIgnoreCase(o2Name);
89 * get array of supported Databases
91 * @return database source string for each database - only the latest version
92 * of a source db is bound to each source.
94 public String[] getSupportedDb()
96 if (fetchableDbs == null)
100 String[] sf = fetchableDbs.keySet()
101 .toArray(new String[fetchableDbs.size()]);
105 public boolean isFetchable(String source)
107 for (String db : fetchableDbs.keySet())
109 if (source.equalsIgnoreCase(db))
114 Cache.log.warn("isFetchable doesn't know about '" + source + "'");
119 * Fetch sequences for the given cross-references
123 * if true, only fetch from nucleotide data sources, else peptide
126 public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
128 Vector<SequenceI> rseqs = new Vector<>();
129 Hashtable<String, List<String>> queries = new Hashtable<>();
130 for (DBRefEntry ref : refs)
132 String canonical = DBRefUtils.getCanonicalName(ref.getSource());
133 if (!queries.containsKey(canonical))
135 queries.put(canonical, new ArrayList<String>());
137 List<String> qset = queries.get(canonical);
138 if (!qset.contains(ref.getAccessionId()))
140 qset.add(ref.getAccessionId());
143 Enumeration<String> e = queries.keys();
144 while (e.hasMoreElements())
146 List<String> query = null;
148 db = e.nextElement();
149 query = queries.get(db);
150 if (!isFetchable(db))
152 reportStdError(db, query, new Exception(
153 "Don't know how to fetch from this database :" + db));
157 Stack<String> queriesLeft = new Stack<>();
158 queriesLeft.addAll(query);
160 List<DbSourceProxy> proxies = getSourceProxy(db);
161 for (DbSourceProxy fetcher : proxies)
163 List<String> queriesMade = new ArrayList<>();
164 HashSet<String> queriesFound = new HashSet<>();
167 if (fetcher.isDnaCoding() != dna)
169 continue; // wrong sort of data
171 boolean doMultiple = fetcher.getMaximumQueryCount() > 1;
172 while (!queriesLeft.isEmpty())
174 StringBuffer qsb = new StringBuffer();
177 if (qsb.length() > 0)
179 qsb.append(fetcher.getAccessionSeparator());
181 String q = queriesLeft.pop();
184 } while (doMultiple && !queriesLeft.isEmpty());
186 AlignmentI seqset = null;
189 // create a fetcher and go to it
190 seqset = fetcher.getSequenceRecords(qsb.toString());
191 } catch (Exception ex)
194 "Failed to retrieve the following from " + db);
195 System.err.println(qsb);
196 ex.printStackTrace(System.err);
198 // TODO: Merge alignment together - perhaps
201 SequenceI seqs[] = seqset.getSequencesArray();
204 for (int is = 0; is < seqs.length; is++)
206 rseqs.addElement(seqs[is]);
207 // BH 2015.01.25 check about version/accessid being null here
208 List<DBRefEntry> frefs = DBRefUtils.searchRefs(
209 seqs[is].getDBRefs(),
210 new DBRefEntry(db, null, null), DBRefUtils.SEARCH_MODE_FULL);
211 for (DBRefEntry dbr : frefs)
213 queriesFound.add(dbr.getAccessionId());
214 queriesMade.remove(dbr.getAccessionId());
221 if (fetcher.getRawRecords() != null)
224 "# Retrieved from " + db + ":" + qsb.toString());
225 StringBuffer rrb = fetcher.getRawRecords();
227 * for (int rr = 0; rr<rrb.length; rr++) {
232 hdr = "# " + db + ":" + qsb.toString();
234 * } else { hdr = "# part "+rr; }
236 System.out.println(hdr);
239 System.out.println(rrb);
241 System.out.println("# end of " + hdr);
248 } catch (Exception ex)
250 reportStdError(db, queriesMade, ex);
252 if (queriesMade.size() > 0)
254 System.out.println("# Adding " + queriesMade.size()
255 + " ids back to queries list for searching again (" + db
257 queriesLeft.addAll(queriesMade);
262 SequenceI[] result = null;
263 if (rseqs.size() > 0)
265 result = new SequenceI[rseqs.size()];
267 for (SequenceI s : rseqs)
276 public void reportStdError(String db, List<String> queriesMade,
281 "Failed to retrieve the following references from " + db);
283 for (String qv : queriesMade)
285 System.err.print(" " + qv + ";");
288 System.err.println();
292 System.err.println();
293 ex.printStackTrace();
297 * Returns a list of proxies for the given source
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
304 public List<DbSourceProxy> getSourceProxy(String db)
306 db = DBRefUtils.getCanonicalName(db);
307 Map<String, DbSourceProxyRoot> dblist = fetchableDbs.get(db);
310 return new ArrayList<>();
314 * sort so that primary sources precede secondary
316 List<DbSourceProxy> dbs = new ArrayList<>();
317 for (Entry<String, DbSourceProxyRoot> entry : dblist.entrySet())
319 DbSourceProxyRoot proxy = entry.getValue();
320 if (proxy instanceof DbRoot)
322 proxy = setProxy((DbRoot) proxy, dblist);
324 dbs.add((DbSourceProxy) proxy);
326 Collections.sort(dbs, proxyComparator);
330 class DbRoot implements DbSourceProxyRoot
333 private String sourceName;
335 private String className;
337 DbRoot(String sourceName, String className)
339 this.sourceName = sourceName;
340 this.className = className;
344 public String getDbSource()
350 * lazy class creation
352 * @return the actual proxy object
354 public DbSourceProxy getProxy()
358 return (DbSourceProxy) Class.forName(className).newInstance();
359 } catch (Exception e)
361 // Serious problems if this happens.
362 throw new Error(MessageManager.getString(
363 "error.dbrefsource_implementation_exception"), e);
370 * constructs an instance of the proxy and registers it as a valid dbrefsource
372 * @param dbSourceProxyClass
373 * reference for class implementing
374 * jalview.ws.seqfetcher.DbSourceProxy
376 protected void addDBRefSourceImpl(
377 Class<? extends DbSourceProxy> dbSourceProxyClass)
378 throws IllegalArgumentException
380 DbSourceProxy proxy = null;
383 proxy = dbSourceProxyClass.getConstructor().newInstance();
384 } catch (IllegalArgumentException e)
387 } catch (Exception e)
389 // Serious problems if this happens.
390 throw new Error(MessageManager
391 .getString("error.dbrefsource_implementation_exception"), e);
393 addDbRefSourceImpl(proxy);
396 public void addDBRefSourceImpl(String sourceName, String className)
398 addDbRefSourceImpl(new DbRoot(sourceName, className));
402 * add the properly initialised DbSourceProxy object 'proxy' to the list of
407 void addDbRefSourceImpl(DbSourceProxyRoot proxy)
411 if (fetchableDbs == null)
413 fetchableDbs = new Hashtable<>();
415 String key = proxy.getDbSource();
416 Map<String, DbSourceProxyRoot> slist = fetchableDbs.get(key);
419 fetchableDbs.put(key, slist = new Hashtable<>());
421 if (proxy instanceof DbRoot)
423 slist.put("", proxy);
427 slist.put(((DbSourceProxy) proxy).getDbName(), proxy);
433 * select sources which are implemented by instances of the given class
436 * that implements DbSourceProxy
437 * @return null or vector of source names for fetchers
439 public String[] getDbInstances(Class<?> class1)
441 if (!DbSourceProxy.class.isAssignableFrom(class1))
443 throw new Error(MessageManager.formatMessage(
444 "error.implementation_error_dbinstance_must_implement_interface",
446 { class1.toString() }));
448 if (fetchableDbs == null)
452 Vector<String> src = new Vector<>();
453 for (String dbSource : fetchableDbs.keySet())
455 Map<String, DbSourceProxyRoot> dblist = fetchableDbs.get(dbSource);
456 for (Entry<String, DbSourceProxyRoot> entry : dblist.entrySet())
458 DbSourceProxyRoot proxy = entry.getValue();
459 if (proxy instanceof DbRoot)
461 proxy = setProxy((DbRoot) proxy, dblist);
463 Class<?> c = proxy.getClass();
464 if (class1 == c || class1.isAssignableFrom(c))
466 src.addElement(dbSource);
470 String[] sources = null;
473 src.copyInto(sources = new String[src.size()]);
478 private DbSourceProxyRoot setProxy(DbRoot root,
479 Map<String, DbSourceProxyRoot> dblist)
481 DbSourceProxy proxy = root.getProxy();
482 // Time to create the actual proxy
484 dblist.put(proxy.getDbName(), proxy);
488 public DbSourceProxy[] getDbSourceProxyInstances(Class<?> class1)
490 if (fetchableDbs == null)
494 List<DbSourceProxy> prlist = new ArrayList<>();
495 for (String fetchable : fetchableDbs.keySet())
497 for (DbSourceProxy pr : getSourceProxy(fetchable))
499 if (class1.isInstance(pr))
505 if (prlist.size() == 0)
509 return prlist.toArray(new DbSourceProxy[0]);
513 * Returns a preferred feature colouring scheme for the given source, or null
514 * if none is defined.
519 public FeatureSettingsModelI getFeatureColourScheme(String source)
522 * return the first non-null colour scheme for any proxy for
523 * this database source
525 for (DbSourceProxy proxy : getSourceProxy(source))
527 FeatureSettingsModelI preferredColours = proxy
528 .getFeatureColourScheme();
529 if (preferredColours != null)
531 return preferredColours;