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.Stack;
40 import java.util.Vector;
42 public class ASequenceFetcher
46 * set of databases we can retrieve entries from
48 protected Hashtable<String, Map<String, DbSourceProxy>> fetchableDbs;
51 * comparator to sort by tier (0/1/2) and name
53 private Comparator<DbSourceProxy> proxyComparator;
58 protected ASequenceFetcher()
63 * comparator to sort proxies by tier and name
65 proxyComparator = new Comparator<DbSourceProxy>()
68 public int compare(DbSourceProxy o1, DbSourceProxy o2)
71 * Tier 0 precedes 1 precedes 2
73 int compared = Integer.compare(o1.getTier(), o2.getTier());
76 // defend against NullPointer - should never happen
77 String o1Name = o1.getDbName();
78 String o2Name = o2.getDbName();
79 if (o1Name != null && o2Name != null)
81 compared = o1Name.compareToIgnoreCase(o2Name);
90 * get array of supported Databases
92 * @return database source string for each database - only the latest version
93 * of a source db is bound to each source.
95 public String[] getSupportedDb()
97 if (fetchableDbs == null)
101 String[] sf = fetchableDbs.keySet()
102 .toArray(new String[fetchableDbs.size()]);
106 public boolean isFetchable(String source)
108 for (String db : fetchableDbs.keySet())
110 if (source.equalsIgnoreCase(db))
115 Cache.log.warn("isFetchable doesn't know about '" + source + "'");
120 * Fetch sequences for the given cross-references
124 * if true, only fetch from nucleotide data sources, else peptide
127 public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)
129 Vector<SequenceI> rseqs = new Vector<SequenceI>();
130 Hashtable<String, List<String>> queries = new Hashtable<String, List<String>>();
131 for (DBRefEntry ref : refs)
133 if (!queries.containsKey(ref.getSource()))
135 queries.put(ref.getSource(), new ArrayList<String>());
137 List<String> qset = queries.get(ref.getSource());
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<String>();
158 queriesLeft.addAll(query);
160 List<DbSourceProxy> proxies = getSourceProxy(db);
161 for (DbSourceProxy fetcher : proxies)
163 List<String> queriesMade = new ArrayList<String>();
164 HashSet<String> queriesFound = new HashSet<String>();
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 List<DBRefEntry> frefs = DBRefUtils.searchRefs(
208 seqs[is].getDBRefs(),
209 new DBRefEntry(db, null, null));
210 for (DBRefEntry dbr : frefs)
212 queriesFound.add(dbr.getAccessionId());
213 queriesMade.remove(dbr.getAccessionId());
220 if (fetcher.getRawRecords() != null)
223 "# Retrieved from " + db + ":" + qsb.toString());
224 StringBuffer rrb = fetcher.getRawRecords();
226 * for (int rr = 0; rr<rrb.length; rr++) {
231 hdr = "# " + db + ":" + qsb.toString();
233 * } else { hdr = "# part "+rr; }
235 System.out.println(hdr);
238 System.out.println(rrb);
240 System.out.println("# end of " + hdr);
247 } catch (Exception ex)
249 reportStdError(db, queriesMade, ex);
251 if (queriesMade.size() > 0)
253 System.out.println("# Adding " + queriesMade.size()
254 + " ids back to queries list for searching again (" + db
256 queriesLeft.addAll(queriesMade);
261 SequenceI[] result = null;
262 if (rseqs.size() > 0)
264 result = new SequenceI[rseqs.size()];
266 for (SequenceI s : rseqs)
275 public void reportStdError(String db, List<String> queriesMade,
280 "Failed to retrieve the following references from " + db);
282 for (String qv : queriesMade)
284 System.err.print(" " + qv + ";");
287 System.err.println();
291 System.err.println();
292 ex.printStackTrace();
296 * Returns a list of proxies for the given source
299 * database source string TODO: add version string/wildcard for
300 * retrieval of specific DB source/version combinations.
301 * @return a list of DbSourceProxy for the db
303 public List<DbSourceProxy> getSourceProxy(String db)
305 db = DBRefUtils.getCanonicalName(db);
306 Map<String, DbSourceProxy> dblist = fetchableDbs.get(db);
309 return new ArrayList<DbSourceProxy>();
313 * sort so that primary sources precede secondary
315 List<DbSourceProxy> dbs = new ArrayList<DbSourceProxy>(dblist.values());
316 Collections.sort(dbs, proxyComparator);
321 * constructs an instance of the proxy and registers it as a valid dbrefsource
323 * @param dbSourceProxy
324 * reference for class implementing
325 * jalview.ws.seqfetcher.DbSourceProxy
327 protected void addDBRefSourceImpl(
328 Class<? extends DbSourceProxy> dbSourceProxy)
329 throws IllegalArgumentException
331 DbSourceProxy proxy = null;
334 DbSourceProxy proxyObj = dbSourceProxy.getConstructor().newInstance();
336 } catch (IllegalArgumentException e)
339 } catch (Exception e)
341 // Serious problems if this happens.
342 throw new Error(MessageManager
343 .getString("error.dbrefsource_implementation_exception"), e);
345 addDbRefSourceImpl(proxy);
349 * add the properly initialised DbSourceProxy object 'proxy' to the list of
354 protected void addDbRefSourceImpl(DbSourceProxy proxy)
358 if (fetchableDbs == null)
360 fetchableDbs = new Hashtable<String, Map<String, DbSourceProxy>>();
362 Map<String, DbSourceProxy> slist = fetchableDbs
363 .get(proxy.getDbSource());
366 fetchableDbs.put(proxy.getDbSource(),
367 slist = new Hashtable<String, DbSourceProxy>());
369 slist.put(proxy.getDbName(), proxy);
374 * select sources which are implemented by instances of the given class
377 * that implements DbSourceProxy
378 * @return null or vector of source names for fetchers
380 public String[] getDbInstances(Class class1)
382 if (!DbSourceProxy.class.isAssignableFrom(class1))
384 throw new Error(MessageManager.formatMessage(
385 "error.implementation_error_dbinstance_must_implement_interface",
387 { class1.toString() }));
389 if (fetchableDbs == null)
393 String[] sources = null;
394 Vector<String> src = new Vector<String>();
395 Enumeration<String> dbs = fetchableDbs.keys();
396 while (dbs.hasMoreElements())
398 String dbn = dbs.nextElement();
399 for (DbSourceProxy dbp : fetchableDbs.get(dbn).values())
401 if (class1.isAssignableFrom(dbp.getClass()))
409 src.copyInto(sources = new String[src.size()]);
414 public DbSourceProxy[] getDbSourceProxyInstances(Class class1)
416 List<DbSourceProxy> prlist = new ArrayList<DbSourceProxy>();
417 for (String fetchable : getSupportedDb())
419 for (DbSourceProxy pr : getSourceProxy(fetchable))
421 if (class1.isInstance(pr))
427 if (prlist.size() == 0)
431 return prlist.toArray(new DbSourceProxy[0]);
435 * Returns a preferred feature colouring scheme for the given source, or null
436 * if none is defined.
441 public FeatureSettingsModelI getFeatureColourScheme(String source)
444 * return the first non-null colour scheme for any proxy for
445 * this database source
447 for (DbSourceProxy proxy : getSourceProxy(source))
449 FeatureSettingsModelI preferredColours = proxy
450 .getFeatureColourScheme();
451 if (preferredColours != null)
453 return preferredColours;