2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.ws.seqfetcher;
20 import jalview.datamodel.AlignmentI;
21 import jalview.datamodel.DBRefEntry;
22 import jalview.datamodel.SequenceI;
23 import jalview.util.DBRefUtils;
25 import java.util.ArrayList;
26 import java.util.Enumeration;
27 import java.util.HashSet;
28 import java.util.Hashtable;
29 import java.util.Iterator;
30 import java.util.List;
32 import java.util.Stack;
33 import java.util.Vector;
35 public class ASequenceFetcher
39 * set of databases we can retrieve entries from
41 protected Hashtable<String, Map<String, DbSourceProxy>> FETCHABLEDBS;
43 public ASequenceFetcher()
49 * get list of supported Databases
51 * @return database source string for each database - only the latest version
52 * of a source db is bound to each source.
54 public String[] getSupportedDb()
56 if (FETCHABLEDBS == null)
58 String[] sf = new String[FETCHABLEDBS.size()];
59 Enumeration e = FETCHABLEDBS.keys();
61 while (e.hasMoreElements())
63 sf[i++] = (String) e.nextElement();
69 public boolean isFetchable(String source)
71 Enumeration e = FETCHABLEDBS.keys();
72 while (e.hasMoreElements())
74 String db = (String) e.nextElement();
75 if (source.compareToIgnoreCase(db) == 0)
78 jalview.bin.Cache.log.warn("isFetchable doesn't know about '" + source
83 public SequenceI[] getSequences(jalview.datamodel.DBRefEntry[] refs)
85 SequenceI[] ret = null;
86 Vector<SequenceI> rseqs = new Vector();
87 Hashtable<String, List<String>> queries = new Hashtable();
88 for (int r = 0; r < refs.length; r++)
90 if (!queries.containsKey(refs[r].getSource()))
92 queries.put(refs[r].getSource(), new ArrayList<String>());
94 List<String> qset = queries.get(refs[r].getSource());
95 if (!qset.contains(refs[r].getAccessionId()))
97 qset.add(refs[r].getAccessionId());
100 Enumeration<String> e = queries.keys();
101 while (e.hasMoreElements())
103 List<String> query = null;
105 db = e.nextElement();
106 query = queries.get(db);
107 if (!isFetchable(db))
109 reportStdError(db, query, new Exception(
110 "Don't know how to fetch from this database :" + db));
113 Iterator<DbSourceProxy> fetchers = getSourceProxy(db).iterator();
114 Stack<String> queriesLeft = new Stack<String>();
115 // List<String> queriesFailed = new ArrayList<String>();
116 queriesLeft.addAll(query);
117 while (fetchers.hasNext())
119 List<String> queriesMade = new ArrayList<String>();
120 HashSet queriesFound = new HashSet<String>();
123 DbSourceProxy fetcher = fetchers.next();
124 boolean doMultiple = fetcher.getAccessionSeparator() != null; // No
129 while (!queriesLeft.isEmpty())
131 StringBuffer qsb = new StringBuffer();
134 if (qsb.length() > 0)
136 qsb.append(fetcher.getAccessionSeparator());
138 String q = queriesLeft.pop();
141 } while (doMultiple && !queriesLeft.isEmpty());
143 AlignmentI seqset = null;
146 // create a fetcher and go to it
147 seqset = fetcher.getSequenceRecords(qsb.toString()); // ,
149 } catch (Exception ex)
151 System.err.println("Failed to retrieve the following from "
153 System.err.println(qsb);
154 ex.printStackTrace(System.err);
156 // TODO: Merge alignment together - perhaps
159 SequenceI seqs[] = seqset.getSequencesArray();
162 for (int is = 0; is < seqs.length; is++)
164 rseqs.addElement(seqs[is]);
165 DBRefEntry[] frefs = DBRefUtils.searchRefs(seqs[is]
166 .getDBRef(), new DBRefEntry(db, null, null));
169 for (DBRefEntry dbr : frefs)
171 queriesFound.add(dbr.getAccessionId());
172 queriesMade.remove(dbr.getAccessionId());
180 if (fetcher.getRawRecords() != null)
182 System.out.println("# Retrieved from " + db + ":"
184 StringBuffer rrb = fetcher.getRawRecords();
186 * for (int rr = 0; rr<rrb.length; rr++) {
191 hdr = "# " + db + ":" + qsb.toString();
193 * } else { hdr = "# part "+rr; }
195 System.out.println(hdr);
197 System.out.println(rrb);
198 System.out.println("# end of " + hdr);
205 } catch (Exception ex)
207 reportStdError(db, queriesMade, ex);
209 if (queriesMade.size() > 0)
211 System.out.println("# Adding " + queriesMade.size()
212 + " ids back to queries list for searching again (" + db
214 queriesLeft.addAll(queriesMade);
218 if (rseqs.size() > 0)
220 ret = new SequenceI[rseqs.size()];
221 Enumeration sqs = rseqs.elements();
223 while (sqs.hasMoreElements())
225 SequenceI s = (SequenceI) sqs.nextElement();
233 public void reportStdError(String db, List<String> queriesMade,
237 System.err.println("Failed to retrieve the following references from "
240 for (String qv : queriesMade)
242 System.err.print(" " + qv + ";");
245 System.err.println();
249 System.err.println();
250 ex.printStackTrace();
254 * Retrieve an instance of the proxy for the given source
257 * database source string TODO: add version string/wildcard for
258 * retrieval of specific DB source/version combinations.
259 * @return an instance of DbSourceProxy for that db.
261 public List<DbSourceProxy> getSourceProxy(String db)
263 List<DbSourceProxy> dbs;
264 Map<String, DbSourceProxy> dblist = FETCHABLEDBS.get(db);
267 return new ArrayList<DbSourceProxy>();
270 if (dblist.size() > 1)
272 DbSourceProxy[] l = dblist.values().toArray(new DbSourceProxy[0]);
274 String[] nm = new String[l.length];
275 for (DbSourceProxy s : l)
277 nm[i++] = s.getDbName().toLowerCase();
279 jalview.util.QuickSort.sort(nm, l);
280 dbs = new ArrayList<DbSourceProxy>();
281 for (i = l.length - 1; i >= 0; i--)
288 dbs = new ArrayList<DbSourceProxy>(dblist.values());
294 * constructs and instance of the proxy and registers it as a valid
297 * @param dbSourceProxy
298 * reference for class implementing
299 * jalview.ws.seqfetcher.DbSourceProxy
300 * @throws java.lang.IllegalArgumentException
301 * if class does not implement jalview.ws.seqfetcher.DbSourceProxy
303 protected void addDBRefSourceImpl(Class dbSourceProxy)
304 throws java.lang.IllegalArgumentException
306 DbSourceProxy proxy = null;
309 Object proxyObj = dbSourceProxy.getConstructor(null)
311 if (!DbSourceProxy.class.isInstance(proxyObj))
313 throw new IllegalArgumentException(
314 dbSourceProxy.toString()
315 + " does not implement the jalview.ws.seqfetcher.DbSourceProxy");
317 proxy = (DbSourceProxy) proxyObj;
318 } catch (IllegalArgumentException e)
321 } catch (Exception e)
323 // Serious problems if this happens.
324 throw new Error("DBRefSource Implementation Exception", e);
326 addDbRefSourceImpl(proxy);
330 * add the properly initialised DbSourceProxy object 'proxy' to the list of
335 protected void addDbRefSourceImpl(DbSourceProxy proxy)
339 if (FETCHABLEDBS == null)
341 FETCHABLEDBS = new Hashtable<String, Map<String, DbSourceProxy>>();
343 Map<String, DbSourceProxy> slist = FETCHABLEDBS.get(proxy
347 FETCHABLEDBS.put(proxy.getDbSource(),
348 slist = new Hashtable<String, DbSourceProxy>());
350 slist.put(proxy.getDbName(), proxy);
355 * test if the database handler for dbName contains the given dbProperty when
356 * a dbName resolves to a set of proxies - this method will return the result
357 * of the test for the first instance. TODO implement additional method to
358 * query all sources for a db to find one with a particular property
362 * @return true if proxy has the given property
364 public boolean hasDbSourceProperty(String dbName, String dbProperty)
366 // TODO: decide if invalidDbName exception is thrown here.
368 List<DbSourceProxy> proxies = getSourceProxy(dbName);
371 for (DbSourceProxy proxy : proxies)
373 if (proxy.getDbSourceProperties() != null)
375 return proxy.getDbSourceProperties().containsKey(dbProperty);
383 * select sources which are implemented by instances of the given class
385 * @param class that implements DbSourceProxy
386 * @return null or vector of source names for fetchers
388 public String[] getDbInstances(Class class1)
390 if (!jalview.ws.seqfetcher.DbSourceProxy.class.isAssignableFrom(class1))
393 "Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given '"
396 if (FETCHABLEDBS == null)
400 String[] sources = null;
401 Vector src = new Vector();
402 Enumeration dbs = FETCHABLEDBS.keys();
403 while (dbs.hasMoreElements())
405 String dbn = (String) dbs.nextElement();
406 for (DbSourceProxy dbp : FETCHABLEDBS.get(dbn).values())
408 if (class1.isAssignableFrom(dbp.getClass()))
416 src.copyInto(sources = new String[src.size()]);
421 public DbSourceProxy[] getDbSourceProxyInstances(Class class1)
423 ArrayList<DbSourceProxy> prlist = new ArrayList<DbSourceProxy>();
424 for (String fetchable : getSupportedDb())
425 for (DbSourceProxy pr : getSourceProxy(fetchable))
427 if (class1.isInstance(pr))
432 if (prlist.size() == 0)
436 return prlist.toArray(new DbSourceProxy[0]);