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package jalview.ws.seqfetcher; |
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import jalview.api.FeatureSettingsModelI; |
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import jalview.bin.Cache; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.DBRefEntry; |
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import jalview.datamodel.SequenceI; |
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import jalview.util.DBRefUtils; |
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import jalview.util.MessageManager; |
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import java.util.ArrayList; |
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import java.util.Collections; |
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import java.util.Comparator; |
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import java.util.Enumeration; |
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import java.util.HashSet; |
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import java.util.Hashtable; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Stack; |
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import java.util.Vector; |
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| 19.6% |
Uncovered Elements: 181 (225) |
Complexity: 50 |
Complexity Density: 0.34 |
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public class ASequenceFetcher |
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{ |
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protected Hashtable<String, Map<String, DbSourceProxy>> fetchableDbs; |
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private Comparator<DbSourceProxy> proxyComparator; |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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protected ASequenceFetcher()... |
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{ |
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super(); |
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proxyComparator = new Comparator<DbSourceProxy>() |
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{ |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 4 |
Complexity Density: 0.57 |
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0 |
@Override... |
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public int compare(DbSourceProxy o1, DbSourceProxy o2) |
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{ |
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int compared = Integer.compare(o1.getTier(), o2.getTier()); |
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if (compared == 0) |
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{ |
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String o1Name = o1.getDbName(); |
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String o2Name = o2.getDbName(); |
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if (o1Name != null && o2Name != null) |
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{ |
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compared = o1Name.compareToIgnoreCase(o2Name); |
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} |
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} |
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return compared; |
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} |
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}; |
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} |
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@return |
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| 66.7% |
Uncovered Elements: 2 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
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public String[] getSupportedDb()... |
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{ |
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if (fetchableDbs == null) |
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{ |
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return null; |
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} |
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String[] sf = fetchableDbs.keySet() |
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.toArray(new String[fetchableDbs.size()]); |
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return sf; |
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} |
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| 0% |
Uncovered Elements: 7 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
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public boolean isFetchable(String source)... |
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{ |
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for (String db : fetchableDbs.keySet()) |
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{ |
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if (source.equalsIgnoreCase(db)) |
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{ |
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return true; |
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} |
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} |
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Cache.log.warn("isFetchable doesn't know about '" + source + "'"); |
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return false; |
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} |
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@param |
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@param |
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@return |
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| 0% |
Uncovered Elements: 103 (103) |
Complexity: 19 |
Complexity Density: 0.26 |
|
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public SequenceI[] getSequences(List<DBRefEntry> refs, boolean dna)... |
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{ |
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Vector<SequenceI> rseqs = new Vector<>(); |
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Hashtable<String, List<String>> queries = new Hashtable<>(); |
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for (DBRefEntry ref : refs) |
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{ |
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String canonical = DBRefUtils.getCanonicalName(ref.getSource()); |
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if (!queries.containsKey(canonical)) |
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{ |
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queries.put(canonical, new ArrayList<String>()); |
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} |
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List<String> qset = queries.get(canonical); |
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if (!qset.contains(ref.getAccessionId())) |
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{ |
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qset.add(ref.getAccessionId()); |
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} |
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} |
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Enumeration<String> e = queries.keys(); |
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while (e.hasMoreElements()) |
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{ |
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List<String> query = null; |
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String db = null; |
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db = e.nextElement(); |
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query = queries.get(db); |
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if (!isFetchable(db)) |
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{ |
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reportStdError(db, query, new Exception( |
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"Don't know how to fetch from this database :" + db)); |
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continue; |
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} |
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Stack<String> queriesLeft = new Stack<>(); |
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queriesLeft.addAll(query); |
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List<DbSourceProxy> proxies = getSourceProxy(db); |
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for (DbSourceProxy fetcher : proxies) |
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{ |
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List<String> queriesMade = new ArrayList<>(); |
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HashSet<String> queriesFound = new HashSet<>(); |
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try |
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{ |
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if (fetcher.isDnaCoding() != dna) |
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{ |
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continue; |
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} |
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boolean doMultiple = fetcher.getMaximumQueryCount() > 1; |
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while (!queriesLeft.isEmpty()) |
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{ |
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StringBuffer qsb = new StringBuffer(); |
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do |
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{ |
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if (qsb.length() > 0) |
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{ |
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qsb.append(fetcher.getAccessionSeparator()); |
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} |
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String q = queriesLeft.pop(); |
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queriesMade.add(q); |
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qsb.append(q); |
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} while (doMultiple && !queriesLeft.isEmpty()); |
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AlignmentI seqset = null; |
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try |
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{ |
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seqset = fetcher.getSequenceRecords(qsb.toString()); |
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} catch (Exception ex) |
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{ |
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System.err.println( |
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"Failed to retrieve the following from " + db); |
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System.err.println(qsb); |
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ex.printStackTrace(System.err); |
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} |
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if (seqset != null) |
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{ |
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SequenceI seqs[] = seqset.getSequencesArray(); |
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if (seqs != null) |
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{ |
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for (int is = 0; is < seqs.length; is++) |
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{ |
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rseqs.addElement(seqs[is]); |
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List<DBRefEntry> frefs = DBRefUtils.searchRefs( |
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seqs[is].getDBRefs(), |
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new DBRefEntry(db, null, null), DBRefUtils.SEARCH_MODE_FULL); |
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for (DBRefEntry dbr : frefs) |
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{ |
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queriesFound.add(dbr.getAccessionId()); |
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queriesMade.remove(dbr.getAccessionId()); |
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} |
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seqs[is] = null; |
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} |
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} |
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else |
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{ |
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if (fetcher.getRawRecords() != null) |
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{ |
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System.out.println( |
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"# Retrieved from " + db + ":" + qsb.toString()); |
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StringBuffer rrb = fetcher.getRawRecords(); |
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String hdr; |
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hdr = "# " + db + ":" + qsb.toString(); |
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System.out.println(hdr); |
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if (rrb != null) |
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{ |
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System.out.println(rrb); |
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} |
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System.out.println("# end of " + hdr); |
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} |
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} |
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} |
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} |
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} catch (Exception ex) |
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{ |
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reportStdError(db, queriesMade, ex); |
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} |
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if (queriesMade.size() > 0) |
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{ |
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System.out.println("# Adding " + queriesMade.size() |
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+ " ids back to queries list for searching again (" + db |
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+ ")"); |
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queriesLeft.addAll(queriesMade); |
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} |
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} |
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} |
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263 |
0 |
SequenceI[] result = null; |
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if (rseqs.size() > 0) |
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{ |
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result = new SequenceI[rseqs.size()]; |
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int si = 0; |
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for (SequenceI s : rseqs) |
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{ |
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result[si++] = s; |
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s.updatePDBIds(); |
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} |
273 |
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} |
274 |
0 |
return result; |
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} |
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| 0% |
Uncovered Elements: 11 (11) |
Complexity: 2 |
Complexity Density: 0.22 |
|
277 |
0 |
public void reportStdError(String db, List<String> queriesMade,... |
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Exception ex) |
279 |
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{ |
280 |
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281 |
0 |
System.err.println( |
282 |
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"Failed to retrieve the following references from " + db); |
283 |
0 |
int n = 0; |
284 |
0 |
for (String qv : queriesMade) |
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{ |
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0 |
System.err.print(" " + qv + ";"); |
287 |
0 |
if (n++ > 10) |
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{ |
289 |
0 |
System.err.println(); |
290 |
0 |
n = 0; |
291 |
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} |
292 |
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} |
293 |
0 |
System.err.println(); |
294 |
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ex.printStackTrace(); |
295 |
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} |
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297 |
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298 |
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299 |
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300 |
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@param |
301 |
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302 |
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@return |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
305 |
22720 |
public List<DbSourceProxy> getSourceProxy(String db)... |
306 |
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{ |
307 |
22720 |
db = DBRefUtils.getCanonicalName(db); |
308 |
22720 |
Map<String, DbSourceProxy> dblist = fetchableDbs.get(db); |
309 |
22720 |
if (dblist == null) |
310 |
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{ |
311 |
1 |
return new ArrayList<>(); |
312 |
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} |
313 |
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314 |
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|
315 |
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|
316 |
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317 |
22719 |
List<DbSourceProxy> dbs = new ArrayList<>(dblist.values()); |
318 |
22719 |
Collections.sort(dbs, proxyComparator); |
319 |
22719 |
return dbs; |
320 |
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} |
321 |
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322 |
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324 |
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325 |
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@param |
326 |
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327 |
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328 |
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| 71.4% |
Uncovered Elements: 2 (7) |
Complexity: 3 |
Complexity Density: 0.43 |
|
329 |
64 |
protected void addDBRefSourceImpl(... |
330 |
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Class<? extends DbSourceProxy> dbSourceProxy) |
331 |
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throws IllegalArgumentException |
332 |
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{ |
333 |
64 |
DbSourceProxy proxy = null; |
334 |
64 |
try |
335 |
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{ |
336 |
64 |
DbSourceProxy proxyObj = dbSourceProxy.getConstructor().newInstance(); |
337 |
64 |
proxy = proxyObj; |
338 |
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} catch (IllegalArgumentException e) |
339 |
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{ |
340 |
0 |
throw e; |
341 |
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} catch (Exception e) |
342 |
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{ |
343 |
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|
344 |
0 |
throw new Error(MessageManager |
345 |
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.getString("error.dbrefsource_implementation_exception"), e); |
346 |
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} |
347 |
64 |
addDbRefSourceImpl(proxy); |
348 |
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} |
349 |
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|
350 |
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|
351 |
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|
352 |
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|
353 |
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|
354 |
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@param |
355 |
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|
|
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| 84.6% |
Uncovered Elements: 2 (13) |
Complexity: 4 |
Complexity Density: 0.57 |
|
356 |
64 |
protected void addDbRefSourceImpl(DbSourceProxy proxy)... |
357 |
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{ |
358 |
64 |
if (proxy != null) |
359 |
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{ |
360 |
64 |
if (fetchableDbs == null) |
361 |
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{ |
362 |
8 |
fetchableDbs = new Hashtable<>(); |
363 |
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} |
364 |
64 |
Map<String, DbSourceProxy> slist = fetchableDbs |
365 |
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.get(proxy.getDbSource()); |
366 |
64 |
if (slist == null) |
367 |
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{ |
368 |
64 |
fetchableDbs.put(proxy.getDbSource(), |
369 |
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slist = new Hashtable<>()); |
370 |
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} |
371 |
64 |
slist.put(proxy.getDbName(), proxy); |
372 |
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} |
373 |
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} |
374 |
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375 |
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376 |
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377 |
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|
378 |
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@param |
379 |
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380 |
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@return |
381 |
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| 0% |
Uncovered Elements: 25 (25) |
Complexity: 6 |
Complexity Density: 0.4 |
|
382 |
0 |
public String[] getDbInstances(Class class1)... |
383 |
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{ |
384 |
0 |
if (!DbSourceProxy.class.isAssignableFrom(class1)) |
385 |
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{ |
386 |
0 |
throw new Error(MessageManager.formatMessage( |
387 |
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"error.implementation_error_dbinstance_must_implement_interface", |
388 |
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new String[] |
389 |
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{ class1.toString() })); |
390 |
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} |
391 |
0 |
if (fetchableDbs == null) |
392 |
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{ |
393 |
0 |
return null; |
394 |
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} |
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 |
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{ |
400 |
0 |
String dbn = dbs.nextElement(); |
401 |
0 |
for (DbSourceProxy dbp : fetchableDbs.get(dbn).values()) |
402 |
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{ |
403 |
0 |
if (class1.isAssignableFrom(dbp.getClass())) |
404 |
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{ |
405 |
0 |
src.addElement(dbn); |
406 |
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} |
407 |
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} |
408 |
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} |
409 |
0 |
if (src.size() > 0) |
410 |
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{ |
411 |
0 |
src.copyInto(sources = new String[src.size()]); |
412 |
|
} |
413 |
0 |
return sources; |
414 |
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} |
415 |
|
|
|
|
| 0% |
Uncovered Elements: 12 (12) |
Complexity: 3 |
Complexity Density: 0.38 |
|
416 |
0 |
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 |
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{ |
423 |
0 |
if (class1.isInstance(pr)) |
424 |
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{ |
425 |
0 |
prlist.add(pr); |
426 |
|
} |
427 |
|
} |
428 |
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} |
429 |
0 |
if (prlist.size() == 0) |
430 |
|
{ |
431 |
0 |
return null; |
432 |
|
} |
433 |
0 |
return prlist.toArray(new DbSourceProxy[0]); |
434 |
|
} |
435 |
|
|
436 |
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|
437 |
|
|
438 |
|
|
439 |
|
|
440 |
|
@param |
441 |
|
@return |
442 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
443 |
4 |
public FeatureSettingsModelI getFeatureColourScheme(String source)... |
444 |
|
{ |
445 |
|
|
446 |
|
|
447 |
|
|
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 |
|
} |