-
- /**
- * simple run method to test dbsources.
- *
- * @param argv
- */
- public static void main(String[] argv)
- {
- AlignmentI ds = null;
- Vector noProds = new Vector();
- String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n"
- + "With no arguments, all DbSources will be queried with their test Accession number.\n"
- + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
- + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
- + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
- boolean withDas=true;
- if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))
- {
- withDas=false;
- String targs[] = new String[argv.length-1];
- System.arraycopy(argv, 1, targs, 0, targs.length);
- argv=targs;
- }
- if (argv != null && argv.length > 0)
- {
- List<DbSourceProxy> sps = new SequenceFetcher(withDas)
- .getSourceProxy(argv[0]);
-
- if (sps != null)
- {
- for (DbSourceProxy sp : sps)
- {
- AlignmentI al = null;
- try
- {
- al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());
- } catch (Exception e)
- {
- e.printStackTrace();
- System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())
- + " from " + argv[0] + "\nUsage: " + usage);
- }
- SequenceI[] prod = al.getSequencesArray();
- if (al != null)
- {
- for (int p = 0; p < prod.length; p++)
- {
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true) + " : "
- + prod[p].getDescription());
- }
- }
- }
- return;
- }
- else
- {
- System.err.println("Can't resolve " + argv[0]
- + " as a database name. Allowed values are :\n"
- + new SequenceFetcher().getSupportedDb());
- }
- System.out.println(usage);
- return;
- }
- ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
- String[] dbSources = sfetcher.getSupportedDb();
- for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
- {
- String db = dbSources[dbsource];
- // skip me
- if (db.equals(DBRefSource.PDB))
- continue;
- for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
- {
- System.out.println("Source: " + sp.getDbName() + " (" + db
- + "): retrieving test:" + sp.getTestQuery());
- AlignmentI al = null;
- try
- {
- al = sp.getSequenceRecords(sp.getTestQuery());
- if (al != null && al.getHeight() > 0
- && sp.getDbSourceProperties() != null)
- {
- boolean dna = sp.getDbSourceProperties().containsKey(
- DBRefSource.DNACODINGSEQDB)
- || sp.getDbSourceProperties().containsKey(
- DBRefSource.DNASEQDB)
- || sp.getDbSourceProperties().containsKey(
- DBRefSource.CODINGSEQDB);
- // try and find products
- String types[] = jalview.analysis.CrossRef
- .findSequenceXrefTypes(dna, al.getSequencesArray());
- if (types != null)
- {
- System.out.println("Xref Types for: "
- + (dna ? "dna" : "prot"));
- for (int t = 0; t < types.length; t++)
- {
- System.out.println("Type: " + types[t]);
- SequenceI[] prod = jalview.analysis.CrossRef
- .findXrefSequences(al.getSequencesArray(), dna,
- types[t]).getSequencesArray();
- System.out.println("Found "
- + ((prod == null) ? "no" : "" + prod.length)
- + " products");
- if (prod != null)
- {
- for (int p = 0; p < prod.length; p++)
- {
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true));
- }
- }
- }
- }
- else
- {
- noProds.addElement((dna ? new Object[]
- { al, al } : new Object[]
- { al }));
- }
-
- }
- } catch (Exception ex)
- {
- System.out.println("ERROR:Failed to retrieve test query.");
- ex.printStackTrace(System.out);
- }
-
- if (al == null)
- {
- System.out.println("ERROR:No alignment retrieved.");
- StringBuffer raw = sp.getRawRecords();
- if (raw != null)
- System.out.println(raw.toString());
- else
- System.out.println("ERROR:No Raw results.");
- }
- else
- {
- System.out.println("Retrieved " + al.getHeight() + " sequences.");
- for (int s = 0; s < al.getHeight(); s++)
- {
- SequenceI sq = al.getSequenceAt(s);
- while (sq.getDatasetSequence() != null)
- {
- sq = sq.getDatasetSequence();
-
- }
- if (ds == null)
- {
- ds = new Alignment(new SequenceI[]
- { sq });
-
- }
- else
- {
- ds.addSequence(sq);
- }
- }
- }
- System.out.flush();
- System.err.flush();
-
- }
- if (noProds.size() > 0)
- {
- Enumeration ts = noProds.elements();
- while (ts.hasMoreElements())
-
- {
- Object[] typeSq = (Object[]) ts.nextElement();
- boolean dna = (typeSq.length > 1);
- AlignmentI al = (AlignmentI) typeSq[0];
- System.out.println("Trying getProducts for "
- + al.getSequenceAt(0).getDisplayId(true));
- System.out.println("Search DS Xref for: "
- + (dna ? "dna" : "prot"));
- // have a bash at finding the products amongst all the retrieved
- // sequences.
- SequenceI[] seqs = al.getSequencesArray();
- Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
- seqs, dna, null, ds);
- System.out.println("Found "
- + ((prodal == null) ? "no" : "" + prodal.getHeight())
- + " products");
- if (prodal != null)
- {
- SequenceI[] prod = prodal.getSequencesArray(); // note
- // should
- // test
- // rather
- // than
- // throw
- // away
- // codon
- // mapping
- // (if
- // present)
- for (int p = 0; p < prod.length; p++)
- {
- System.out.println("Prod " + p + ": "
- + prod[p].getDisplayId(true));
- }
- }
- }
-
- }
-
- }
- }
-
- /**
- * query the currently defined DAS source registry for sequence sources and
- * add a DasSequenceSource instance for each source to the SequenceFetcher
- * source list.
- */
- public void registerDasSequenceSources()
- {
- // TODO: define a context as a registry provider (either desktop,
- // jalview.bin.cache, or something else).
- for (jalviewSourceI source : jalview.bin.Cache.getDasSourceRegistry()
- .getSources())
- {
- if (source.isSequenceSource())
- {
- List<DbSourceProxy> dassources = source.getSequenceSourceProxies();
- for (DbSourceProxy seqsrc : dassources)
- {
- addDbRefSourceImpl(seqsrc);
- }
- }
- }
- }
-