package jalview.ws; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.DBRefSource; import jalview.datamodel.SequenceI; import jalview.ws.seqfetcher.ASequenceFetcher; import jalview.ws.seqfetcher.DbSourceProxy; import java.util.Enumeration; import java.util.List; import java.util.Vector; public class SequenceFetcherTest { /** * simple run method to test dbsources. * * @param argv */ public static void main(String[] argv) { // TODO: extracted from SequenceFetcher - convert to proper unit test with // assertions AlignmentI ds = null; Vector noProds = new Vector(); String usage = "SequenceFetcher.main [-nodas] [ []]\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 and retrieve 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 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) { boolean dna = sp.isDnaCoding(); // 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], null) .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 = 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)); } } } } } } }