+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ws;
-
-import jalview.analysis.CrossRef;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefSource;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-import jalview.ws.seqfetcher.ASequenceFetcher;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
-import java.util.Enumeration;
-import java.util.List;
-import java.util.Vector;
-
-import org.testng.annotations.BeforeClass;
-
-public class SequenceFetcherTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- /**
- * simple run method to test dbsources.
- *
- * @param argv
- * @j2sIgnore
- */
- public static void main(String[] argv)
- {
- // TODO: extracted from SequenceFetcher - convert to network dependent
- // functional integration test with
- // assertions
-
- 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.";
-
- if (argv != null && argv.length > 0)
- {
- 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 = SequenceFetcher.getInstance()
- .getSourceProxy(argv[0]);
-
- if (sps != null)
- {
- for (DbSourceProxy sp : sps)
- {
- // AlignmentI al = null;
- try
- {
- testRetrieval(argv[0], sp,
- 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);
- }
- }
- return;
- }
- else
- {
- System.err.println("Can't resolve " + argv[0]
- + " as a database name. Allowed values are :\n"
- + SequenceFetcher.getInstance().getSupportedDb());
- }
- System.out.println(usage);
- return;
- }
- ASequenceFetcher sfetcher = SequenceFetcher.getInstance();
- 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))
- {
- testRetrieval(db, sp, sp.getTestQuery());
- }
- }
-
- }
-
- private static void testRetrieval(String db, DbSourceProxy sp,
- String testQuery)
- {
- AlignmentI ds = null;
- Vector<Object[]> noProds = new Vector<>();
- System.out.println("Source: " + sp.getDbName() + " (" + db
- + "): retrieving test:" + sp.getTestQuery());
- {
- AlignmentI al = null;
- try
- {
- al = sp.getSequenceRecords(testQuery);
- if (al != null && al.getHeight() > 0)
- {
- boolean dna = sp.isDnaCoding();
- al.setDataset(null);
- AlignmentI alds = al.getDataset();
- // try and find products
- CrossRef crossRef = new CrossRef(al.getSequencesArray(), alds);
- List<String> types = crossRef.findXrefSourcesForSequences(dna);
- if (types != null)
- {
- System.out.println("Xref Types for: " + (dna ? "dna" : "prot"));
- for (String source : types)
- {
- System.out.println("Type: " + source);
- SequenceI[] prod = crossRef.findXrefSequences(source, dna)
- .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.");
- if (ds == null)
- {
- ds = al.getDataset();
- }
- else
- {
- ds.append(al.getDataset());
- al.setDataset(ds);
- }
- }
- System.out.flush();
- System.err.flush();
- }
- if (noProds.size() > 0)
- {
- Enumeration<Object[]> 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 = new CrossRef(seqs, ds).findXrefSequences(null,
- dna);
- 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));
- }
- }
- }
- }
- }
-}
git://source.jalview.org / jalview.git / blobdiff