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package jalview.ws; |
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import jalview.analysis.CrossRef; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.DBRefSource; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.JvOptionPane; |
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import jalview.ws.seqfetcher.ASequenceFetcher; |
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import jalview.ws.seqfetcher.DbSourceProxy; |
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import java.util.Enumeration; |
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import java.util.HashMap; |
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import java.util.List; |
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import java.util.Map; |
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import java.util.Vector; |
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import org.testng.Assert; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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| 9.6% |
Uncovered Elements: 132 (146) |
Complexity: 35 |
Complexity Density: 0.39 |
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public class SequenceFetcherTest |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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| 62.5% |
Uncovered Elements: 6 (16) |
Complexity: 4 |
Complexity Density: 0.4 |
1PASS
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@Test(groups = "Functional")... |
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public void testNoDuplicatesInFetchDbRefs() |
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{ |
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Map<String, List<DbSourceProxy>> seen = new HashMap<>(); |
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jalview.ws.SequenceFetcher sfetcher = new jalview.ws.SequenceFetcher(); |
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String dupes = ""; |
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for (String src : sfetcher.getNonAlignmentSources()) |
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{ |
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List<DbSourceProxy> seenitem = seen.get(src); |
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if (seenitem != null) |
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{ |
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dupes += (dupes.length() > 0 ? "," : "") + src; |
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} |
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else |
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{ |
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seen.put(src, sfetcher.getSourceProxy(src)); |
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} |
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} |
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if (dupes.length() > 0) |
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{ |
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Assert.fail("Duplicate sources : " + dupes); |
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} |
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} |
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@param |
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| 0% |
Uncovered Elements: 40 (40) |
Complexity: 11 |
Complexity Density: 0.42 |
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public static void main(String[] argv)... |
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{ |
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String usage = "SequenceFetcher.main [-nodas] [<DBNAME> [<ACCNO>]]\n" |
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+ "With no arguments, all DbSources will be queried with their test Accession number.\n" |
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+ "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" |
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+ "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it."; |
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if (argv != null && argv.length > 0) |
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{ |
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String targs[] = new String[argv.length - 1]; |
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System.arraycopy(argv, 1, targs, 0, targs.length); |
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argv = targs; |
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} |
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if (argv != null && argv.length > 0) |
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{ |
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List<DbSourceProxy> sps = new SequenceFetcher() |
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.getSourceProxy(argv[0]); |
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if (sps != null) |
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{ |
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for (DbSourceProxy sp : sps) |
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{ |
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AlignmentI al = null; |
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try |
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{ |
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testRetrieval(argv[0], sp, |
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argv.length > 1 ? argv[1] : sp.getTestQuery()); |
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} catch (Exception e) |
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{ |
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e.printStackTrace(); |
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System.err.println("Error when retrieving " |
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+ (argv.length > 1 ? argv[1] : sp.getTestQuery()) |
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+ " from " + argv[0] + "\nUsage: " + usage); |
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} |
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} |
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return; |
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} |
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else |
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{ |
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System.err.println("Can't resolve " + argv[0] |
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+ " as a database name. Allowed values are :\n" |
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+ new SequenceFetcher().getSupportedDb()); |
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} |
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System.out.println(usage); |
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return; |
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} |
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ASequenceFetcher sfetcher = new SequenceFetcher(); |
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String[] dbSources = sfetcher.getSupportedDb(); |
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for (int dbsource = 0; dbsource < dbSources.length; dbsource++) |
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{ |
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String db = dbSources[dbsource]; |
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if (db.equals(DBRefSource.PDB)) |
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{ |
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continue; |
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} |
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for (DbSourceProxy sp : sfetcher.getSourceProxy(db)) |
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{ |
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testRetrieval(db, sp, sp.getTestQuery()); |
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} |
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} |
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} |
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| 0% |
Uncovered Elements: 84 (84) |
Complexity: 19 |
Complexity Density: 0.37 |
|
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private static void testRetrieval(String db, DbSourceProxy sp,... |
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String testQuery) |
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{ |
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AlignmentI ds = null; |
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Vector<Object[]> noProds = new Vector<>(); |
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System.out.println("Source: " + sp.getDbName() + " (" + db |
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+ "): retrieving test:" + sp.getTestQuery()); |
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{ |
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AlignmentI al = null; |
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try |
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{ |
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al = sp.getSequenceRecords(testQuery); |
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if (al != null && al.getHeight() > 0) |
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{ |
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boolean dna = sp.isDnaCoding(); |
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al.setDataset(null); |
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AlignmentI alds = al.getDataset(); |
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CrossRef crossRef = new CrossRef(al.getSequencesArray(), alds); |
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List<String> types = crossRef.findXrefSourcesForSequences(dna); |
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if (types != null) |
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{ |
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System.out.println("Xref Types for: " + (dna ? "dna" : "prot")); |
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for (String source : types) |
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{ |
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System.out.println("Type: " + source); |
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SequenceI[] prod = crossRef.findXrefSequences(source, dna) |
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.getSequencesArray(); |
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System.out.println( |
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"Found " + ((prod == null) ? "no" : "" + prod.length) |
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+ " products"); |
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if (prod != null) |
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{ |
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for (int p = 0; p < prod.length; p++) |
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{ |
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System.out.println( |
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"Prod " + p + ": " + prod[p].getDisplayId(true)); |
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} |
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} |
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} |
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} |
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else |
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{ |
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noProds.addElement( |
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(dna ? new Object[] |
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{ al, al } : new Object[] { al })); |
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} |
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} |
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} catch (Exception ex) |
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{ |
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System.out.println("ERROR:Failed to retrieve test query."); |
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ex.printStackTrace(System.out); |
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} |
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if (al == null) |
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{ |
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System.out.println("ERROR:No alignment retrieved."); |
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StringBuffer raw = sp.getRawRecords(); |
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if (raw != null) |
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{ |
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System.out.println(raw.toString()); |
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} |
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else |
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{ |
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System.out.println("ERROR:No Raw results."); |
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} |
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} |
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else |
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{ |
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System.out.println("Retrieved " + al.getHeight() + " sequences."); |
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if (ds == null) |
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{ |
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ds = al.getDataset(); |
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} |
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else |
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{ |
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ds.append(al.getDataset()); |
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al.setDataset(ds); |
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} |
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} |
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System.out.flush(); |
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System.err.flush(); |
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} |
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if (noProds.size() > 0) |
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{ |
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Enumeration<Object[]> ts = noProds.elements(); |
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while (ts.hasMoreElements()) |
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{ |
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Object[] typeSq = ts.nextElement(); |
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boolean dna = (typeSq.length > 1); |
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AlignmentI al = (AlignmentI) typeSq[0]; |
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System.out.println("Trying getProducts for " |
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+ al.getSequenceAt(0).getDisplayId(true)); |
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System.out.println("Search DS Xref for: " + (dna ? "dna" : "prot")); |
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SequenceI[] seqs = al.getSequencesArray(); |
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Alignment prodal = new CrossRef(seqs, ds).findXrefSequences(null, |
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dna); |
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System.out.println("Found " |
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+ ((prodal == null) ? "no" : "" + prodal.getHeight()) |
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+ " products"); |
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if (prodal != null) |
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{ |
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SequenceI[] prod = prodal.getSequencesArray(); |
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for (int p = 0; p < prod.length; p++) |
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{ |
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System.out.println( |
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"Prod " + p + ": " + prod[p].getDisplayId(true)); |
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} |
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} |
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} |
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} |
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} |
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} |