X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2FSequenceFetcherTest.java;h=a54ce8b203f3e0e1e5a7b20e0ddcf95c3d1256f9;hb=e66e65a8aa126254d4c45240bc28e1281d3c0825;hp=7a9b5532ac96e1cbb7d2d14de407971acabfbab3;hpb=409fd993c6e32e999b24082aae107a043a590f8f;p=jalview.git diff --git a/test/jalview/ws/SequenceFetcherTest.java b/test/jalview/ws/SequenceFetcherTest.java index 7a9b553..a54ce8b 100644 --- a/test/jalview/ws/SequenceFetcherTest.java +++ b/test/jalview/ws/SequenceFetcherTest.java @@ -25,7 +25,7 @@ public class SequenceFetcherTest // assertions AlignmentI ds = null; - Vector noProds = new Vector(); + 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" @@ -116,7 +116,8 @@ public class SequenceFetcherTest System.out.println("Type: " + types[t]); SequenceI[] prod = jalview.analysis.CrossRef .findXrefSequences(al.getSequencesArray(), dna, - types[t]).getSequencesArray(); + types[t], null) + .getSequencesArray(); System.out.println("Found " + ((prod == null) ? "no" : "" + prod.length) + " products"); @@ -184,11 +185,11 @@ public class SequenceFetcherTest } if (noProds.size() > 0) { - Enumeration ts = noProds.elements(); + Enumeration ts = noProds.elements(); while (ts.hasMoreElements()) { - Object[] typeSq = (Object[]) ts.nextElement(); + Object[] typeSq = ts.nextElement(); boolean dna = (typeSq.length > 1); AlignmentI al = (AlignmentI) typeSq[0]; System.out.println("Trying getProducts for "