From 84478e43fc8694f4c0c4c16515faf813744194da Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 3 Aug 2020 12:06:42 +0100 Subject: [PATCH] JAL-3692 fix up test for 2.11.1 series datamodel API --- test/jalview/io/EmblFlatFileTest.java | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java index 4ca826c..35b378b 100644 --- a/test/jalview/io/EmblFlatFileTest.java +++ b/test/jalview/io/EmblFlatFileTest.java @@ -18,7 +18,6 @@ import org.testng.annotations.Test; import jalview.datamodel.DBRefEntry; import jalview.datamodel.Mapping; -import jalview.datamodel.Sequence.DBModList; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.datamodel.features.SequenceFeatures; @@ -37,7 +36,7 @@ public class EmblFlatFileTest public void testParse() throws MalformedURLException, IOException { File dataFile = new File("test/jalview/io/J03321.embl.txt"); - FileParse fp = new FileParse(dataFile, DataSourceType.FILE); + FileParse fp = new FileParse(dataFile.getAbsolutePath(), DataSourceType.FILE); EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest"); parser.parse(); List seqs = parser.getSeqs(); @@ -127,7 +126,8 @@ public class EmblFlatFileTest * (some e.g. INTERPRO are duplicates). Jalview adds a dbref to 'self'. * Sample a few here. Note DBRefEntry constructor capitalises source. */ - List dbrefs = seq.getDBRefs(); + List dbrefs = Arrays.asList(seq.getDBRefs()); + assertEquals(dbrefs.size(), 32); // xref to 'self': DBRefEntry selfRef = new DBRefEntry("EMBLTEST", "1", "J03321"); @@ -256,7 +256,7 @@ public class EmblFlatFileTest List seqs = parser.getSeqs(); assertEquals(seqs.size(), 1); SequenceI seq = seqs.get(0); - DBModList dbrefs = seq.getDBRefs(); + List dbrefs = Arrays.asList(seq.getDBRefs()); /* * dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1 -- 1.7.10.2