From 0c43b6471604ebf707b0f592ad9bdbe932910a86 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 29 Aug 2016 12:10:10 +0100 Subject: [PATCH] JAL-2154 catch insertion of duplicate CDS after retrieve cross-references with Alignment.assertDatasetIsNormaised --- test/jalview/io/CrossRef2xmlTests.java | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index e7a6950..080bda8 100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@ -114,6 +114,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase AlignmentTest.assertAlignmentDatasetRefs(af.getViewport() .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + pass3 + "): Fetch " + first + ":"); + AlignmentTest.assertDatasetIsNormalised(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Fetch " + first + ":"); dna = af.getViewport().getAlignment().isNucleotide(); retral = af.getViewport().getAlignment(); dataset = retral.getDataset(); @@ -137,6 +140,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase AlignmentTest.assertAlignmentDatasetRefs(af.getViewport() .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + pass3 + "): Recover " + first + ":"); + AlignmentTest.assertDatasetIsNormalised(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Recover " + first + ":"); } @@ -229,6 +235,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase "Pass (" + pass1 + "," + pass2 + "," + pass3 + "): before start of pass3: " + nextxref + ":"); + AlignmentTest.assertDatasetIsNormalised(avp.getAlignment(), + "Pass (" + pass1 + "," + pass2 + "," + pass3 + + "): before start of pass3: " + nextxref + + ":"); SequenceI[] xrseqs = avp.getAlignment().getSequencesArray(); @@ -341,6 +351,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase nextavp.getAlignment(), "" + "Pass (" + pass1 + "," + pass2 + "): For " + nextnextxref + ":"); + AlignmentTest.assertDatasetIsNormalised( + nextavp.getAlignment(), "" + "Pass (" + pass1 + + "," + pass2 + "): For " + + nextnextxref + ":"); stringify(dbtoviewBit, savedProjects, nextnextxref, nextavp); -- 1.7.10.2