X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=0e066c28fc03cb97ce1875394bf24ae4c14d65a7;hb=d53fdb7d3610e7f8287f3c76592dd3c2b2aa03f3;hp=18e008ec823a91c96d5341f95f4ce8d0d0de7813;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java index 18e008e..0e066c2 100644 --- a/test/jalview/io/AnnotationFileIOTest.java +++ b/test/jalview/io/AnnotationFileIOTest.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -24,8 +24,11 @@ import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.io.AnnotationFile.ViewDef; import java.io.File; +import java.util.Hashtable; import org.junit.Test; @@ -44,7 +47,9 @@ public class AnnotationFileIOTest "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" }, { "Test group only annotation file parsing results in parser indicating annotation was parsed", - "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" } }; + "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" }, + { "Test hiding/showing of insertions on sequence_ref", + "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } }; @Test public void exampleAnnotationFileIO() throws Exception @@ -102,17 +107,20 @@ public class AnnotationFileIOTest try { AlignmentI al = readAlignmentFile(f); - + ColumnSelection cs = new ColumnSelection(); assertTrue( "Test " + testname + "\nAlignment was not annotated - annotation file not imported.", - new AnnotationFile().readAnnotationFile(al, af, + new AnnotationFile().readAnnotationFile(al, cs, af, FormatAdapter.FILE)); + AnnotationFile aff = new AnnotationFile(); + ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs, + new Hashtable()); String anfileout = new AnnotationFile().printAnnotations( al.getAlignmentAnnotation(), al.getGroups(), - al.getProperties()); + al.getProperties(), null, al, v); assertTrue( "Test " + testname @@ -136,7 +144,7 @@ public class AnnotationFileIOTest FormatAdapter.PASTE)); // test for consistency in io - StockholmFileTest.testAlignmentEquivalence(al, al_new); + StockholmFileTest.testAlignmentEquivalence(al, al_new, false); return; } catch (Exception e) {