X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FGff3tests.java;h=faa4d430d73538f769f2db6024e212cfdb2f459d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=8df44df1519c36d8a17c2223e91679caf3c43e6c;hpb=12e8812e5c9d01ad910e6e1161d7b8886fd94f0e;p=jalview.git diff --git a/test/jalview/io/Gff3tests.java b/test/jalview/io/Gff3tests.java index 8df44df..faa4d43 100644 --- a/test/jalview/io/Gff3tests.java +++ b/test/jalview/io/Gff3tests.java @@ -1,5 +1,31 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.io; +import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertFalse; +import static org.testng.AssertJUnit.assertNotNull; +import static org.testng.AssertJUnit.assertNull; +import static org.testng.AssertJUnit.assertTrue; + import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceDummy; @@ -8,8 +34,7 @@ import jalview.gui.AlignFrame; import java.io.IOException; -import org.junit.Assert; -import org.junit.Test; +import org.testng.annotations.Test; public class Gff3tests { @@ -18,7 +43,7 @@ public class Gff3tests exonerateOutput = "examples/testdata/exonerateoutput.gff", simpleGff3file = "examples/testdata/simpleGff3.gff"; - @Test + @Test(groups = { "Functional" }) public void testExonerateImport() { // exonerate does not tag sequences after features, so we have a more @@ -29,64 +54,61 @@ public class Gff3tests AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs, FormatAdapter.FILE); - Assert.assertEquals("Unexpected number of DNA protein associations", 0, - af.getViewport().getAlignment().getCodonFrames().size()); + assertEquals("Unexpected number of DNA protein associations", 0, af + .getViewport().getAlignment().getCodonFrames().size()); af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null); - Assert.assertNotEquals("Expected at least one DNA protein association", - 0, af.getViewport().getAlignment().getDataset() - .getCodonFrames().size()); + assertTrue("Expected at least one DNA protein association", af + .getViewport().getAlignment().getDataset().getCodonFrames() + .size() > 0); } - @Test + @Test(groups = { "Functional" }) public void simpleGff3FileIdentify() { - Assert.assertEquals("Didn't recognise file correctly.", - IdentifyFile.GFF3File, + assertEquals("Didn't recognise file correctly.", IdentifyFile.GFF3File, new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE)); } - @Test + @Test(groups = { "Functional" }) public void simpleGff3FileClass() throws IOException { - AlignmentI dataset = new Alignment(new SequenceI[] - {}); + AlignmentI dataset = new Alignment(new SequenceI[] {}); FeaturesFile ffile = new FeaturesFile(simpleGff3file, FormatAdapter.FILE); boolean parseResult = ffile.parse(dataset, null, null, false, false); - Assert.assertTrue("return result should be true", parseResult); + assertTrue("return result should be true", parseResult); checkDatasetfromSimpleGff3(dataset); } - @Test + @Test(groups = { "Functional" }) public void simpleGff3FileLoader() throws IOException { AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( simpleGff3file, FormatAdapter.FILE); - Assert.assertTrue( + assertTrue( "Didn't read the alignment into an alignframe from Gff3 File", af != null); checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset()); } - @Test + @Test(groups = { "Functional" }) public void simpleGff3RelaxedIdMatching() throws IOException { - AlignmentI dataset = new Alignment(new SequenceI[] - {}); + AlignmentI dataset = new Alignment(new SequenceI[] {}); FeaturesFile ffile = new FeaturesFile(simpleGff3file, FormatAdapter.FILE); boolean parseResult = ffile.parse(dataset, null, null, false, true); - Assert.assertTrue("return result (relaxedID matching) should be true", + assertTrue("return result (relaxedID matching) should be true", parseResult); checkDatasetfromSimpleGff3(dataset); } - @Test + @Test(groups = { "Functional" }) public void readGff3File() throws IOException { Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE); @@ -98,47 +120,49 @@ public class Gff3tests private void checkDatasetfromSimpleGff3(AlignmentI dataset) { - Assert.assertEquals("no sequences extracted from GFF3 file", 2, + assertEquals("no sequences extracted from GFF3 file", 2, dataset.getHeight()); SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset .findName("seq2"); - Assert.assertNotNull(seq1); - Assert.assertNotNull(seq2); - Assert.assertFalse( + assertNotNull(seq1); + assertNotNull(seq2); + assertFalse( "Failed to replace dummy seq1 with real sequence", seq1 instanceof SequenceDummy && ((SequenceDummy) seq1).isDummy()); - Assert.assertFalse( + assertFalse( "Failed to replace dummy seq2 with real sequence", seq2 instanceof SequenceDummy && ((SequenceDummy) seq2).isDummy()); String placeholderseq = new SequenceDummy("foo").getSequenceAsString(); - Assert.assertFalse("dummy replacement buggy for seq1", + assertFalse("dummy replacement buggy for seq1", placeholderseq.equals(seq1.getSequenceAsString())); - Assert.assertNotEquals("dummy replacement buggy for seq2", + assertFalse("dummy replacement buggy for seq2", placeholderseq.equals(seq2.getSequenceAsString())); - Assert.assertNotNull("No features added to seq1", - seq1.getSequenceFeatures());// != null); - Assert.assertEquals("Wrong number of features", 3, + assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// != + // null); + assertEquals("Wrong number of features", 3, seq1.getSequenceFeatures().length); - Assert.assertNull(seq2.getSequenceFeatures()); - Assert.assertEquals("Wrong number of features", 0, seq2 - .getSequenceFeatures() == null ? 0 - : seq2.getSequenceFeatures().length); - Assert.assertTrue( + assertNull(seq2.getSequenceFeatures()); + assertEquals( + "Wrong number of features", + 0, + seq2.getSequenceFeatures() == null ? 0 : seq2 + .getSequenceFeatures().length); + assertTrue( "Expected at least one CDNA/Protein mapping for seq1", dataset.getCodonFrame(seq1) != null && dataset.getCodonFrame(seq1).size() > 0); } - // @Test + // @Test(groups ={ "Functional" }) // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject() // { // fail("Not yet implemented"); // } // - // @Test + // @Test(groups ={ "Functional" }) // public final void testAlignFileBooleanStringString() // { // fail("Not yet implemented");