From: Jim Procter Date: Thu, 15 Oct 2015 18:28:27 +0000 (+0100) Subject: Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport X-Git-Tag: Release_2_10_0~296^2~134 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c75ca41e87495a7d86ebc3c8cbeb56610ac48758;p=jalview.git Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport --- c75ca41e87495a7d86ebc3c8cbeb56610ac48758 diff --cc .classpath index 255010a,473d937..9164f3d --- a/.classpath +++ b/.classpath @@@ -48,10 -46,9 +46,10 @@@ - + + diff --cc test/jalview/datamodel/SequenceDummyTest.java index ca1ac7d,229d0b1..e263843 --- a/test/jalview/datamodel/SequenceDummyTest.java +++ b/test/jalview/datamodel/SequenceDummyTest.java @@@ -1,10 -1,30 +1,31 @@@ + /* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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.datamodel; - import org.testng.Assert; - import org.testng.annotations.Test; + import static org.testng.AssertJUnit.assertFalse; + import static org.testng.AssertJUnit.assertTrue; + import org.testng.annotations.Test; +@Test public class SequenceDummyTest { /** diff --cc test/jalview/io/Gff3tests.java index 56b57af,b78a004..e4a6119 --- a/test/jalview/io/Gff3tests.java +++ b/test/jalview/io/Gff3tests.java @@@ -34,10 -59,9 +59,10 @@@ public class Gff3test af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null); - Assert.assertNotEquals( - assertTrue("Expected at least one DNA protein association", af - .getViewport().getAlignment().getDataset().getCodonFrames() - .size() > 0); ++ assertNotEquals("Expected at least one DNA protein association", + 0, af.getViewport().getAlignment().getDataset() + .getCodonFrames().size(), - "Expected at least one DNA protein association"); ++ ); } @@@ -103,39 -125,38 +126,39 @@@ 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(), - "Failed to replace dummy seq1 with real sequence"); - Assert.assertFalse( + && ((SequenceDummy) seq1).isDummy()); + assertFalse( + "Failed to replace dummy seq2 with real sequence", seq2 instanceof SequenceDummy - && ((SequenceDummy) seq2).isDummy()); + && ((SequenceDummy) seq2).isDummy(), + "Failed to replace dummy seq2 with real sequence"); String placeholderseq = new SequenceDummy("foo").getSequenceAsString(); - Assert.assertFalse(placeholderseq.equals(seq1.getSequenceAsString()), - "dummy replacement buggy for seq1"); - Assert.assertNotEquals("dummy replacement buggy for seq2", + assertFalse("dummy replacement buggy for seq1", + placeholderseq.equals(seq1.getSequenceAsString())); + assertFalse("dummy replacement buggy for seq2", placeholderseq.equals(seq2.getSequenceAsString())); - Assert.assertNotNull(seq1.getSequenceFeatures(), - "No features added to seq1"); - Assert.assertEquals(seq1.getSequenceFeatures().length, 3, - "Wrong number of features"); - Assert.assertNull(seq2.getSequenceFeatures()); - Assert.assertEquals( - seq2 - .getSequenceFeatures() == null ? 0 - : seq2 - .getSequenceFeatures().length, 0, - "Wrong number of features"); - Assert.assertTrue( - assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// != - // null); ++ assertNotNull("No features added to seq1", seq1.getSequenceFeatures()); + assertEquals("Wrong number of features", 3, + seq1.getSequenceFeatures().length); + 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); + && dataset.getCodonFrame(seq1).size() > 0, + "Expected at least one CDNA/Protein mapping for seq1"); } - // @Test + // @Test(groups ={ "Functional" }) // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject() // { // fail("Not yet implemented"); diff --cc test/jalview/io/HtmlFileTest.java index 09b8990,3b99208..6c13e26 --- a/test/jalview/io/HtmlFileTest.java +++ b/test/jalview/io/HtmlFileTest.java @@@ -1,14 -1,36 +1,34 @@@ + /* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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.junit.Assert.fail; - import org.testng.annotations.Test; public class HtmlFileTest { - @Test(enabled = false) + @Test(groups = { "Functional" }, enabled = false) public void test() { - fail("Not yet implemented"); + org.testng.AssertJUnit.fail("Not yet implemented"); } } diff --cc test/jalview/ws/jabaws/JalviewJabawsTestUtils.java index 91e9244,5426fce..46feebc --- a/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java +++ b/test/jalview/ws/jabaws/JalviewJabawsTestUtils.java @@@ -45,14 -47,14 +45,14 @@@ public class JalviewJabawsTestUtil /** * test servers */ - private static String[] serviceUrls = new String[] - { "http://localhost:8080/jabaws", + private static String[] serviceUrls = new String[] { + "http://localhost:8080/jabaws", "http://www.compbio.dundee.ac.uk/jabaws" }; - @Test(enabled = false) + @Test(groups = { "Functional" }, enabled = false) public void testAnnotExport() { - fail("Not yet implemented"); + Assert.fail("Not yet implemented"); } public static jalview.ws.jws2.Jws2Discoverer getJabawsDiscoverer() diff --cc utils/InstallAnywhere/Jalview.iap_xml index 4a9d96b,cd9987c..83d1a98 --- a/utils/InstallAnywhere/Jalview.iap_xml +++ b/utils/InstallAnywhere/Jalview.iap_xml @@@ -6775,11 -7306,16 +7358,17 @@@ and any path to a file to read from tha