From 5ddab6dda9d0e32e9b2d36cea1b41a7cd4a5371e Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Mon, 17 Dec 2018 15:16:57 +0000 Subject: [PATCH] JAL-3174 Merging in some test filename-case fixes --- test/jalview/ext/htsjdk/TestHtsContigDb.java | 20 ++++++++------ test/jalview/ext/jmol/JmolParserTest.java | 36 ++++++++++++++------------ 2 files changed, 31 insertions(+), 25 deletions(-) diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java index 28c5cf0..ad9bf03 100644 --- a/test/jalview/ext/htsjdk/TestHtsContigDb.java +++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java @@ -44,12 +44,12 @@ public class TestHtsContigDb @Test(groups = "Functional") public final void testGetSequenceProxy() throws Exception { - String pathname = "test/jalview/ext/htsjdk/pgmb.fasta"; + String pathname = "test/jalview/ext/htsjdk/pgmB.fasta"; HtsContigDb db = new HtsContigDb("ADB", new File(pathname)); - + assertTrue(db.isValid()); assertTrue(db.isIndexed()); // htsjdk opens the .fai file - + SequenceI sq = db.getSequenceProxy("Deminut"); assertNotNull(sq); assertEquals(sq.getLength(), 606); @@ -60,7 +60,7 @@ public class TestHtsContigDb sq = db.getSequenceProxy("PPL_06716"); assertNotNull(sq); assertEquals(sq.getLength(), 602); - + // dict = db.getDictionary(f, truncate)) } @@ -73,7 +73,7 @@ public class TestHtsContigDb expectedExceptions = java.lang.IllegalArgumentException.class) public final void testGetSequenceProxy_indexed() { - String pathname = "test/jalview/ext/htsjdk/pgmb.fasta.fai"; + String pathname = "test/jalview/ext/htsjdk/pgmB.fasta.fai"; new HtsContigDb("ADB", new File(pathname)); fail("Expected exception opening .fai file"); } @@ -92,16 +92,20 @@ public class TestHtsContigDb @Test(groups = "Functional") public void testCreateFastaSequenceIndex() throws IOException { - File fasta = new File("test/jalview/ext/htsjdk/pgmb.fasta"); - + File fasta = new File("test/jalview/ext/htsjdk/pgmB.fasta"); + /* * create .fai with no overwrite fails if it exists */ - try { + try + { HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false); fail("Expected exception"); } catch (IOException e) { + System.out.println( + "Caught IOException in testCreateFastaSequenceIndex"); + e.printStackTrace(); // expected } diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java index f5e637c..bcad464 100644 --- a/test/jalview/ext/jmol/JmolParserTest.java +++ b/test/jalview/ext/jmol/JmolParserTest.java @@ -62,9 +62,9 @@ public class JmolParserTest * 1GAQ has been reduced to alpha carbons only * 1QCF is the full PDB file including headers, HETATM etc */ - String[] testFile = new String[] { "./examples/1GAQ.txt", + String[] testFile = new String[] { "./examples/1gaq.txt", "./test/jalview/ext/jmol/1xyz.pdb", - "./test/jalview/ext/jmol/1qcf.pdb" }; + "./test/jalview/ext/jmol/1QCF.pdb" }; //@formatter:off // a modified and very cut-down extract of 4UJ4 @@ -130,17 +130,17 @@ public class JmolParserTest JmolParser jtest = new JmolParser(pdbStr, DataSourceType.FILE); Vector seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs(); - assertTrue( - "No sequences extracted from testfile\n" - + (jtest.hasWarningMessage() ? jtest.getWarningMessage() - : "(No warnings raised)"), seqs != null - && seqs.size() > 0); + assertTrue("No sequences extracted from testfile\n" + + (jtest.hasWarningMessage() ? jtest.getWarningMessage() + : "(No warnings raised)"), + seqs != null && seqs.size() > 0); for (SequenceI sq : seqs) { - assertEquals("JMol didn't process " + pdbStr - + " to the same sequence as MCView", - sq.getSequenceAsString(), mcseqs.remove(0) - .getSequenceAsString()); + assertEquals( + "JMol didn't process " + pdbStr + + " to the same sequence as MCView", + sq.getSequenceAsString(), + mcseqs.remove(0).getSequenceAsString()); AlignmentI al = new Alignment(new SequenceI[] { sq }); validateSecStrRows(al); } @@ -175,13 +175,15 @@ public class JmolParserTest private void checkFirstAAIsAssoc(SequenceI sq) { - assertTrue("No secondary structure assigned for protein sequence for " - + sq.getName(), + assertTrue( + "No secondary structure assigned for protein sequence for " + + sq.getName(), sq.getAnnotation() != null && sq.getAnnotation().length >= 1 && sq.getAnnotation()[0].hasIcons); assertTrue( "Secondary structure not associated for sequence " - + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq); + + sq.getName(), + sq.getAnnotation()[0].sequenceRef == sq); } /** @@ -194,7 +196,8 @@ public class JmolParserTest { PDBfile mctest = new PDBfile(false, false, false, pastePDBDataWithChainBreak, DataSourceType.PASTE); - JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak, DataSourceType.PASTE); + JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak, + DataSourceType.PASTE); Vector seqs = jtest.getSeqs(); Vector mcseqs = mctest.getSeqs(); @@ -216,8 +219,7 @@ public class JmolParserTest { PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc, DataSourceType.PASTE); - JmolParser jtest = new JmolParser(pdbWithAltLoc, - DataSourceType.PASTE); + JmolParser jtest = new JmolParser(pdbWithAltLoc, DataSourceType.PASTE); Vector seqs = jtest.getSeqs(); Vector mcseqs = mctest.getSeqs(); -- 1.7.10.2