From: Ben Soares Date: Thu, 13 Dec 2018 14:50:02 +0000 (+0000) Subject: JAL-3130 Fixing a few more tests that pass on a Mac but not on linux (e.g. jv-bamboo) X-Git-Tag: Release_2_11_0~17^2~7^2~58^2~7 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=aa548e5d9f568e4c5456d1670c297deae9cae0f2 JAL-3130 Fixing a few more tests that pass on a Mac but not on linux (e.g. jv-bamboo) --- diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java index 09a9713..22c9098 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/StructureManager.java @@ -121,8 +121,8 @@ public class StructureManager for (String chimObjName : names) { // get or open the corresponding models if they already exist - List currentModels = chimeraManager.getChimeraModels( - chimObjName, type); + List currentModels = chimeraManager + .getChimeraModels(chimObjName, type); if (currentModels.size() == 0) { // open and return models @@ -562,11 +562,11 @@ public class StructureManager // Get the corresponding "real" model if (chimeraManager.hasChimeraModel(modelNumber, subModelNumber)) { - ChimeraModel dataModel = chimeraManager.getChimeraModel( - modelNumber, subModelNumber); - if (dataModel.getResidueCount() == selectedModel - .getResidueCount() - || dataModel.getModelType() == StructureManager.ModelType.SMILES) + ChimeraModel dataModel = chimeraManager + .getChimeraModel(modelNumber, subModelNumber); + if (dataModel.getResidueCount() == selectedModel.getResidueCount() + || dataModel + .getModelType() == StructureManager.ModelType.SMILES) { // Select the entire model addChimSelection(dataModel); @@ -576,8 +576,8 @@ public class StructureManager { for (ChimeraChain selectedChain : selectedModel.getChains()) { - ChimeraChain dataChain = dataModel.getChain(selectedChain - .getChainId()); + ChimeraChain dataChain = dataModel + .getChain(selectedChain.getChainId()); if (selectedChain.getResidueCount() == dataChain .getResidueCount()) { @@ -931,6 +931,7 @@ public class StructureManager pathList.add("/usr/local/chimera/bin/chimera"); pathList.add("/usr/local/bin/chimera"); pathList.add("/usr/bin/chimera"); + pathList.add(System.getProperty("user.home") + "/opt/bin/chimera"); } else if (os.startsWith("Windows")) { 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(); diff --git a/test/jalview/io/IdentifyFileTest.java b/test/jalview/io/IdentifyFileTest.java index dd4f6ba..cf7f58f 100644 --- a/test/jalview/io/IdentifyFileTest.java +++ b/test/jalview/io/IdentifyFileTest.java @@ -89,12 +89,11 @@ public class IdentifyFileTest @DataProvider(name = "identifyFiles") public Object[][] IdentifyFileDP() { - return new Object[][] { - { "examples/example.json", FileFormat.Json }, + return new Object[][] { { "examples/example.json", FileFormat.Json }, { "examples/plantfdx.fa", FileFormat.Fasta }, { "examples/dna_interleaved.phy", FileFormat.Phylip }, { "examples/2GIS.pdb", FileFormat.PDB }, - { "examples/rf00031_folded.stk", FileFormat.Stockholm }, + { "examples/RF00031_folded.stk", FileFormat.Stockholm }, { "examples/testdata/test.rnaml", FileFormat.Rnaml }, { "examples/testdata/test.aln", FileFormat.Clustal }, { "examples/testdata/test.pfam", FileFormat.Pfam }, @@ -107,13 +106,12 @@ public class IdentifyFileTest { "examples/testdata/simpleGff3.gff", FileFormat.Features }, { "examples/testdata/test.jvp", FileFormat.Jalview }, { "examples/testdata/test.cif", FileFormat.MMCif }, - { - "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316", + { "examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316", FileFormat.Fasta }, { "resources/scoreModel/pam250.scm", FileFormat.ScoreMatrix }, { "resources/scoreModel/blosum80.scm", FileFormat.ScoreMatrix } - // { "examples/testdata/test.amsa", "AMSA" }, - // { "examples/test.jnet", "JnetFile" }, + // { "examples/testdata/test.amsa", "AMSA" }, + // { "examples/test.jnet", "JnetFile" }, }; } @@ -126,8 +124,8 @@ public class IdentifyFileTest // too few columns: assertFalse(id.looksLikeFeatureData("1 \t 2 \t 3 \t 4 \t 5")); // GFF format: - assertTrue(id - .looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss")); + assertTrue( + id.looksLikeFeatureData("Seq1\tlocal\tHelix\t2456\t2462\tss")); // Jalview format: assertTrue(id.looksLikeFeatureData("Helix\tSeq1\t-1\t2456\t2462\tss")); // non-numeric start column: diff --git a/test/jalview/util/PlatformTest.java b/test/jalview/util/PlatformTest.java index 470e64d..2e5a786 100644 --- a/test/jalview/util/PlatformTest.java +++ b/test/jalview/util/PlatformTest.java @@ -61,11 +61,11 @@ public class PlatformTest assertFalse(Platform.isControlDown(new MouseEvent(b, 0, 0L, mods, 0, 0, 0, 0, clickCount, isPopupTrigger, buttonNo), mac)); - mods = InputEvent.CTRL_DOWN_MASK; + mods = InputEvent.CTRL_DOWN_MASK | InputEvent.BUTTON1_DOWN_MASK; assertFalse(Platform.isControlDown(new MouseEvent(b, 0, 0L, mods, 0, 0, 0, 0, clickCount, isPopupTrigger, buttonNo), mac)); - mods = InputEvent.META_DOWN_MASK; + mods = InputEvent.META_DOWN_MASK | InputEvent.BUTTON1_DOWN_MASK; assertTrue(Platform.isControlDown(new MouseEvent(b, 0, 0L, mods, 0, 0, 0, 0, clickCount, isPopupTrigger, buttonNo), mac));