From cf26b5f11d6edc9a83324fe8d0752e8a5de984fa Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 7 Sep 2016 10:26:25 +0100 Subject: [PATCH] JAL-2164 fix failing test --- test/jalview/io/Jalview2xmlTests.java | 162 ++++++++++++++++----------------- 1 file changed, 77 insertions(+), 85 deletions(-) diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index 39d2c89..3d53234 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -33,6 +33,7 @@ import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenSequences; import jalview.datamodel.PDBEntry; +import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; @@ -42,6 +43,8 @@ import jalview.gui.Desktop; import jalview.gui.Jalview2XML; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.TCoffeeColourScheme; import jalview.structure.StructureImportSettings; import jalview.viewmodel.AlignmentViewport; @@ -65,9 +68,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase String inFile = "examples/RF00031_folded.stk"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - inFile, FormatAdapter.FILE); - assertTrue("Didn't read input file " + inFile, af != null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, + FormatAdapter.FILE); + assertNotNull("Didn't read input file " + inFile, af); int olddsann = countDsAnn(af.getViewport()); assertTrue("Didn't find any dataset annotations", olddsann > 0); af.rnahelicesColour_actionPerformed(null); @@ -78,9 +81,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase af.saveAlignment(tfile, "Jalview")); af.closeMenuItem_actionPerformed(true); af = null; - af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - FormatAdapter.FILE); - assertTrue("Failed to import new project", af != null); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE); + assertNotNull("Failed to import new project", af); int newdsann = countDsAnn(af.getViewport()); assertTrue( "Differing numbers of dataset sequence annotation\nOriginally " @@ -100,32 +102,26 @@ public class Jalview2xmlTests extends Jalview2xmlBase String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - inFile, FormatAdapter.FILE); - assertTrue("Didn't read input file " + inFile, af != null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, + FormatAdapter.FILE); + assertNotNull("Didn't read input file " + inFile, af); af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null); - assertTrue( - "Didn't set T-coffee colourscheme", - af.getViewport().getGlobalColourScheme().getClass() - .equals(jalview.schemes.TCoffeeColourScheme.class)); - assertTrue( - "Recognise T-Coffee score from string", + assertSame("Didn't set T-coffee colourscheme", af.getViewport() + .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class); + assertNotNull("Recognise T-Coffee score from string", jalview.schemes.ColourSchemeProperty.getColour(af.getViewport() - .getAlignment(), - jalview.schemes.ColourSchemeProperty.getColourName(af - .getViewport().getGlobalColourScheme())) != null); + .getAlignment(), ColourSchemeProperty.getColourName(af + .getViewport().getGlobalColourScheme()))); assertTrue("Failed to store as a project.", af.saveAlignment(tfile, "Jalview")); af.closeMenuItem_actionPerformed(true); af = null; - af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - FormatAdapter.FILE); - assertTrue("Failed to import new project", af != null); - assertTrue( - "Didn't set T-coffee colourscheme for imported project.", - af.getViewport().getGlobalColourScheme().getClass() - .equals(jalview.schemes.TCoffeeColourScheme.class)); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE); + assertNotNull("Failed to import new project", af); + assertSame("Didn't set T-coffee colourscheme for imported project.", af + .getViewport().getGlobalColourScheme().getClass(), + TCoffeeColourScheme.class); System.out .println("T-Coffee score shading successfully recovered from project."); } @@ -136,19 +132,19 @@ public class Jalview2xmlTests extends Jalview2xmlBase String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - inFile, FormatAdapter.FILE); - assertTrue("Didn't read input file " + inFile, af != null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, + FormatAdapter.FILE); + assertNotNull("Didn't read input file " + inFile, af); af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null); AlignmentAnnotation[] aa = af.getViewport().getAlignment() .getSequenceAt(0).getAnnotation("IUPredWS (Short)"); assertTrue( "Didn't find any IUPred annotation to use to shade alignment.", aa != null && aa.length > 0); - AnnotationColourGradient cs = new jalview.schemes.AnnotationColourGradient( - aa[0], null, AnnotationColourGradient.ABOVE_THRESHOLD); - AnnotationColourGradient gcs = new jalview.schemes.AnnotationColourGradient( - aa[0], null, AnnotationColourGradient.BELOW_THRESHOLD); + AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null, + AnnotationColourGradient.ABOVE_THRESHOLD); + AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0], + null, AnnotationColourGradient.BELOW_THRESHOLD); cs.setSeqAssociated(true); gcs.setSeqAssociated(true); af.changeColour(cs); @@ -164,16 +160,15 @@ public class Jalview2xmlTests extends Jalview2xmlBase af.saveAlignment(tfile, "Jalview")); af.closeMenuItem_actionPerformed(true); af = null; - af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - FormatAdapter.FILE); - assertTrue("Failed to import new project", af != null); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE); + assertNotNull("Failed to import new project", af); // check for group and alignment colourschemes ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme(); ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups() .get(0).cs; - assertTrue("Didn't recover global colourscheme", _rcs != null); + assertNotNull("Didn't recover global colourscheme", _rcs); assertTrue("Didn't recover annotation colour global scheme", _rcs instanceof AnnotationColourGradient); AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs; @@ -195,7 +190,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase System.out .println("Per sequence colourscheme (Background) successfully applied and recovered."); - assertTrue("Didn't recover group colourscheme", _rgcs != null); + assertNotNull("Didn't recover group colourscheme", _rgcs); assertTrue("Didn't recover annotation colour group colourscheme", _rgcs instanceof AnnotationColourGradient); __rcs = (AnnotationColourGradient) _rgcs; @@ -221,9 +216,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase { int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop .getAlignFrames().length; - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); assertTrue("Didn't gather the views in the example file.", Desktop.getAlignFrames().length == 1 + origCount); @@ -232,14 +227,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void viewRefPdbAnnotation() throws Exception { - // TODO: Make this pass without setting StructureParser.JALVIEW_PARSER - // StructureImportSettings - // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER); StructureImportSettings.setProcessSecondaryStructure(true); StructureImportSettings.setVisibleChainAnnotation(true); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); AlignmentViewPanel sps = null; for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) { @@ -249,8 +241,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase break; } } - assertTrue("Couldn't find the structure view", sps != null); - SequenceI sq = sps.getAlignment().findName("1A70|"); + assertNotNull("Couldn't find the structure view", sps); AlignmentAnnotation refan = null; for (AlignmentAnnotation ra : sps.getAlignment() .getAlignmentAnnotation()) @@ -261,10 +252,13 @@ public class Jalview2xmlTests extends Jalview2xmlBase break; } } - assertTrue("Annotation secondary structure not found.", refan != null); - assertTrue("Couldn't find 1a70 null chain", sq != null); + assertNotNull("Annotation secondary structure not found.", refan); + SequenceI sq = sps.getAlignment().findName("1A70|"); + assertNotNull("Couldn't find 1a70 null chain", sq); // compare the manually added temperature factor annotation // to the track automatically transferred from the pdb structure on load + assertNotNull("1a70 has no annotation", sq.getDatasetSequence() + .getAnnotation()); for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation()) { AlignmentAnnotation alaa; @@ -296,9 +290,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void testCopyViewSettings() throws Exception { - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); AlignmentViewPanel sps = null, groups = null; for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) { @@ -311,8 +305,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase groups = ap; } } - assertTrue("Couldn't find the structure view", sps != null); - assertTrue("Couldn't find the MAFFT view", groups != null); + assertNotNull("Couldn't find the structure view", sps); + assertNotNull("Couldn't find the MAFFT view", groups); ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle(); ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle(); @@ -336,9 +330,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase { Desktop.instance.closeAll_actionPerformed(null); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); Assert.assertEquals(Desktop.getAlignFrames().length, 1); String afid = af.getViewport().getSequenceSetId(); @@ -369,8 +362,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase { Assert.assertEquals(Desktop.getAlignFrames().length, 0); } - af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - tfile.getAbsolutePath(), FormatAdapter.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + FormatAdapter.FILE); Assert.assertNotNull(af); Assert.assertEquals( Desktop.getAlignFrames().length, @@ -392,7 +385,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase Desktop.instance.closeAll_actionPerformed(null); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); String afid = af.getViewport().getSequenceSetId(); // remember reference sequence for each panel @@ -434,8 +427,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.assertEquals(Desktop.getAlignFrames().length, 0); } - af = new FileLoader().LoadFileWaitTillLoaded( - tfile.getAbsolutePath(), FormatAdapter.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + FormatAdapter.FILE); afid = af.getViewport().getSequenceSetId(); for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) @@ -525,18 +518,18 @@ public class Jalview2xmlTests extends Jalview2xmlBase Desktop.instance.closeAll_actionPerformed(null); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( "examples/uniref50.fa", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); String afid = af.getViewport().getSequenceSetId(); // make a second view of the alignment af.newView_actionPerformed(null); - + /* * remember representative and hidden sequences marked * on each panel */ Map repSeqs = new HashMap(); Map> hiddenSeqNames = new HashMap>(); - + /* * mark sequence 2, 3, 4.. in panels 1, 2, 3... * as reference sequence for itself and the preceding sequence @@ -553,7 +546,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase repSeqs.put(ap.getViewName(), repSeq); List hiddenNames = new ArrayList(); hiddenSeqNames.put(ap.getViewName(), hiddenNames); - + /* * have rep sequence represent itself and the one before it * this hides the group (except for the rep seq) @@ -577,7 +570,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(sg.getSequences().contains(repSeq)); assertTrue(sg.getSequences().contains(precedingSeq)); assertTrue("alignment has groups", alignment.getGroups().isEmpty()); - Map hiddenRepSeqsMap = av.getHiddenRepSequences(); + Map hiddenRepSeqsMap = av + .getHiddenRepSequences(); assertNotNull(hiddenRepSeqsMap); assertEquals(1, hiddenRepSeqsMap.size()); assertSame(sg, hiddenRepSeqsMap.get(repSeq)); @@ -588,8 +582,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase n++; } File tfile = File - .createTempFile("testStoreAndRecoverGroupReps", - ".jvp"); + .createTempFile("testStoreAndRecoverGroupReps", ".jvp"); try { new Jalview2XML(false).saveState(tfile); @@ -602,11 +595,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase { Assert.assertEquals(Desktop.getAlignFrames().length, 0); } - - af = new FileLoader().LoadFileWaitTillLoaded( - tfile.getAbsolutePath(), FormatAdapter.FILE); + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + FormatAdapter.FILE); afid = af.getViewport().getSequenceSetId(); - + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) { String viewName = ap.getViewName(); @@ -630,8 +623,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase HiddenSequences hs = alignment.getHiddenSequences(); assertEquals( "wrong number of restored hidden sequences in " - + ap.getViewName(), - hidden.size(), hs.getSize()); + + ap.getViewName(), hidden.size(), hs.getSize()); } } @@ -647,7 +639,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase String exampleFile = "examples/3W5V.pdb"; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile, FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + assertNotNull("Didn't read in the example file correctly.", af); String afid = af.getViewport().getSequenceSetId(); AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid); @@ -667,18 +659,18 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.assertNotNull(seqs[2].getDatasetSequence()); Assert.assertNotNull(seqs[3].getDatasetSequence()); PDBEntry[] pdbEntries = new PDBEntry[4]; - pdbEntries[0] = new PDBEntry("3W5V", "A", null, testFile); - pdbEntries[1] = new PDBEntry("3W5V", "B", null, testFile); - pdbEntries[2] = new PDBEntry("3W5V", "C", null, testFile); - pdbEntries[3] = new PDBEntry("3W5V", "D", null, testFile); - Assert.assertTrue(seqs[0].getDatasetSequence().getAllPDBEntries() - .get(0).equals(pdbEntries[0])); - Assert.assertTrue(seqs[1].getDatasetSequence().getAllPDBEntries() - .get(0).equals(pdbEntries[1])); - Assert.assertTrue(seqs[2].getDatasetSequence().getAllPDBEntries() - .get(0).equals(pdbEntries[2])); - Assert.assertTrue(seqs[3].getDatasetSequence().getAllPDBEntries() - .get(0).equals(pdbEntries[3])); + pdbEntries[0] = new PDBEntry("3W5V", "A", Type.PDB, testFile); + pdbEntries[1] = new PDBEntry("3W5V", "B", Type.PDB, testFile); + pdbEntries[2] = new PDBEntry("3W5V", "C", Type.PDB, testFile); + pdbEntries[3] = new PDBEntry("3W5V", "D", Type.PDB, testFile); + Assert.assertEquals(seqs[0].getDatasetSequence().getAllPDBEntries() + .get(0), pdbEntries[0]); + Assert.assertEquals(seqs[1].getDatasetSequence().getAllPDBEntries() + .get(0), pdbEntries[1]); + Assert.assertEquals(seqs[2].getDatasetSequence().getAllPDBEntries() + .get(0), pdbEntries[2]); + Assert.assertEquals(seqs[3].getDatasetSequence().getAllPDBEntries() + .get(0), pdbEntries[3]); File tfile = File.createTempFile("testStoreAndRecoverPDBEntry", ".jvp"); try -- 1.7.10.2