X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=de1208675cbc52ad687dc9acbf290c74ba105464;hb=80ff57c095b792b8e8e123ddb0eff4d1780d6cbd;hp=a54d1902efcd07f8c65eb682ce5e5329c1bd1a17;hpb=309af01a4a460b17ef6b924a20057b372d8fbeac;p=jalview.git diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index a54d190..de12086 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -32,14 +32,20 @@ import jalview.api.ViewStyleI; 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; import jalview.gui.AlignFrame; +import jalview.gui.AlignmentPanel; import jalview.gui.Desktop; import jalview.gui.Jalview2XML; +import jalview.gui.JvOptionPane; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.TCoffeeColourScheme; import jalview.structure.StructureImportSettings; import jalview.viewmodel.AlignmentViewport; @@ -51,20 +57,28 @@ import java.util.Map; import org.testng.Assert; import org.testng.AssertJUnit; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @Test(singleThreaded = true) public class Jalview2xmlTests extends Jalview2xmlBase { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Test(groups = { "Functional" }) public void testRNAStructureRecovery() throws Exception { String inFile = "examples/RF00031_folded.stk"; String tfile = File.createTempFile("JalviewTest", ".jvp") .getAbsolutePath(); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - inFile, FormatAdapter.FILE); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + inFile, DataSourceType.FILE); assertTrue("Didn't read input file " + inFile, af != null); int olddsann = countDsAnn(af.getViewport()); assertTrue("Didn't find any dataset annotations", olddsann > 0); @@ -73,11 +87,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase "Couldn't apply RNA helices colourscheme", af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); assertTrue("Failed to store as a project.", - af.saveAlignment(tfile, "Jalview")); + af.saveAlignment(tfile, FileFormat.Jalview)); af.closeMenuItem_actionPerformed(true); af = null; - af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - FormatAdapter.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); assertTrue("Failed to import new project", af != null); int newdsann = countDsAnn(af.getViewport()); assertTrue( @@ -98,32 +111,27 @@ 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); - 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", - jalview.schemes.ColourSchemeProperty.getColour(af.getViewport() - .getAlignment(), - jalview.schemes.ColourSchemeProperty.getColourName(af - .getViewport().getGlobalColourScheme())) != null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + inFile, DataSourceType.FILE); + assertNotNull("Didn't read input file " + inFile, af); + af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); + assertSame("Didn't set T-coffee colourscheme", af.getViewport() + .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class); + assertNotNull("Recognise T-Coffee score from string", + ColourSchemeProperty.getColour(af.getViewport() + .getAlignment(), ColourSchemeProperty.getColourName(af + .getViewport().getGlobalColourScheme()))); assertTrue("Failed to store as a project.", - af.saveAlignment(tfile, "Jalview")); + af.saveAlignment(tfile, FileFormat.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, + DataSourceType.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."); } @@ -134,19 +142,18 @@ 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); - af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, DataSourceType.FILE); + assertNotNull("Didn't read input file " + inFile, af); + af.loadJalviewDataFile(inAnnot, DataSourceType.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); @@ -159,11 +166,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true); af.alignPanel.alignmentChanged(); assertTrue("Failed to store as a project.", - af.saveAlignment(tfile, "Jalview")); + af.saveAlignment(tfile, FileFormat.Jalview)); af.closeMenuItem_actionPerformed(true); af = null; - af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, - FormatAdapter.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); assertTrue("Failed to import new project", af != null); // check for group and alignment colourschemes @@ -171,7 +177,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase 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; @@ -193,7 +199,7 @@ 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; @@ -219,9 +225,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase { int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop .getAlignFrames().length; - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile_2_7.jar", DataSourceType.FILE); + 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); @@ -230,14 +236,11 @@ 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( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile_2_7.jar", DataSourceType.FILE); + assertNotNull("Didn't read in the example file correctly.", af); AlignmentViewPanel sps = null; for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) { @@ -247,8 +250,7 @@ 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()) @@ -259,10 +261,13 @@ 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; @@ -294,9 +299,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase @Test(groups = { "Functional" }) public void testCopyViewSettings() throws Exception { - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile_2_7.jar", DataSourceType.FILE); + assertNotNull("Didn't read in the example file correctly.", af); AlignmentViewPanel sps = null, groups = null; for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) { @@ -309,8 +314,8 @@ 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(); @@ -334,9 +339,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase { Desktop.instance.closeAll_actionPerformed(null); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile_2_7.jar", DataSourceType.FILE); Assert.assertEquals(Desktop.getAlignFrames().length, 1); String afid = af.getViewport().getSequenceSetId(); @@ -367,8 +371,8 @@ 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(), DataSourceType.FILE); Assert.assertNotNull(af); Assert.assertEquals( Desktop.getAlignFrames().length, @@ -389,8 +393,8 @@ 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); + "examples/exampleFile_2_7.jar", DataSourceType.FILE); + assertNotNull("Didn't read in the example file correctly.", af); String afid = af.getViewport().getSequenceSetId(); // remember reference sequence for each panel @@ -433,7 +437,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase } af = new FileLoader().LoadFileWaitTillLoaded( - tfile.getAbsolutePath(), FormatAdapter.FILE); + tfile.getAbsolutePath(), DataSourceType.FILE); afid = af.getViewport().getSequenceSetId(); for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) @@ -522,19 +526,19 @@ 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); + "examples/uniref50.fa", DataSourceType.FILE); + 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 @@ -551,7 +555,7 @@ 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) @@ -575,7 +579,8 @@ 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)); @@ -586,8 +591,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase n++; } File tfile = File - .createTempFile("testStoreAndRecoverGroupReps", - ".jvp"); + .createTempFile("testStoreAndRecoverGroupReps", ".jvp"); try { new Jalview2XML(false).saveState(tfile); @@ -602,9 +606,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase } af = new FileLoader().LoadFileWaitTillLoaded( - tfile.getAbsolutePath(), FormatAdapter.FILE); + tfile.getAbsolutePath(), DataSourceType.FILE); afid = af.getViewport().getSequenceSetId(); - + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) { String viewName = ap.getViewName(); @@ -628,8 +632,101 @@ 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()); + } + } + + /** + * Test save and reload of PDBEntry in Jalview project + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testStoreAndRecoverPDBEntry() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + String exampleFile = "examples/3W5V.pdb"; + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile, + DataSourceType.FILE); + assertNotNull("Didn't read in the example file correctly.", af); + String afid = af.getViewport().getSequenceSetId(); + + AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid); + System.out.println(); + AlignmentViewPanel ap = alignPanels[0]; + String tfileBase = new File(".").getAbsolutePath().replace(".", ""); + String testFile = tfileBase + exampleFile; + AlignmentI alignment = ap.getAlignment(); + System.out.println("blah"); + SequenceI[] seqs = alignment.getSequencesArray(); + Assert.assertNotNull(seqs[0]); + Assert.assertNotNull(seqs[1]); + Assert.assertNotNull(seqs[2]); + Assert.assertNotNull(seqs[3]); + Assert.assertNotNull(seqs[0].getDatasetSequence()); + Assert.assertNotNull(seqs[1].getDatasetSequence()); + Assert.assertNotNull(seqs[2].getDatasetSequence()); + Assert.assertNotNull(seqs[3].getDatasetSequence()); + PDBEntry[] pdbEntries = new PDBEntry[4]; + 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 + { + new Jalview2XML(false).saveState(tfile); + } catch (Throwable e) + { + Assert.fail("Didn't save the state", e); + } + Desktop.instance.closeAll_actionPerformed(null); + if (Desktop.getAlignFrames() != null) + { + Assert.assertEquals(Desktop.getAlignFrames().length, 0); + } + + AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded( + tfile.getAbsolutePath(), DataSourceType.FILE); + String rfid = restoredFrame.getViewport().getSequenceSetId(); + AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid); + AlignmentViewPanel rap = rAlignPanels[0]; + AlignmentI rAlignment = rap.getAlignment(); + System.out.println("blah"); + SequenceI[] rseqs = rAlignment.getSequencesArray(); + Assert.assertNotNull(rseqs[0]); + Assert.assertNotNull(rseqs[1]); + Assert.assertNotNull(rseqs[2]); + Assert.assertNotNull(rseqs[3]); + Assert.assertNotNull(rseqs[0].getDatasetSequence()); + Assert.assertNotNull(rseqs[1].getDatasetSequence()); + Assert.assertNotNull(rseqs[2].getDatasetSequence()); + Assert.assertNotNull(rseqs[3].getDatasetSequence()); + + // The Asserts below are expected to fail until the PDB chainCode is + // recoverable from a Jalview projects + for (int chain = 0; chain < 4; chain++) + { + PDBEntry recov = rseqs[chain].getDatasetSequence().getAllPDBEntries() + .get(0); + PDBEntry expected = pdbEntries[chain]; + Assert.assertEquals(recov.getId(), expected.getId(), + "Mismatch PDB ID"); + Assert.assertEquals(recov.getChainCode(), expected.getChainCode(), + "Mismatch PDB ID"); + Assert.assertEquals(recov.getType(), expected.getType(), + "Mismatch PDBEntry 'Type'"); + Assert.assertNotNull(recov.getFile(), + "Recovered PDBEntry should have a non-null file entry"); } } }