X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=3d53234fc634d316e1f5ae1a105d159a410d7ff6;hb=3e29fb36af9c48e07837e32b7e99c081b2461b2f;hp=38153df44959f69daef08227e56ea89e800cda2f;hpb=e56b8db4f9c6e0a51cf538d95bd2e007a2c92495;p=jalview.git diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index 38153df..3d53234 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -29,18 +29,23 @@ import static org.testng.AssertJUnit.assertTrue; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.ViewStyleI; -import jalview.bin.Cache; 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.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.TCoffeeColourScheme; +import jalview.structure.StructureImportSettings; import jalview.viewmodel.AlignmentViewport; import java.io.File; @@ -51,61 +56,21 @@ import java.util.Map; import org.testng.Assert; import org.testng.AssertJUnit; -import org.testng.annotations.AfterClass; -import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @Test(singleThreaded = true) -public class Jalview2xmlTests +public class Jalview2xmlTests extends Jalview2xmlBase { - /** - * @throws java.lang.Exception - */ - @BeforeClass(alwaysRun = true) - public static void setUpBeforeClass() throws Exception - { - jalview.bin.Jalview.main(new String[] { "-props", - "test/jalview/io/testProps.jvprops" }); - } - - /** - * @throws java.lang.Exception - */ - @AfterClass(alwaysRun = true) - public static void tearDownAfterClass() throws Exception - { - jalview.gui.Desktop.instance.closeAll_actionPerformed(null); - } - - int countDsAnn(jalview.viewmodel.AlignmentViewport avp) - { - int numdsann = 0; - for (SequenceI sq : avp.getAlignment().getDataset().getSequences()) - { - if (sq.getAnnotation() != null) - { - for (AlignmentAnnotation dssa : sq.getAnnotation()) - { - if (dssa.isValidStruc()) - { - numdsann++; - } - } - } - } - return numdsann; - } - @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); - 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); @@ -116,9 +81,8 @@ public class Jalview2xmlTests 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 " @@ -138,32 +102,26 @@ public class Jalview2xmlTests 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."); } @@ -174,19 +132,19 @@ public class Jalview2xmlTests 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); @@ -202,16 +160,15 @@ public class Jalview2xmlTests 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; @@ -233,7 +190,7 @@ public class Jalview2xmlTests 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; @@ -259,9 +216,9 @@ public class Jalview2xmlTests { 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); @@ -270,13 +227,11 @@ public class Jalview2xmlTests @Test(groups = { "Functional" }) public void viewRefPdbAnnotation() throws Exception { - Cache.applicationProperties.setProperty("STRUCT_FROM_PDB", - Boolean.TRUE.toString()); - Cache.applicationProperties.setProperty("ADD_SS_ANN", - Boolean.TRUE.toString()); - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + StructureImportSettings.setProcessSecondaryStructure(true); + StructureImportSettings.setVisibleChainAnnotation(true); + 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()) { @@ -286,8 +241,7 @@ public class Jalview2xmlTests 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()) @@ -298,10 +252,13 @@ public class Jalview2xmlTests 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; @@ -333,9 +290,9 @@ public class Jalview2xmlTests @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()) { @@ -348,8 +305,8 @@ public class Jalview2xmlTests 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(); @@ -364,37 +321,28 @@ public class Jalview2xmlTests } /** - * test store and recovery of expanded views - currently this is disabled - * since the Desktop.explodeViews method doesn't seem to result in the views - * being expanded to distinct align frames when executed programmatically. + * test store and recovery of expanded views * * @throws Exception */ @Test(groups = { "Functional" }, enabled = true) public void testStoreAndRecoverExpandedviews() throws Exception { - AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + 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); + Assert.assertEquals(Desktop.getAlignFrames().length, 1); String afid = af.getViewport().getSequenceSetId(); - { - final AlignFrame xaf = af; - af = null; - new Thread(new Runnable() - { - @Override - public void run() - { - Desktop.instance.explodeViews(xaf); - } - }).start(); - Thread.sleep(1000); - } - // int times = 0; - // while (++times < 5 && Desktop.getAlignFrames().length < ) - // { - // Thread.sleep(300); - // } + + // check FileLoader returned a reference to the one alignFrame that is + // actually on the Desktop + assertTrue( + "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window", + af == Desktop.getAlignFrameFor(af.getViewport())); + + Desktop.explodeViews(af); + int oldviews = Desktop.getAlignFrames().length; Assert.assertEquals(Desktop.getAlignFrames().length, Desktop.getAlignmentPanels(afid).length); @@ -414,8 +362,8 @@ public class Jalview2xmlTests { 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, @@ -437,7 +385,7 @@ public class Jalview2xmlTests 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 @@ -479,8 +427,8 @@ public class Jalview2xmlTests 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)) @@ -570,18 +518,18 @@ public class Jalview2xmlTests 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 @@ -598,7 +546,7 @@ public class Jalview2xmlTests 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) @@ -622,7 +570,8 @@ public class Jalview2xmlTests 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)); @@ -633,8 +582,7 @@ public class Jalview2xmlTests n++; } File tfile = File - .createTempFile("testStoreAndRecoverGroupReps", - ".jvp"); + .createTempFile("testStoreAndRecoverGroupReps", ".jvp"); try { new Jalview2XML(false).saveState(tfile); @@ -647,11 +595,11 @@ public class Jalview2xmlTests { 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(); @@ -675,8 +623,101 @@ public class Jalview2xmlTests 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, + FormatAdapter.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(), FormatAdapter.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"); } } }