X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=434619ec59f1ea6bf0b1fe7dff586458582ed9fe;hb=b0cee3aaf7d8873910939f97b6acb217d518968d;hp=784f3dd11fc3893b22eb92b93e079303dfca2bbc;hpb=7e73e392838bbaaaff162532ef8e3e251b11f94a;p=jalview.git diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index 784f3dd..434619e 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -29,12 +29,11 @@ import static org.testng.AssertJUnit.assertTrue; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.ViewStyleI; -import jalview.bin.Cache; -import jalview.bin.Jalview; 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; @@ -42,75 +41,35 @@ 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; import java.io.File; import java.util.ArrayList; -import java.util.Date; import java.util.HashMap; import java.util.List; 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 - */ + @Override @BeforeClass(alwaysRun = true) - public static void setUpBeforeClass() throws Exception - { - /* - * use read-only test properties file - */ - Cache.loadProperties("test/jalview/io/testProps.jvprops"); - - /* - * set news feed last read to a future time to ensure no - * 'unread' news item is displayed - */ - Date oneHourFromNow = new Date(System.currentTimeMillis() + 3600 * 1000); - Cache.setDateProperty("JALVIEW_NEWS_RSS_LASTMODIFIED", oneHourFromNow); - - Jalview.main(new String[] {}); - } - - /** - * @throws java.lang.Exception - */ - @AfterClass(alwaysRun = true) - public static void tearDownAfterClass() throws Exception + public void setUpJvOptionPane() { - 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; + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } @Test(groups = { "Functional" }) @@ -119,21 +78,20 @@ public class Jalview2xmlTests 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); - af.rnahelicesColour_actionPerformed(null); + af.rnahelicesColour_actionPerformed(); assertTrue( "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( @@ -154,32 +112,27 @@ 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); - 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(), af.getViewport() + .getGlobalColourScheme().getSchemeName())); 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."); } @@ -190,19 +143,18 @@ 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); - 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); @@ -215,11 +167,10 @@ public class Jalview2xmlTests 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 @@ -227,7 +178,7 @@ public class Jalview2xmlTests 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; @@ -249,7 +200,7 @@ 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; @@ -275,9 +226,9 @@ public class Jalview2xmlTests { 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); @@ -286,14 +237,11 @@ public class Jalview2xmlTests @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()) { @@ -303,8 +251,7 @@ 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()) @@ -315,10 +262,13 @@ 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; @@ -350,9 +300,9 @@ public class Jalview2xmlTests @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()) { @@ -365,8 +315,8 @@ 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(); @@ -390,9 +340,8 @@ public class Jalview2xmlTests { 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(); @@ -423,8 +372,8 @@ 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(), DataSourceType.FILE); Assert.assertNotNull(af); Assert.assertEquals( Desktop.getAlignFrames().length, @@ -445,8 +394,8 @@ 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); + "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 @@ -489,7 +438,7 @@ public class Jalview2xmlTests } af = new FileLoader().LoadFileWaitTillLoaded( - tfile.getAbsolutePath(), FormatAdapter.FILE); + tfile.getAbsolutePath(), DataSourceType.FILE); afid = af.getViewport().getSequenceSetId(); for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) @@ -578,19 +527,19 @@ 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); + "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 @@ -607,7 +556,7 @@ 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) @@ -631,7 +580,8 @@ 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)); @@ -642,8 +592,7 @@ public class Jalview2xmlTests n++; } File tfile = File - .createTempFile("testStoreAndRecoverGroupReps", - ".jvp"); + .createTempFile("testStoreAndRecoverGroupReps", ".jvp"); try { new Jalview2XML(false).saveState(tfile); @@ -658,9 +607,9 @@ public class Jalview2xmlTests } 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(); @@ -684,8 +633,7 @@ 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()); } } @@ -700,8 +648,8 @@ public class Jalview2xmlTests Desktop.instance.closeAll_actionPerformed(null); String exampleFile = "examples/3W5V.pdb"; AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile, - FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + DataSourceType.FILE); + assertNotNull("Didn't read in the example file correctly.", af); String afid = af.getViewport().getSequenceSetId(); AlignmentPanel[] alignPanels = Desktop.getAlignmentPanels(afid); @@ -721,18 +669,18 @@ public class Jalview2xmlTests 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 @@ -749,7 +697,7 @@ public class Jalview2xmlTests } AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded( - tfile.getAbsolutePath(), FormatAdapter.FILE); + tfile.getAbsolutePath(), DataSourceType.FILE); String rfid = restoredFrame.getViewport().getSequenceSetId(); AlignmentPanel[] rAlignPanels = Desktop.getAlignmentPanels(rfid); AlignmentViewPanel rap = rAlignPanels[0]; @@ -767,13 +715,19 @@ public class Jalview2xmlTests // The Asserts below are expected to fail until the PDB chainCode is // recoverable from a Jalview projects - Assert.assertTrue(rseqs[0].getDatasetSequence().getAllPDBEntries() - .get(0).equals(pdbEntries[0])); - Assert.assertTrue(rseqs[1].getDatasetSequence().getAllPDBEntries() - .get(0).equals(pdbEntries[1])); - Assert.assertTrue(rseqs[2].getDatasetSequence().getAllPDBEntries() - .get(0).equals(pdbEntries[2])); - Assert.assertTrue(rseqs[3].getDatasetSequence().getAllPDBEntries() - .get(0).equals(pdbEntries[3])); + 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"); + } } }