X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=3baacc85452cf3117a8d91af99e7c50ea7f290ee;hb=ac5f0c912a1c7819530456bab13942ad3734460b;hp=38153df44959f69daef08227e56ea89e800cda2f;hpb=e56b8db4f9c6e0a51cf538d95bd2e007a2c92495;p=jalview.git diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java index 38153df..3baacc8 100644 --- a/test/jalview/io/Jalview2xmlTests.java +++ b/test/jalview/io/Jalview2xmlTests.java @@ -20,81 +20,102 @@ */ package jalview.io; -import static org.testng.AssertJUnit.assertEquals; -import static org.testng.AssertJUnit.assertFalse; -import static org.testng.AssertJUnit.assertNotNull; -import static org.testng.AssertJUnit.assertSame; -import static org.testng.AssertJUnit.assertTrue; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertFalse; +import static org.testng.Assert.assertNotNull; +import static org.testng.Assert.assertNull; +import static org.testng.Assert.assertSame; +import static org.testng.Assert.assertTrue; +import static org.testng.Assert.fail; +import jalview.analysis.PCA; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureColourI; 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.Point; import jalview.datamodel.SequenceCollectionI; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.datamodel.SequencePoint; +import jalview.datamodel.features.FeatureMatcher; +import jalview.datamodel.features.FeatureMatcherSet; +import jalview.datamodel.features.FeatureMatcherSetI; import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; +import jalview.gui.AlignmentPanel; +import jalview.gui.CalculationChooser; import jalview.gui.Desktop; +import jalview.gui.FeatureRenderer; import jalview.gui.Jalview2XML; +import jalview.gui.JvOptionPane; +import jalview.gui.PCAPanel; +import jalview.gui.PopupMenu; +import jalview.gui.RotatableCanvas; +import jalview.gui.SliderPanel; +import jalview.math.MatrixTest; +import jalview.renderer.ResidueShaderI; import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.BuriedColourScheme; import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.schemes.FeatureColour; +import jalview.schemes.JalviewColourScheme; +import jalview.schemes.RNAHelicesColour; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TCoffeeColourScheme; +import jalview.structure.StructureImportSettings; +import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.PCAModel; +import java.awt.Color; import java.io.File; +import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; +import javax.swing.JInternalFrame; +import javax.swing.JRadioButton; + import org.testng.Assert; import org.testng.AssertJUnit; -import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; +import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; +import junit.extensions.PA; + @Test(singleThreaded = true) -public class Jalview2xmlTests +public class Jalview2xmlTests extends Jalview2xmlBase { - - /** - * @throws java.lang.Exception - */ @BeforeClass(alwaysRun = true) - public static void setUpBeforeClass() throws Exception + public void setUp() { - jalview.bin.Jalview.main(new String[] { "-props", - "test/jalview/io/testProps.jvprops" }); + Cache.loadProperties("test/jalview/io/testProps.jvprops"); } - /** - * @throws java.lang.Exception - */ - @AfterClass(alwaysRun = true) - public static void tearDownAfterClass() throws Exception + @BeforeMethod(alwaysRun = true) + public void setUpMethod() { - jalview.gui.Desktop.instance.closeAll_actionPerformed(null); + Desktop.instance.closeAll_actionPerformed(null); } - int countDsAnn(jalview.viewmodel.AlignmentViewport avp) + @Override + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() { - 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" }) @@ -103,33 +124,34 @@ 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); - assertTrue("Didn't read input file " + inFile, af != null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, + DataSourceType.FILE); + assertNotNull(af, "Didn't read input file " + inFile); int olddsann = countDsAnn(af.getViewport()); - assertTrue("Didn't find any dataset annotations", olddsann > 0); - af.rnahelicesColour_actionPerformed(null); + assertTrue(olddsann > 0, "Didn't find any dataset annotations"); + af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices + .toString()); 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.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour, + "Couldn't apply RNA helices colourscheme"); + assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + "Failed to store as a project."); 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, DataSourceType.FILE); + assertNotNull(af, "Failed to import new project"); int newdsann = countDsAnn(af.getViewport()); - assertTrue( + assertEquals(olddsann, newdsann, "Differing numbers of dataset sequence annotation\nOriginally " - + olddsann + " and now " + newdsann, - olddsann == newdsann); + + olddsann + " and now " + newdsann); System.out .println("Read in same number of annotations as originally present (" + olddsann + ")"); assertTrue( - "RNA helices colourscheme was not applied on import.", - af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour); + + af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour, + "RNA helices colourscheme was not applied on import."); } @Test(groups = { "Functional" }) @@ -138,32 +160,26 @@ 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); - 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); - - assertTrue("Failed to store as a project.", - af.saveAlignment(tfile, "Jalview")); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile, + DataSourceType.FILE); + assertNotNull(af, "Didn't read input file " + inFile); + af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null); + assertSame(af.getViewport().getGlobalColourScheme().getClass(), + TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme"); + assertNotNull(ColourSchemeProperty.getColourScheme(af.getViewport() + .getAlignment(), af.getViewport().getGlobalColourScheme() + .getSchemeName()), "Recognise T-Coffee score from string"); + + assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + "Failed to store as a project."); 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(af, "Failed to import new project"); + assertSame(af.getViewport().getGlobalColourScheme().getClass(), + TCoffeeColourScheme.class, + "Didn't set T-coffee colourscheme for imported project."); System.out .println("T-Coffee score shading successfully recovered from project."); } @@ -174,82 +190,83 @@ 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(af, "Didn't read input file " + inFile); + 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); + + aa != null && aa.length > 0, + "Didn't find any IUPred annotation to use to shade alignment."); + 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); SequenceGroup sg = new SequenceGroup(); sg.setStartRes(57); sg.setEndRes(92); - sg.cs = gcs; + sg.cs.setColourScheme(gcs); af.getViewport().getAlignment().addGroup(sg); sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false); sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true); af.alignPanel.alignmentChanged(); - assertTrue("Failed to store as a project.", - af.saveAlignment(tfile, "Jalview")); + assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + "Failed to store as a project."); 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, DataSourceType.FILE); + assertNotNull(af, "Failed to import new project"); // 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); - assertTrue("Didn't recover annotation colour global scheme", - _rcs instanceof AnnotationColourGradient); + .get(0).getColourScheme(); + assertNotNull(_rcs, "Didn't recover global colourscheme"); + assertTrue(_rcs instanceof AnnotationColourGradient, + "Didn't recover annotation colour global scheme"); AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs; - assertTrue("Annotation colourscheme wasn't sequence associated", - __rcs.isSeqAssociated()); + assertTrue(__rcs.isSeqAssociated(), + "Annotation colourscheme wasn't sequence associated"); boolean diffseqcols = false, diffgseqcols = false; SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) { - if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs - .findColour(sqs[5].getCharAt(p), p, sqs[5])) + if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs + .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f)) { diffseqcols = true; } } - assertTrue("Got Different sequence colours", diffseqcols); + assertTrue(diffseqcols, "Got Different sequence colours"); System.out .println("Per sequence colourscheme (Background) successfully applied and recovered."); - assertTrue("Didn't recover group colourscheme", _rgcs != null); - assertTrue("Didn't recover annotation colour group colourscheme", - _rgcs instanceof AnnotationColourGradient); + assertNotNull(_rgcs, "Didn't recover group colourscheme"); + assertTrue(_rgcs instanceof AnnotationColourGradient, + "Didn't recover annotation colour group colourscheme"); __rcs = (AnnotationColourGradient) _rgcs; - assertTrue("Group Annotation colourscheme wasn't sequence associated", - __rcs.isSeqAssociated()); + assertTrue(__rcs.isSeqAssociated(), + "Group Annotation colourscheme wasn't sequence associated"); for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) { - if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs - .findColour(sqs[2].getCharAt(p), p, sqs[2])) + if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs + .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f)) { diffgseqcols = true; } } - assertTrue("Got Different group sequence colours", diffgseqcols); + assertTrue(diffgseqcols, "Got Different group sequence colours"); System.out .println("Per sequence (Group) colourscheme successfully applied and recovered."); } @@ -259,24 +276,47 @@ 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); - assertTrue("Didn't gather the views in the example file.", - Desktop.getAlignFrames().length == 1 + origCount); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile_2_7.jar", DataSourceType.FILE); + assertNotNull(af, "Didn't read in the example file correctly."); + assertTrue(Desktop.getAlignFrames().length == 1 + origCount, + "Didn't gather the views in the example file."); + + } + + /** + * Test for JAL-2223 - multiple mappings in View Mapping report + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void noDuplicatePdbMappingsMade() throws Exception + { + StructureImportSettings.setProcessSecondaryStructure(true); + StructureImportSettings.setVisibleChainAnnotation(true); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile_2_7.jar", DataSourceType.FILE); + assertNotNull(af, "Didn't read in the example file correctly."); + + // locate Jmol viewer + // count number of PDB mappings the structure selection manager holds - + String pdbFile = af.getCurrentView().getStructureSelectionManager() + .findFileForPDBId("1A70"); + assertEquals( + af.getCurrentView().getStructureSelectionManager() + .getMapping(pdbFile).length, + 2, "Expected only two mappings for 1A70"); } @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( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + StructureImportSettings.setProcessSecondaryStructure(true); + StructureImportSettings.setVisibleChainAnnotation(true); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile_2_7.jar", DataSourceType.FILE); + assertNotNull(af, "Didn't read in the example file correctly."); AlignmentViewPanel sps = null; for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) { @@ -286,8 +326,7 @@ public class Jalview2xmlTests break; } } - assertTrue("Couldn't find the structure view", sps != null); - SequenceI sq = sps.getAlignment().findName("1A70|"); + assertNotNull(sps, "Couldn't find the structure view"); AlignmentAnnotation refan = null; for (AlignmentAnnotation ra : sps.getAlignment() .getAlignmentAnnotation()) @@ -298,10 +337,13 @@ public class Jalview2xmlTests break; } } - assertTrue("Annotation secondary structure not found.", refan != null); - assertTrue("Couldn't find 1a70 null chain", sq != null); + assertNotNull(refan, "Annotation secondary structure not found."); + SequenceI sq = sps.getAlignment().findName("1A70|"); + assertNotNull(sq, "Couldn't find 1a70 null chain"); // compare the manually added temperature factor annotation // to the track automatically transferred from the pdb structure on load + assertNotNull(sq.getDatasetSequence().getAnnotation(), + "1a70 has no annotation"); for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation()) { AlignmentAnnotation alaa; @@ -315,9 +357,9 @@ public class Jalview2xmlTests try { assertTrue( - "Mismatch at alignment position " + p, (alaa.annotations[p] == null && refan.annotations[p] == null) - || alaa.annotations[p].value == refan.annotations[p].value); + || alaa.annotations[p].value == refan.annotations[p].value, + "Mismatch at alignment position " + p); } catch (NullPointerException q) { Assert.fail("Mismatch of alignment annotations at position " @@ -333,9 +375,9 @@ 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(af, "Didn't read in the example file correctly."); AlignmentViewPanel sps = null, groups = null; for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels()) { @@ -348,8 +390,8 @@ public class Jalview2xmlTests groups = ap; } } - assertTrue("Couldn't find the structure view", sps != null); - assertTrue("Couldn't find the MAFFT view", groups != null); + assertNotNull(sps, "Couldn't find the structure view"); + assertNotNull(groups, "Couldn't find the MAFFT view"); ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle(); ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle(); @@ -364,37 +406,29 @@ 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( - "examples/exampleFile_2_7.jar", FormatAdapter.FILE); - assertTrue("Didn't read in the example file correctly.", af != null); + Desktop.instance.closeAll_actionPerformed(null); + + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/exampleFile_2_7.jar", DataSourceType.FILE); + 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 + assertSame( + af, + Desktop.getAlignFrameFor(af.getViewport()), + "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window"); + + Desktop.explodeViews(af); + int oldviews = Desktop.getAlignFrames().length; Assert.assertEquals(Desktop.getAlignFrames().length, Desktop.getAlignmentPanels(afid).length); @@ -414,15 +448,15 @@ 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, Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length); Assert.assertEquals( - oldviews, - Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length); + Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length, + oldviews); } /** @@ -436,12 +470,12 @@ 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(af, "Didn't read in the example file correctly."); String afid = af.getViewport().getSequenceSetId(); // remember reference sequence for each panel - Map refseqs = new HashMap(); + Map refseqs = new HashMap<>(); /* * mark sequence 2, 3, 4.. in panels 1, 2, 3... @@ -479,8 +513,8 @@ public class Jalview2xmlTests Assert.assertEquals(Desktop.getAlignFrames().length, 0); } - af = new FileLoader().LoadFileWaitTillLoaded( - tfile.getAbsolutePath(), FormatAdapter.FILE); + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); afid = af.getViewport().getSequenceSetId(); for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) @@ -569,19 +603,19 @@ 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(af, "Didn't read in the example file correctly."); 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>(); - + 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 @@ -596,9 +630,9 @@ public class Jalview2xmlTests repIndex = Math.max(repIndex, 1); SequenceI repSeq = alignment.getSequenceAt(repIndex); repSeqs.put(ap.getViewName(), repSeq); - List hiddenNames = new ArrayList(); + 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) @@ -621,8 +655,9 @@ public class Jalview2xmlTests assertSame(repSeq, sg.getSeqrep()); assertTrue(sg.getSequences().contains(repSeq)); assertTrue(sg.getSequences().contains(precedingSeq)); - assertTrue("alignment has groups", alignment.getGroups().isEmpty()); - Map hiddenRepSeqsMap = av.getHiddenRepSequences(); + assertTrue(alignment.getGroups().isEmpty(), "alignment has groups"); + Map hiddenRepSeqsMap = av + .getHiddenRepSequences(); assertNotNull(hiddenRepSeqsMap); assertEquals(1, hiddenRepSeqsMap.size()); assertSame(sg, hiddenRepSeqsMap.get(repSeq)); @@ -633,8 +668,7 @@ public class Jalview2xmlTests n++; } File tfile = File - .createTempFile("testStoreAndRecoverGroupReps", - ".jvp"); + .createTempFile("testStoreAndRecoverGroupReps", ".jvp"); try { new Jalview2XML(false).saveState(tfile); @@ -647,11 +681,11 @@ public class Jalview2xmlTests { Assert.assertEquals(Desktop.getAlignFrames().length, 0); } - - af = new FileLoader().LoadFileWaitTillLoaded( - tfile.getAbsolutePath(), FormatAdapter.FILE); + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); afid = af.getViewport().getSequenceSetId(); - + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) { String viewName = ap.getViewName(); @@ -659,10 +693,10 @@ public class Jalview2xmlTests AlignmentI alignment = ap.getAlignment(); List groups = alignment.getGroups(); assertNotNull(groups); - assertTrue("Alignment has groups", groups.isEmpty()); + assertTrue(groups.isEmpty(), "Alignment has groups"); Map hiddenRepSeqsMap = av .getHiddenRepSequences(); - assertNotNull("No hidden represented sequences", hiddenRepSeqsMap); + assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences"); assertEquals(1, hiddenRepSeqsMap.size()); assertEquals(repSeqs.get(viewName).getDisplayId(true), hiddenRepSeqsMap.keySet().iterator().next() @@ -674,9 +708,488 @@ public class Jalview2xmlTests List hidden = hiddenSeqNames.get(ap.getViewName()); HiddenSequences hs = alignment.getHiddenSequences(); assertEquals( + hidden.size(), + hs.getSize(), "wrong number of restored hidden sequences in " - + ap.getViewName(), - hidden.size(), hs.getSize()); + + ap.getViewName()); + } + } + + /** + * 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(af, "Didn't read in the example file correctly."); + 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"); + } + } + + /** + * Configure an alignment and a sub-group each with distinct colour schemes, + * Conservation and PID thresholds, and confirm these are restored from the + * saved project. + * + * @throws IOException + */ + @Test(groups = { "Functional" }) + public void testStoreAndRecoverColourThresholds() throws IOException + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + + AlignViewport av = af.getViewport(); + AlignmentI al = av.getAlignment(); + + /* + * Colour alignment by Buried Index, Above 10% PID, By Conservation 20% + */ + af.changeColour_actionPerformed(JalviewColourScheme.Buried.toString()); + assertTrue(av.getGlobalColourScheme() instanceof BuriedColourScheme); + af.abovePIDThreshold_actionPerformed(true); + SliderPanel sp = SliderPanel.getSliderPanel(); + assertFalse(sp.isForConservation()); + sp.valueChanged(10); + af.conservationMenuItem_actionPerformed(true); + sp = SliderPanel.getSliderPanel(); + assertTrue(sp.isForConservation()); + sp.valueChanged(20); + ResidueShaderI rs = av.getResidueShading(); + assertEquals(rs.getThreshold(), 10); + assertTrue(rs.conservationApplied()); + assertEquals(rs.getConservationInc(), 20); + + /* + * create a group with Strand colouring, 30% Conservation + * and 40% PID threshold + */ + SequenceGroup sg = new SequenceGroup(); + sg.addSequence(al.getSequenceAt(0), false); + sg.setStartRes(15); + sg.setEndRes(25); + av.setSelectionGroup(sg); + PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null); + popupMenu.changeColour_actionPerformed(JalviewColourScheme.Strand + .toString()); + assertTrue(sg.getColourScheme() instanceof StrandColourScheme); + assertEquals(al.getGroups().size(), 1); + assertSame(al.getGroups().get(0), sg); + popupMenu.conservationMenuItem_actionPerformed(true); + sp = SliderPanel.getSliderPanel(); + assertTrue(sp.isForConservation()); + sp.valueChanged(30); + popupMenu.abovePIDColour_actionPerformed(true); + sp = SliderPanel.getSliderPanel(); + assertFalse(sp.isForConservation()); + sp.valueChanged(40); + assertTrue(sg.getGroupColourScheme().conservationApplied()); + assertEquals(sg.getGroupColourScheme().getConservationInc(), 30); + assertEquals(sg.getGroupColourScheme().getThreshold(), 40); + + /* + * save project, close windows, reload project, verify + */ + File tfile = File.createTempFile("testStoreAndRecoverColourThresholds", + ".jvp"); + tfile.deleteOnExit(); + new Jalview2XML(false).saveState(tfile); + Desktop.instance.closeAll_actionPerformed(null); + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + Assert.assertNotNull(af, "Failed to reload project"); + + /* + * verify alignment (background) colouring + */ + rs = af.getViewport().getResidueShading(); + assertTrue(rs.getColourScheme() instanceof BuriedColourScheme); + assertEquals(rs.getThreshold(), 10); + assertTrue(rs.conservationApplied()); + assertEquals(rs.getConservationInc(), 20); + + /* + * verify group colouring + */ + assertEquals(1, af.getViewport().getAlignment().getGroups().size(), 1); + rs = af.getViewport().getAlignment().getGroups().get(0) + .getGroupColourScheme(); + assertTrue(rs.getColourScheme() instanceof StrandColourScheme); + assertEquals(rs.getThreshold(), 40); + assertTrue(rs.conservationApplied()); + assertEquals(rs.getConservationInc(), 30); + } + + /** + * Test save and reload of feature colour schemes and filter settings + * + * @throws IOException + */ + @Test(groups = { "Functional" }) + public void testSaveLoadFeatureColoursAndFilters() throws IOException + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE); + SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0); + + /* + * add some features to the sequence + */ + int score = 1; + addFeatures(seq1, "type1", score++); + addFeatures(seq1, "type2", score++); + addFeatures(seq1, "type3", score++); + addFeatures(seq1, "type4", score++); + addFeatures(seq1, "type5", score++); + + /* + * set colour schemes for features + */ + FeatureRenderer fr = af.getFeatureRenderer(); + fr.findAllFeatures(true); + + // type1: red + fr.setColour("type1", new FeatureColour(Color.red)); + + // type2: by label + FeatureColourI byLabel = new FeatureColour(); + byLabel.setColourByLabel(true); + fr.setColour("type2", byLabel); + + // type3: by score above threshold + FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1, + 10); + byScore.setAboveThreshold(true); + byScore.setThreshold(2f); + fr.setColour("type3", byScore); + + // type4: by attribute AF + FeatureColourI byAF = new FeatureColour(); + byAF.setColourByLabel(true); + byAF.setAttributeName("AF"); + fr.setColour("type4", byAF); + + // type5: by attribute CSQ:PolyPhen below threshold + FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE, + 1, 10); + byPolyPhen.setBelowThreshold(true); + byPolyPhen.setThreshold(3f); + byPolyPhen.setAttributeName("CSQ", "PolyPhen"); + fr.setColour("type5", byPolyPhen); + + /* + * set filters for feature types + */ + + // filter type1 features by (label contains "x") + FeatureMatcherSetI filterByX = new FeatureMatcherSet(); + filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x")); + fr.setFeatureFilter("type1", filterByX); + + // filter type2 features by (score <= 2.4 and score > 1.1) + FeatureMatcherSetI filterByScore = new FeatureMatcherSet(); + filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4")); + filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1")); + fr.setFeatureFilter("type2", filterByScore); + + // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0) + FeatureMatcherSetI filterByXY = new FeatureMatcherSet(); + filterByXY + .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF")); + filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ", + "PolyPhen")); + fr.setFeatureFilter("type3", filterByXY); + + /* + * save as Jalview project + */ + File tfile = File.createTempFile("JalviewTest", ".jvp"); + tfile.deleteOnExit(); + String filePath = tfile.getAbsolutePath(); + assertTrue(af.saveAlignment(filePath, FileFormat.Jalview), + "Failed to store as a project."); + + /* + * close current alignment and load the saved project + */ + af.closeMenuItem_actionPerformed(true); + af = null; + af = new FileLoader() + .LoadFileWaitTillLoaded(filePath, DataSourceType.FILE); + assertNotNull(af, "Failed to import new project"); + + /* + * verify restored feature colour schemes and filters + */ + fr = af.getFeatureRenderer(); + FeatureColourI fc = fr.getFeatureStyle("type1"); + assertTrue(fc.isSimpleColour()); + assertEquals(fc.getColour(), Color.red); + fc = fr.getFeatureStyle("type2"); + assertTrue(fc.isColourByLabel()); + fc = fr.getFeatureStyle("type3"); + assertTrue(fc.isGraduatedColour()); + assertNull(fc.getAttributeName()); + assertTrue(fc.isAboveThreshold()); + assertEquals(fc.getThreshold(), 2f); + fc = fr.getFeatureStyle("type4"); + assertTrue(fc.isColourByLabel()); + assertTrue(fc.isColourByAttribute()); + assertEquals(fc.getAttributeName(), new String[] { "AF" }); + fc = fr.getFeatureStyle("type5"); + assertTrue(fc.isGraduatedColour()); + assertTrue(fc.isColourByAttribute()); + assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" }); + assertTrue(fc.isBelowThreshold()); + assertEquals(fc.getThreshold(), 3f); + + assertEquals(fr.getFeatureFilter("type1").toStableString(), + "Label Contains x"); + assertEquals(fr.getFeatureFilter("type2").toStableString(), + "(Score LE 2.4) AND (Score GT 1.1)"); + assertEquals(fr.getFeatureFilter("type3").toStableString(), + "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)"); + } + + private void addFeature(SequenceI seq, String featureType, int score) + { + SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2, + score, "grp"); + sf.setValue("AF", score); + sf.setValue("CSQ", new HashMap() + { + { + put("PolyPhen", Integer.toString(score)); + } + }); + seq.addSequenceFeature(sf); + } + + /** + * Adds two features of the given type to the given sequence, also setting the + * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen" + * + * @param seq + * @param featureType + * @param score + */ + private void addFeatures(SequenceI seq, String featureType, int score) + { + addFeature(seq, featureType, score++); + addFeature(seq, featureType, score); + } + + /** + * Test save and reload of a PCA viewer + * + * @throws IOException + */ + @Test(groups = { "Functional" }) + public void testSaveLoadPCA() throws IOException + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + assertEquals(af.getViewport().getAlignment().getHeight(), 15); + + /* + * calculate and open PCA (calculates in a separate thread) + */ + CalculationChooser chooser = new CalculationChooser(af); + ((JRadioButton) PA.getValue(chooser, "pca")).setSelected(true); + PA.invokeMethod(chooser, "calculate_actionPerformed()"); + PCAPanel pcaPanel = (PCAPanel) PA.getValue(chooser, "pcaPanel"); + assertNotNull(pcaPanel); + waitFor(50); // let it get started!! + while (pcaPanel.isWorking()) + { + waitFor(50); + } + PA.invokeMethod(chooser, "close_actionPerformed()"); + + /* + * rotate, zoom in, change background colour + */ + RotatableCanvas rc = (RotatableCanvas) PA.getValue(pcaPanel, "rc"); + PA.setValue(rc, "bgColour", Color.PINK); + rc.zoom(1.9f); + rc.rotate(20, 40f); + + /* + * save as Jalview project + */ + File tfile = File.createTempFile("JalviewTest", ".jvp"); + tfile.deleteOnExit(); + String filePath = tfile.getAbsolutePath(); + assertTrue(af.saveAlignment(filePath, FileFormat.Jalview), + "Failed to store as a project."); + + /* + * load the saved project and locate the restored PCA panel + */ + new FileLoader().LoadFileWaitTillLoaded(filePath, DataSourceType.FILE); + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + PCAPanel pcaPanel2 = null; + for (JInternalFrame frame : frames) + { + if (frame instanceof PCAPanel && frame != pcaPanel) + { + pcaPanel2 = (PCAPanel) frame; + } + } + assertNotNull(pcaPanel2); + + /* + * compare restored and original PCA + */ + PCAModel pcaModel = (PCAModel) PA.getValue(pcaPanel, "pcaModel"); + PCAModel pcaModel2 = (PCAModel) PA.getValue(pcaPanel2, "pcaModel"); + RotatableCanvas rc2 = (RotatableCanvas) PA.getValue(pcaPanel2, "rc"); + assertNotNull(pcaModel); + assertNotNull(pcaModel2); + assertNotNull(rc2); + assertEquals(rc2.getBackgroundColour(), Color.PINK); + assertEquals(PA.getValue(rc2, "scaleFactor"), 1.9f); + + // original has input data + assertNotNull(pcaModel.getInputData()); + // restored has no input data (JAL-2647 to do) + assertNull(pcaModel2.getInputData()); + + // verify sequence points are at the same positions + List seqPts = pcaModel.getSequencePoints(); + List seqPts2 = pcaModel2.getSequencePoints(); + assertEquals(seqPts.size(), seqPts2.size()); + for (int i = 0; i < seqPts.size(); i++) + { + SequencePoint sp = seqPts.get(i); + SequencePoint sp2 = seqPts2.get(i); + assertEquals(sp.getSequence().getName(), sp2.getSequence().getName()); + assertEquals(sp.coord, sp2.coord); + } + + // verify axis end points are at the same positions + Point[] axes = (Point[]) PA.getValue(rc, "axisEndPoints"); + Point[] axes2 = (Point[]) PA.getValue(rc2, "axisEndPoints"); + assertEquals(axes.length, 3); + assertEquals(axes2.length, 3); + for (int i = 0; i < 3; i++) + { + assertEquals(axes[i], axes2[i]); + } + + // compare PCA data + PCA pca = (PCA) PA.getValue(pcaModel, "pca"); + PCA pca2 = (PCA) PA.getValue(pcaModel2, "pca"); + assertNotNull(pca); + assertNotNull(pca2); + // same (BLOSUM62) score model (a singleton object) + assertSame(PA.getValue(pca, "scoreModel"), + PA.getValue(pca2, "scoreModel")); + assertEquals(PA.getValue(pca, "similarityParams"), + PA.getValue(pca2, "similarityParams")); + MatrixTest.assertMatricesMatch(pca.getPairwiseScores(), + pca2.getPairwiseScores()); + MatrixTest.assertMatricesMatch(pca.getTridiagonal(), + pca2.getTridiagonal()); + MatrixTest.assertMatricesMatch(pca.getEigenmatrix(), + pca2.getEigenmatrix()); + } + + protected void waitFor(long t) + { + synchronized (this) + { + try + { + wait(t); + } catch (InterruptedException e) + { + fail(e.getMessage()); + } } } }