From bd75c84346a9d63341d2cf3826ce99a2b37bcace Mon Sep 17 00:00:00 2001 From: gmungoc Date: Wed, 19 Sep 2018 08:03:38 +0100 Subject: [PATCH] JAL-3063 unit test for save/load project switched to JAXB --- test/jalview/project/Jalview2xmlTests.java | 1041 ++++++++++++++++++++++++++++ 1 file changed, 1041 insertions(+) create mode 100644 test/jalview/project/Jalview2xmlTests.java diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java new file mode 100644 index 0000000..f0fc3fd --- /dev/null +++ b/test/jalview/project/Jalview2xmlTests.java @@ -0,0 +1,1041 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.project; + +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 jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureColourI; +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.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +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.Desktop; +import jalview.gui.FeatureRenderer; +import jalview.gui.JvOptionPane; +import jalview.gui.PopupMenu; +import jalview.gui.SliderPanel; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileLoader; +import jalview.io.Jalview2xmlBase; +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 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 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 +{ + + @Override + @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 FileLoader().LoadFileWaitTillLoaded(inFile, + DataSourceType.FILE); + assertNotNull(af, "Didn't read input file " + inFile); + int olddsann = countDsAnn(af.getViewport()); + assertTrue(olddsann > 0, "Didn't find any dataset annotations"); + af.changeColour_actionPerformed(JalviewColourScheme.RNAHelices + .toString()); + assertTrue( + 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 FileLoader() + .LoadFileWaitTillLoaded(tfile, DataSourceType.FILE); + assertNotNull(af, "Failed to import new project"); + int newdsann = countDsAnn(af.getViewport()); + assertEquals(olddsann, newdsann, + "Differing numbers of dataset sequence annotation\nOriginally " + + olddsann + " and now " + newdsann); + System.out + .println("Read in same number of annotations as originally present (" + + olddsann + ")"); + assertTrue( + + af.getViewport().getGlobalColourScheme() instanceof RNAHelicesColour, + "RNA helices colourscheme was not applied on import."); + } + + @Test(groups = { "Functional" }) + public void testTCoffeeScores() throws Exception + { + String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii"; + String tfile = File.createTempFile("JalviewTest", ".jvp") + .getAbsolutePath(); + 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 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."); + } + + @Test(groups = { "Functional" }) + public void testColourByAnnotScores() throws Exception + { + String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva"; + String tfile = File.createTempFile("JalviewTest", ".jvp") + .getAbsolutePath(); + 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( + + 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.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(af.saveAlignment(tfile, FileFormat.Jalview), + "Failed to store as a project."); + af.closeMenuItem_actionPerformed(true); + 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).getColourScheme(); + assertNotNull(_rcs, "Didn't recover global colourscheme"); + assertTrue(_rcs instanceof AnnotationColourGradient, + "Didn't recover annotation colour global scheme"); + AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs; + 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], null, 0f) != _rcs + .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f)) + { + diffseqcols = true; + } + } + assertTrue(diffseqcols, "Got Different sequence colours"); + System.out + .println("Per sequence colourscheme (Background) successfully applied and recovered."); + + assertNotNull(_rgcs, "Didn't recover group colourscheme"); + assertTrue(_rgcs instanceof AnnotationColourGradient, + "Didn't recover annotation colour group colourscheme"); + __rcs = (AnnotationColourGradient) _rgcs; + 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], null, 0f) != _rgcs + .findColour(sqs[2].getCharAt(p), p, sqs[2], null, 0f)) + { + diffgseqcols = true; + } + } + assertTrue(diffgseqcols, "Got Different group sequence colours"); + System.out + .println("Per sequence (Group) colourscheme successfully applied and recovered."); + } + + @Test(groups = { "Functional" }) + public void gatherViewsHere() throws Exception + { + int origCount = Desktop.getAlignFrames() == null ? 0 : Desktop + .getAlignFrames().length; + 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 + { + 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()) + { + if ("Spinach Feredoxin Structure".equals(ap.getViewName())) + { + sps = ap; + break; + } + } + assertNotNull(sps, "Couldn't find the structure view"); + AlignmentAnnotation refan = null; + for (AlignmentAnnotation ra : sps.getAlignment() + .getAlignmentAnnotation()) + { + if (ra.graph != 0) + { + refan = ra; + break; + } + } + 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; + sq.addAlignmentAnnotation(alaa = new AlignmentAnnotation(ala)); + alaa.adjustForAlignment(); + if (ala.graph == refan.graph) + { + for (int p = 0; p < ala.annotations.length; p++) + { + sq.findPosition(p); + try + { + assertTrue( + (alaa.annotations[p] == null && refan.annotations[p] == null) + || alaa.annotations[p].value == refan.annotations[p].value, + "Mismatch at alignment position " + p); + } catch (NullPointerException q) + { + Assert.fail("Mismatch of alignment annotations at position " + + p + " Ref seq ann: " + refan.annotations[p] + + " alignment " + alaa.annotations[p]); + } + } + } + } + + } + + @Test(groups = { "Functional" }) + public void testCopyViewSettings() throws Exception + { + 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()) + { + if ("Spinach Feredoxin Structure".equals(ap.getViewName())) + { + sps = ap; + } + if (ap.getViewName().contains("MAFFT")) + { + groups = ap; + } + } + 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(); + AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle)); + + groups.getAlignViewport().setViewStyle(structureStyle); + AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport() + .getViewStyle())); + Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport() + .getViewStyle())); + + } + + /** + * test store and recovery of expanded views + * + * @throws Exception + */ + @Test(groups = { "Functional" }, enabled = true) + public void testStoreAndRecoverExpandedviews() throws Exception + { + 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(); + + // 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); + File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp"); + try + { + new Jalview2XML(false).saveState(tfile); + } catch (Error e) + { + Assert.fail("Didn't save the expanded view state", e); + } catch (Exception e) + { + Assert.fail("Didn't save the expanded view state", e); + } + Desktop.instance.closeAll_actionPerformed(null); + if (Desktop.getAlignFrames() != null) + { + Assert.assertEquals(Desktop.getAlignFrames().length, 0); + } + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + Assert.assertNotNull(af); + Assert.assertEquals( + Desktop.getAlignFrames().length, + Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length); + Assert.assertEquals( + Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length, + oldviews); + } + + /** + * Test save and reload of a project with a different representative sequence + * in each view. + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testStoreAndRecoverReferenceSeqSettings() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "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<>(); + + /* + * mark sequence 2, 3, 4.. in panels 1, 2, 3... + * as reference sequence for itself and the preceding sequence + */ + int n = 1; + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) + { + AlignViewportI av = ap.getAlignViewport(); + AlignmentI alignment = ap.getAlignment(); + int repIndex = n % alignment.getHeight(); + SequenceI rep = alignment.getSequenceAt(repIndex); + refseqs.put(ap.getViewName(), rep); + + // code from mark/unmark sequence as reference in jalview.gui.PopupMenu + // todo refactor this to an alignment view controller + av.setDisplayReferenceSeq(true); + av.setColourByReferenceSeq(true); + av.getAlignment().setSeqrep(rep); + + n++; + } + File tfile = File.createTempFile("testStoreAndRecoverReferenceSeq", + ".jvp"); + try + { + new Jalview2XML(false).saveState(tfile); + } catch (Throwable e) + { + Assert.fail("Didn't save the expanded view state", e); + } + Desktop.instance.closeAll_actionPerformed(null); + if (Desktop.getAlignFrames() != null) + { + Assert.assertEquals(Desktop.getAlignFrames().length, 0); + } + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + afid = af.getViewport().getSequenceSetId(); + + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) + { + // check representative + AlignmentI alignment = ap.getAlignment(); + SequenceI rep = alignment.getSeqrep(); + Assert.assertNotNull(rep, + "Couldn't restore sequence representative from project"); + // can't use a strong equals here, because by definition, the sequence IDs + // will be different. + // could set vamsas session save/restore flag to preserve IDs across + // load/saves. + Assert.assertEquals(refseqs.get(ap.getViewName()).toString(), + rep.toString(), + "Representative wasn't the same when recovered."); + Assert.assertTrue(ap.getAlignViewport().isDisplayReferenceSeq(), + "Display reference sequence view setting not set."); + Assert.assertTrue(ap.getAlignViewport().isColourByReferenceSeq(), + "Colour By Reference Seq view setting not set."); + } + } + + @Test(groups = { "Functional" }) + public void testIsVersionStringLaterThan() + { + /* + * No version / development / test / autobuild is leniently assumed to be + * compatible + */ + assertTrue(Jalview2XML.isVersionStringLaterThan(null, null)); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", null)); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, "2.8.3")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, + "Development Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, + "DEVELOPMENT BUILD")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", + "Development Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, "Test")); + assertTrue(Jalview2XML.isVersionStringLaterThan(null, "TEST")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "Test")); + assertTrue(Jalview2XML + .isVersionStringLaterThan(null, "Automated Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", + "Automated Build")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", + "AUTOMATED BUILD")); + + /* + * same version returns true i.e. compatible + */ + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3b1")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3B1", "2.8.3b1")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3B1")); + + /* + * later version returns true + */ + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.4")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.9.2")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8", "2.8.3")); + assertTrue(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.3b1")); + + /* + * earlier version returns false + */ + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.4", "2.8.3")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3b1", "2.8.3")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.3", "2.8.2b1")); + assertFalse(Jalview2XML.isVersionStringLaterThan("2.8.0b2", "2.8.0b1")); + } + + /** + * Test save and reload of a project with a different sequence group (and + * representative sequence) in each view. + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testStoreAndRecoverGroupRepSeqs() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "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<>(); + + /* + * mark sequence 2, 3, 4.. in panels 1, 2, 3... + * as reference sequence for itself and the preceding sequence + */ + int n = 1; + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) + { + AlignViewportI av = ap.getAlignViewport(); + AlignmentI alignment = ap.getAlignment(); + int repIndex = n % alignment.getHeight(); + // ensure at least one preceding sequence i.e. index >= 1 + repIndex = Math.max(repIndex, 1); + SequenceI repSeq = alignment.getSequenceAt(repIndex); + 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) + */ + SequenceGroup sg = new SequenceGroup(); + sg.addSequence(repSeq, false); + SequenceI precedingSeq = alignment.getSequenceAt(repIndex - 1); + sg.addSequence(precedingSeq, false); + sg.setSeqrep(repSeq); + assertTrue(sg.getSequences().contains(repSeq)); + assertTrue(sg.getSequences().contains(precedingSeq)); + av.setSelectionGroup(sg); + assertSame(repSeq, sg.getSeqrep()); + + /* + * represent group with sequence adds to a map of hidden rep sequences + * (it does not create a group on the alignment) + */ + ((AlignmentViewport) av).hideSequences(repSeq, true); + assertSame(repSeq, sg.getSeqrep()); + assertTrue(sg.getSequences().contains(repSeq)); + assertTrue(sg.getSequences().contains(precedingSeq)); + assertTrue(alignment.getGroups().isEmpty(), "alignment has groups"); + Map hiddenRepSeqsMap = av + .getHiddenRepSequences(); + assertNotNull(hiddenRepSeqsMap); + assertEquals(1, hiddenRepSeqsMap.size()); + assertSame(sg, hiddenRepSeqsMap.get(repSeq)); + assertTrue(alignment.getHiddenSequences().isHidden(precedingSeq)); + assertFalse(alignment.getHiddenSequences().isHidden(repSeq)); + hiddenNames.add(precedingSeq.getName()); + + n++; + } + File tfile = File + .createTempFile("testStoreAndRecoverGroupReps", ".jvp"); + try + { + new Jalview2XML(false).saveState(tfile); + } catch (Throwable e) + { + Assert.fail("Didn't save the expanded view state", e); + } + Desktop.instance.closeAll_actionPerformed(null); + if (Desktop.getAlignFrames() != null) + { + Assert.assertEquals(Desktop.getAlignFrames().length, 0); + } + + af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + afid = af.getViewport().getSequenceSetId(); + + for (AlignmentViewPanel ap : Desktop.getAlignmentPanels(afid)) + { + String viewName = ap.getViewName(); + AlignViewportI av = ap.getAlignViewport(); + AlignmentI alignment = ap.getAlignment(); + List groups = alignment.getGroups(); + assertNotNull(groups); + assertTrue(groups.isEmpty(), "Alignment has groups"); + Map hiddenRepSeqsMap = av + .getHiddenRepSequences(); + assertNotNull(hiddenRepSeqsMap, "No hidden represented sequences"); + assertEquals(1, hiddenRepSeqsMap.size()); + assertEquals(repSeqs.get(viewName).getDisplayId(true), + hiddenRepSeqsMap.keySet().iterator().next() + .getDisplayId(true)); + + /* + * verify hidden sequences in restored panel + */ + List hidden = hiddenSeqNames.get(ap.getViewName()); + HiddenSequences hs = alignment.getHiddenSequences(); + assertEquals( + hidden.size(), + hs.getSize(), + "wrong number of restored hidden sequences in " + + 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); + } +} -- 1.7.10.2