X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;fp=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=830a75913c76b08f8f43df0803dc8eebcccf55b1;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
deleted file mode 100644
index 830a759..0000000
--- a/test/jalview/project/Jalview2xmlTests.java
+++ /dev/null
@@ -1,1186 +0,0 @@
-/*
- * 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 <http://www.gnu.org/licenses/>.
- * 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.analysis.scoremodels.SimilarityParams;
-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.PCAPanel;
-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 javax.swing.JInternalFrame;
-
-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");
-    af.saveAlignment(tfile, FileFormat.Jalview);
-    assertTrue(af.isSaveAlignmentSuccessful(),
-            "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);
-    AlignViewport viewport = af.getViewport();
-    assertSame(viewport.getGlobalColourScheme().getClass(),
-            TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
-    assertNotNull(
-            ColourSchemeProperty.getColourScheme(viewport,
-                    viewport.getAlignment(),
-                    viewport.getGlobalColourScheme()
-                            .getSchemeName()),
-            "Recognise T-Coffee score from string");
-
-    af.saveAlignment(tfile, FileFormat.Jalview);
-    assertTrue(af.isSaveAlignmentSuccessful(),
-            "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();
-    af.saveAlignment(tfile, FileFormat.Jalview);
-    assertTrue(af.isSaveAlignmentSuccessful(),
-            "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.getInstance().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.getInstance().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.getInstance().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<String, SequenceI> 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.getInstance().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.getInstance().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<String, SequenceI> repSeqs = new HashMap<>();
-    Map<String, List<String>> 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<String> 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<SequenceI, SequenceCollectionI> 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.getInstance().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<SequenceGroup> groups = alignment.getGroups();
-      assertNotNull(groups);
-      assertTrue(groups.isEmpty(), "Alignment has groups");
-      Map<SequenceI, SequenceCollectionI> 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<String> 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.getInstance().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.getInstance().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.getInstance().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%
-     */
-    av.setColourAppliesToAllGroups(false);
-    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.getInstance().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(null, Color.BLACK,
-            Color.BLUE, null, 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(null, Color.BLACK,
-            Color.BLUE, null, 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();
-    af.saveAlignment(filePath, FileFormat.Jalview);
-    assertTrue(af.isSaveAlignmentSuccessful(),
-            "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<String, String>()
-    {
-      {
-        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);
-  }
-
-  /**
-   * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
-   * view (JAL-3171) this test ensures we can import and merge those views
-   */
-  @Test(groups = { "Functional" })
-  public void testMergeDatasetsforViews() throws IOException
-  {
-    // simple project - two views on one alignment
-    AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
-            "examples/testdata/projects/twoViews.jvp", DataSourceType.FILE);
-    assertNotNull(af);
-    assertTrue(af.getAlignPanels().size() > 1);
-    verifyDs(af);
-  }
-
-  /**
-   * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
-   * view (JAL-3171) this test ensures we can import and merge those views This
-   * is a more complex project
-   */
-  @Test(groups = { "Functional" })
-  public void testMergeDatasetsforManyViews() throws IOException
-  {
-    Desktop.getInstance().closeAll_actionPerformed(null);
-
-    // complex project - one dataset, several views on several alignments
-    AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
-            "examples/testdata/projects/manyViews.jvp",
-            DataSourceType.FILE);
-    assertNotNull(af);
-
-    AlignmentI ds = null;
-    for (AlignFrame alignFrame : Desktop.getAlignFrames())
-    {
-      if (ds == null)
-      {
-        ds = verifyDs(alignFrame);
-      }
-      else
-      {
-        // check that this frame's dataset matches the last
-        assertTrue(ds == verifyDs(alignFrame));
-      }
-    }
-  }
-
-  private AlignmentI verifyDs(AlignFrame af)
-  {
-    AlignmentI ds = null;
-    for (AlignmentViewPanel ap : af.getAlignPanels())
-    {
-      if (ds == null)
-      {
-        ds = ap.getAlignment().getDataset();
-      }
-      else
-      {
-        assertTrue(ap.getAlignment().getDataset() == ds,
-                "Dataset was not the same for imported 2.10.5 project with several alignment views");
-      }
-    }
-    return ds;
-  }
-
-  @Test(groups = "Functional")
-  public void testPcaViewAssociation() throws IOException
-  {
-    Desktop.getInstance().closeAll_actionPerformed(null);
-    final String PCAVIEWNAME = "With PCA";
-    // create a new tempfile
-    File tempfile = File.createTempFile("jvPCAviewAssoc", "jvp");
-
-    {
-      String exampleFile = "examples/uniref50.fa";
-      AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(exampleFile,
-              DataSourceType.FILE);
-      assertNotNull(af, "Didn't read in the example file correctly.");
-      AlignmentPanel origView = (AlignmentPanel) af.getAlignPanels().get(0);
-      AlignmentPanel newview = af.newView(PCAVIEWNAME, true);
-      // create another for good measure
-      af.newView("Not the PCA View", true);
-      PCAPanel pcaPanel = new PCAPanel(origView, "BLOSUM62",
-              new SimilarityParams(true, true, true, false));
-      // we're in the test exec thread, so we can just run synchronously here
-      pcaPanel.run();
-
-      // now switch the linked view
-      pcaPanel.selectAssociatedView(newview);
-
-      assertTrue(pcaPanel.getAlignViewport() == newview.getAlignViewport(),
-              "PCA should be associated with 'With PCA' view: test is broken");
-
-      // now save and reload project
-      Jalview2XML jv2xml = new jalview.project.Jalview2XML(false);
-      tempfile.delete();
-      jv2xml.saveState(tempfile);
-      assertTrue(jv2xml.errorMessage == null,
-              "Failed to save dummy project with PCA: test broken");
-    }
-
-    // load again.
-    Desktop.getInstance().closeAll_actionPerformed(null);
-    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            tempfile.getCanonicalPath(), DataSourceType.FILE);
-    JInternalFrame[] frames = Desktop.getInstance().getAllFrames();
-    // PCA and the tabbed alignment view should be the only two windows on the
-    // desktop
-    assertEquals(frames.length, 2,
-            "PCA and the tabbed alignment view should be the only two windows on the desktop");
-    PCAPanel pcaPanel = (PCAPanel) frames[frames[0] == af ? 1 : 0];
-
-    AlignmentViewPanel restoredNewView = null;
-    for (AlignmentViewPanel alignpanel : Desktop.getAlignmentPanels(null))
-    {
-      if (alignpanel.getAlignViewport() == pcaPanel.getAlignViewport())
-      {
-        restoredNewView = alignpanel;
-      }
-    }
-    assertEquals(restoredNewView.getViewName(), PCAVIEWNAME);
-    assertTrue(
-            restoredNewView.getAlignViewport() == pcaPanel
-                    .getAlignViewport(),
-            "Didn't restore correct view association for the PCA view");
-  }
-}