X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=3baacc85452cf3117a8d91af99e7c50ea7f290ee;hb=ac5f0c912a1c7819530456bab13942ad3734460b;hp=4ef038a3a393747fc1df0cfc4b2d148d058f4d98;hpb=d9e91b5fc027ec6099585c3c7f69c73d7832e540;p=jalview.git

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 4ef038a..3baacc8 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -1,97 +1,1195 @@
+/*
+ * 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.io;
 
-import static org.junit.Assert.*;
+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.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
-public class Jalview2xmlTests
+import junit.extensions.PA;
+
+@Test(singleThreaded = true)
+public class Jalview2xmlTests extends Jalview2xmlBase
 {
+  @BeforeClass(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+  }
 
-  /**
-   * @throws java.lang.Exception
-   */
-  @BeforeClass
-  public static void setUpBeforeClass() throws Exception
+  @BeforeMethod(alwaysRun = true)
+  public void setUpMethod()
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+  }
+
+  @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
   {
-    jalview.bin.Jalview.main(new String[] {"-props","test/src/jalview/io/testProps.jvprops"});
+    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.");
+
   }
 
   /**
-   * @throws java.lang.Exception
+   * Test for JAL-2223 - multiple mappings in View Mapping report
+   * 
+   * @throws Exception
    */
-  @AfterClass
-  public static void tearDownAfterClass() throws Exception
+  @Test(groups = { "Functional" })
+  public void noDuplicatePdbMappingsMade() throws Exception
   {
-    jalview.gui.Desktop.instance.quit();
+    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");
+
   }
-  public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
+
+  @Test(groups = { "Functional" })
+  public void viewRefPdbAnnotation() throws Exception
   {
-    int numdsann=0;
-    for (SequenceI sq: avp.getAlignment().getDataset().getSequences()) {
-      if (sq.getAnnotation() != 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())
+    {
+      if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
       {
-        for (AlignmentAnnotation dssa : sq.getAnnotation())
+        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++)
         {
-          if (dssa.isValidStruc())
+          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)
           {
-            numdsann++;
+            Assert.fail("Mismatch of alignment annotations at position "
+                    + p + " Ref seq ann: " + refan.annotations[p]
+                    + " alignment " + alaa.annotations[p]);
           }
         }
       }
     }
-    return numdsann;
+
   }
-  @Test
-  public void testRNAStructureRecovery() throws Exception
+
+  @Test(groups = { "Functional" })
+  public void testCopyViewSettings() throws Exception
   {
-    String inFile = "examples/RF00031_folded.stk";
-    String tfile = File.createTempFile("JalviewTest", ".jvp").getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(inFile, FormatAdapter.FILE);
-    assertTrue("Didn't read input file "+inFile, af!=null);
-    int olddsann=countDsAnn(af.getViewport());
-    assertTrue("Didn't find any dataset annotations",olddsann>0);
-    assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview"));
-    af.closeMenuItem_actionPerformed(true);
-    af=null;
-    af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
-    assertTrue("Failed to import new project", af!=null);
-    int newdsann=countDsAnn(af.getViewport());
-    assertTrue("Differing numbers of dataset sequence annotation\nOriginally "+olddsann+" and now "+newdsann,olddsann==newdsann);
-    System.out.println("Read in same number of annotations as originally present ("+olddsann+")");
-  }
-  @Test
-  public void testTCoffeeScores() 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
   {
-    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);
+    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();
 
-    assertTrue("Failed to store as a project.",af.saveAlignment(tfile, "Jalview"));
+    // 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.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<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.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<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.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 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));
-    System.out.println("T-Coffee score shading successfully recovered from project.");
+    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);
+  }
+
+  /**
+   * 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<SequencePoint> seqPts = pcaModel.getSequencePoints();
+    List<SequencePoint> 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());
+      }
+    }
+  }
 }