X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJalview2xmlTests.java;h=3d53234fc634d316e1f5ae1a105d159a410d7ff6;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=4ef038a3a393747fc1df0cfc4b2d148d058f4d98;hpb=d9e91b5fc027ec6099585c3c7f69c73d7832e540;p=jalview.git

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 4ef038a..3d53234 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -1,97 +1,723 @@
+/*
+ * 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.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+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.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.structure.StructureImportSettings;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
 
-public class Jalview2xmlTests
+@Test(singleThreaded = true)
+public class Jalview2xmlTests extends Jalview2xmlBase
 {
 
-  /**
-   * @throws java.lang.Exception
-   */
-  @BeforeClass
-  public static void setUpBeforeClass() throws Exception
+  @Test(groups = { "Functional" })
+  public void testRNAStructureRecovery() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] {"-props","test/src/jalview/io/testProps.jvprops"});
+    String inFile = "examples/RF00031_folded.stk";
+    String tfile = File.createTempFile("JalviewTest", ".jvp")
+            .getAbsolutePath();
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read input file " + inFile, af);
+    int olddsann = countDsAnn(af.getViewport());
+    assertTrue("Didn't find any dataset annotations", olddsann > 0);
+    af.rnahelicesColour_actionPerformed(null);
+    assertTrue(
+            "Couldn't apply RNA helices colourscheme",
+            af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
+    assertTrue("Failed to store as a project.",
+            af.saveAlignment(tfile, "Jalview"));
+    af.closeMenuItem_actionPerformed(true);
+    af = null;
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    assertNotNull("Failed to import new project", af);
+    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 + ")");
+    assertTrue(
+            "RNA helices colourscheme was not applied on import.",
+            af.getViewport().getGlobalColourScheme() instanceof jalview.schemes.RNAHelicesColour);
   }
 
-  /**
-   * @throws java.lang.Exception
-   */
-  @AfterClass
-  public static void tearDownAfterClass() throws Exception
+  @Test(groups = { "Functional" })
+  public void testTCoffeeScores() throws Exception
   {
-    jalview.gui.Desktop.instance.quit();
+    String inFile = "examples/uniref50.fa", inAnnot = "examples/uniref50.score_ascii";
+    String tfile = File.createTempFile("JalviewTest", ".jvp")
+            .getAbsolutePath();
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read input file " + inFile, af);
+    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+    assertSame("Didn't set T-coffee colourscheme", af.getViewport()
+            .getGlobalColourScheme().getClass(), TCoffeeColourScheme.class);
+    assertNotNull("Recognise T-Coffee score from string",
+            jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
+                    .getAlignment(), ColourSchemeProperty.getColourName(af
+                    .getViewport().getGlobalColourScheme())));
+
+    assertTrue("Failed to store as a project.",
+            af.saveAlignment(tfile, "Jalview"));
+    af.closeMenuItem_actionPerformed(true);
+    af = null;
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    assertNotNull("Failed to import new project", af);
+    assertSame("Didn't set T-coffee colourscheme for imported project.", af
+            .getViewport().getGlobalColourScheme().getClass(),
+            TCoffeeColourScheme.class);
+    System.out
+            .println("T-Coffee score shading successfully recovered from project.");
   }
-  public int countDsAnn(jalview.viewmodel.AlignmentViewport avp)
+
+  @Test(groups = { "Functional" })
+  public void testColourByAnnotScores() throws Exception
   {
-    int numdsann=0;
-    for (SequenceI sq: avp.getAlignment().getDataset().getSequences()) {
-      if (sq.getAnnotation() != null)
+    String inFile = "examples/uniref50.fa", inAnnot = "examples/testdata/uniref50_iupred.jva";
+    String tfile = File.createTempFile("JalviewTest", ".jvp")
+            .getAbsolutePath();
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(inFile,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read input file " + inFile, af);
+    af.loadJalviewDataFile(inAnnot, FormatAdapter.FILE, null, null);
+    AlignmentAnnotation[] aa = af.getViewport().getAlignment()
+            .getSequenceAt(0).getAnnotation("IUPredWS (Short)");
+    assertTrue(
+            "Didn't find any IUPred annotation to use to shade alignment.",
+            aa != null && aa.length > 0);
+    AnnotationColourGradient cs = new AnnotationColourGradient(aa[0], null,
+            AnnotationColourGradient.ABOVE_THRESHOLD);
+    AnnotationColourGradient gcs = new AnnotationColourGradient(aa[0],
+            null, AnnotationColourGradient.BELOW_THRESHOLD);
+    cs.setSeqAssociated(true);
+    gcs.setSeqAssociated(true);
+    af.changeColour(cs);
+    SequenceGroup sg = new SequenceGroup();
+    sg.setStartRes(57);
+    sg.setEndRes(92);
+    sg.cs = gcs;
+    af.getViewport().getAlignment().addGroup(sg);
+    sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
+    sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
+    af.alignPanel.alignmentChanged();
+    assertTrue("Failed to store as a project.",
+            af.saveAlignment(tfile, "Jalview"));
+    af.closeMenuItem_actionPerformed(true);
+    af = null;
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile, FormatAdapter.FILE);
+    assertNotNull("Failed to import new project", af);
+
+    // check for group and alignment colourschemes
+
+    ColourSchemeI _rcs = af.getViewport().getGlobalColourScheme();
+    ColourSchemeI _rgcs = af.getViewport().getAlignment().getGroups()
+            .get(0).cs;
+    assertNotNull("Didn't recover global colourscheme", _rcs);
+    assertTrue("Didn't recover annotation colour global scheme",
+            _rcs instanceof AnnotationColourGradient);
+    AnnotationColourGradient __rcs = (AnnotationColourGradient) _rcs;
+    assertTrue("Annotation colourscheme wasn't sequence associated",
+            __rcs.isSeqAssociated());
+
+    boolean diffseqcols = false, diffgseqcols = false;
+    SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
+    for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+            && (!diffseqcols || !diffgseqcols); p++)
+    {
+      if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0]) != _rcs
+              .findColour(sqs[5].getCharAt(p), p, sqs[5]))
       {
-        for (AlignmentAnnotation dssa : sq.getAnnotation())
+        diffseqcols = true;
+      }
+    }
+    assertTrue("Got Different sequence colours", diffseqcols);
+    System.out
+            .println("Per sequence colourscheme (Background) successfully applied and recovered.");
+
+    assertNotNull("Didn't recover group colourscheme", _rgcs);
+    assertTrue("Didn't recover annotation colour group colourscheme",
+            _rgcs instanceof AnnotationColourGradient);
+    __rcs = (AnnotationColourGradient) _rgcs;
+    assertTrue("Group Annotation colourscheme wasn't sequence associated",
+            __rcs.isSeqAssociated());
+
+    for (int p = 0, pSize = af.getViewport().getAlignment().getWidth(); p < pSize
+            && (!diffseqcols || !diffgseqcols); p++)
+    {
+      if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1]) != _rgcs
+              .findColour(sqs[2].getCharAt(p), p, sqs[2]))
+      {
+        diffgseqcols = true;
+      }
+    }
+    assertTrue("Got Different group sequence colours", diffgseqcols);
+    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", FormatAdapter.FILE);
+    assertNotNull("Didn't read in the example file correctly.", af);
+    assertTrue("Didn't gather the views in the example file.",
+            Desktop.getAlignFrames().length == 1 + origCount);
+
+  }
+
+  @Test(groups = { "Functional" })
+  public void viewRefPdbAnnotation() throws Exception
+  {
+    StructureImportSettings.setProcessSecondaryStructure(true);
+    StructureImportSettings.setVisibleChainAnnotation(true);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+    assertNotNull("Didn't read in the example file correctly.", af);
+    AlignmentViewPanel sps = null;
+    for (AlignmentViewPanel ap : af.alignPanel.alignFrame.getAlignPanels())
+    {
+      if ("Spinach Feredoxin Structure".equals(ap.getViewName()))
+      {
+        sps = ap;
+        break;
+      }
+    }
+    assertNotNull("Couldn't find the structure view", sps);
+    AlignmentAnnotation refan = null;
+    for (AlignmentAnnotation ra : sps.getAlignment()
+            .getAlignmentAnnotation())
+    {
+      if (ra.graph != 0)
+      {
+        refan = ra;
+        break;
+      }
+    }
+    assertNotNull("Annotation secondary structure not found.", refan);
+    SequenceI sq = sps.getAlignment().findName("1A70|");
+    assertNotNull("Couldn't find 1a70 null chain", sq);
+    // compare the manually added temperature factor annotation
+    // to the track automatically transferred from the pdb structure on load
+    assertNotNull("1a70 has no annotation", sq.getDatasetSequence()
+            .getAnnotation());
+    for (AlignmentAnnotation ala : sq.getDatasetSequence().getAnnotation())
+    {
+      AlignmentAnnotation alaa;
+      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
           {
-            numdsann++;
+            assertTrue(
+                    "Mismatch at alignment position " + p,
+                    (alaa.annotations[p] == null && refan.annotations[p] == null)
+                            || alaa.annotations[p].value == refan.annotations[p].value);
+          } catch (NullPointerException q)
+          {
+            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+")");
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile_2_7.jar", FormatAdapter.FILE);
+    assertNotNull("Didn't read in the example file correctly.", af);
+    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("Couldn't find the structure view", sps);
+    assertNotNull("Couldn't find the MAFFT view", groups);
+
+    ViewStyleI structureStyle = sps.getAlignViewport().getViewStyle();
+    ViewStyleI groupStyle = groups.getAlignViewport().getViewStyle();
+    AssertJUnit.assertFalse(structureStyle.sameStyle(groupStyle));
+
+    groups.getAlignViewport().setViewStyle(structureStyle);
+    AssertJUnit.assertFalse(groupStyle.sameStyle(groups.getAlignViewport()
+            .getViewStyle()));
+    Assert.assertTrue(structureStyle.sameStyle(groups.getAlignViewport()
+            .getViewStyle()));
+
   }
-  @Test
-  public void testTCoffeeScores() throws Exception
+
+  /**
+   * 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));
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile_2_7.jar", FormatAdapter.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
     assertTrue(
-            "Recognise T-Coffee score from string",
-            jalview.schemes.ColourSchemeProperty.getColour(af.getViewport()
-                    .getAlignment(),
-                    jalview.schemes.ColourSchemeProperty.getColourName(af
-                            .getViewport().getGlobalColourScheme())) != null);
+            "Jalview2XML.loadAlignFrame() didn't return correct AlignFrame reference for multiple view window",
+            af == Desktop.getAlignFrameFor(af.getViewport()));
 
-    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);
-    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.");
+    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(),
+            FormatAdapter.FILE);
+    Assert.assertNotNull(af);
+    Assert.assertEquals(
+            Desktop.getAlignFrames().length,
+            Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
+    Assert.assertEquals(
+            oldviews,
+            Desktop.getAlignmentPanels(af.getViewport().getSequenceSetId()).length);
+  }
+
+  /**
+   * 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", FormatAdapter.FILE);
+    assertNotNull("Didn't read in the example file correctly.", af);
+    String afid = af.getViewport().getSequenceSetId();
+
+    // remember reference sequence for each panel
+    Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
+
+    /*
+     * 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(),
+            FormatAdapter.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", FormatAdapter.FILE);
+    assertNotNull("Didn't read in the example file correctly.", af);
+    String afid = af.getViewport().getSequenceSetId();
+    // make a second view of the alignment
+    af.newView_actionPerformed(null);
+
+    /*
+     * remember representative and hidden sequences marked 
+     * on each panel
+     */
+    Map<String, SequenceI> repSeqs = new HashMap<String, SequenceI>();
+    Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
+
+    /*
+     * 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<String>();
+      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 has groups", alignment.getGroups().isEmpty());
+      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(),
+            FormatAdapter.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("Alignment has groups", groups.isEmpty());
+      Map<SequenceI, SequenceCollectionI> hiddenRepSeqsMap = av
+              .getHiddenRepSequences();
+      assertNotNull("No hidden represented sequences", hiddenRepSeqsMap);
+      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(
+              "wrong number of restored hidden sequences in "
+                      + ap.getViewName(), hidden.size(), hs.getSize());
+    }
+  }
+
+  /**
+   * 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,
+            FormatAdapter.FILE);
+    assertNotNull("Didn't read in the example file correctly.", af);
+    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(), FormatAdapter.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");
+    }
+  }
 }