From 7e73e392838bbaaaff162532ef8e3e251b11f94a Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 19 Aug 2016 15:13:01 +0100
Subject: [PATCH] JAL-1803 unit test for PDB chainCode save/restore from
 Jalview project

---
 test/jalview/io/Jalview2xmlTests.java |   90 +++++++++++++++++++++++++++++++++
 1 file changed, 90 insertions(+)

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index c2e3a66..784f3dd 100644
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -34,10 +34,12 @@ import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
 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;
@@ -686,4 +688,92 @@ public class Jalview2xmlTests
               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);
+    assertTrue("Didn't read in the example file correctly.", af != null);
+    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", null, testFile);
+    pdbEntries[1] = new PDBEntry("3W5V", "B", null, testFile);
+    pdbEntries[2] = new PDBEntry("3W5V", "C", null, testFile);
+    pdbEntries[3] = new PDBEntry("3W5V", "D", null, testFile);
+    Assert.assertTrue(seqs[0].getDatasetSequence().getAllPDBEntries()
+            .get(0).equals(pdbEntries[0]));
+    Assert.assertTrue(seqs[1].getDatasetSequence().getAllPDBEntries()
+            .get(0).equals(pdbEntries[1]));
+    Assert.assertTrue(seqs[2].getDatasetSequence().getAllPDBEntries()
+            .get(0).equals(pdbEntries[2]));
+    Assert.assertTrue(seqs[3].getDatasetSequence().getAllPDBEntries()
+            .get(0).equals(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
+    Assert.assertTrue(rseqs[0].getDatasetSequence().getAllPDBEntries()
+            .get(0).equals(pdbEntries[0]));
+    Assert.assertTrue(rseqs[1].getDatasetSequence().getAllPDBEntries()
+            .get(0).equals(pdbEntries[1]));
+    Assert.assertTrue(rseqs[2].getDatasetSequence().getAllPDBEntries()
+            .get(0).equals(pdbEntries[2]));
+    Assert.assertTrue(rseqs[3].getDatasetSequence().getAllPDBEntries()
+            .get(0).equals(pdbEntries[3]));
+  }
 }
-- 
1.7.10.2