From 716b7ed46ecee85d5a5ced3e2c0cf65523b278ae Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 9 Jan 2019 17:29:21 +0000
Subject: [PATCH] JAL-1767 failing test to check if the PCA view association
 is correctly saved and restored

---
 test/jalview/project/Jalview2xmlTests.java |   56 ++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 6739cab..a0f1f6d 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -27,6 +27,7 @@ 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;
@@ -49,6 +50,7 @@ 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;
@@ -77,6 +79,8 @@ 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;
@@ -1102,4 +1106,56 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     }
     return ds;
   }
+
+  @Test(groups = "Functional")
+  public void testPcaViewAssociation() throws IOException
+  {
+    Desktop.instance.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 newview = af.newView(PCAVIEWNAME, true);
+      // create another for good measure
+      af.newView("Not the PCA View", true);
+      PCAPanel pcaPanel = new PCAPanel(newview, "BLOSUM62",
+              new SimilarityParams(true, true, true, false));
+
+      // we're in the test exec thread, so we can just run synchronously here
+      pcaPanel.run();
+
+      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.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            tempfile.getCanonicalPath(), DataSourceType.FILE);
+    JInternalFrame[] frames = Desktop.instance.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 = af.getAlignPanels().get(1);
+    assertEquals(restoredNewView.getViewName(), PCAVIEWNAME);
+    assertTrue(
+            restoredNewView.getAlignViewport() == pcaPanel
+                    .getAlignViewport(),
+            "Didn't restore correct view association for the PCA view");
+  }
 }
-- 
1.7.10.2