JAL-1767 failing test to check if the PCA view association is correctly saved and...

[jalview.git] / test / jalview / project / Jalview2xmlTests.java

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 72cbc50..a0f1f6d 100644 (file)
--- 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;
@@ -1043,12 +1047,50 @@ public class Jalview2xmlTests extends Jalview2xmlBase
    * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
    * view (JAL-3171) this test ensures we can import and merge those views
    */
+  @Test(groups = { "Functional" })
   public void testMergeDatasetsforViews() throws IOException
   {
+    // simple project - two views on one alignment
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
             "examples/testdata/projects/twoViews.jvp", DataSourceType.FILE);
     assertNotNull(af);
     assertTrue(af.getAlignPanels().size() > 1);
+    verifyDs(af);
+  }
+
+  /**
+   * pre 2.11 - jalview 2.10 erroneously created new dataset entries for each
+   * view (JAL-3171) this test ensures we can import and merge those views This
+   * is a more complex project
+   */
+  @Test(groups = { "Functional" })
+  public void testMergeDatasetsforManyViews() throws IOException
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    // complex project - one dataset, several views on several alignments
+    AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+            "examples/testdata/projects/manyViews.jvp",
+            DataSourceType.FILE);
+    assertNotNull(af);
+
+    AlignmentI ds = null;
+    for (AlignFrame alignFrame : Desktop.getAlignFrames())
+    {
+      if (ds == null)
+      {
+        ds = verifyDs(alignFrame);
+      }
+      else
+      {
+        // check that this frame's dataset matches the last
+        assertTrue(ds == verifyDs(alignFrame));
+      }
+    }
+  }
+
+  private AlignmentI verifyDs(AlignFrame af)
+  {
     AlignmentI ds = null;
     for (AlignmentViewPanel ap : af.getAlignPanels())
     {
@@ -1062,5 +1104,58 @@ public class Jalview2xmlTests extends Jalview2xmlBase
                 "Dataset was not the same for imported 2.10.5 project with several alignment views");
       }
     }
+    return ds;
+  }
+
+  @Test(groups = "Functional")
+  public void testPcaViewAssociation() throws IOException
+  {
+    Desktop.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");
   }
 }