Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

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

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index e0930c9..644761e 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -33,12 +33,14 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
 import javax.swing.JInternalFrame;
 
 import org.testng.Assert;
 import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -51,6 +53,7 @@ import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.GeneLocus;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
@@ -64,7 +67,6 @@ 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.Desktop;
 import jalview.gui.JvOptionPane;
@@ -91,9 +93,16 @@ import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
+import junit.extensions.PA;
+
 @Test(singleThreaded = true)
 public class Jalview2xmlTests extends Jalview2xmlBase
 {
+  @AfterMethod(alwaysRun = true)
+  public void tearDown()
+  {
+    Desktop.getInstance().closeAll_actionPerformed(null);
+  }
 
   @Override
   @BeforeClass(alwaysRun = true)
@@ -153,7 +162,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             DataSourceType.FILE);
     assertNotNull(af, "Didn't read input file " + inFile);
     af.loadJalviewDataFile(inAnnot, DataSourceType.FILE, null, null);
-    AlignViewport viewport = af.getViewport();
+    AlignViewportI viewport = af.getViewport();
     assertSame(viewport.getGlobalColourScheme().getClass(),
             TCoffeeColourScheme.class, "Didn't set T-coffee colourscheme");
     assertNotNull(
@@ -276,9 +285,9 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     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,
+    assertEquals(Desktop.getAlignFrames().length,
+            1 + origCount,
             "Didn't gather the views in the example file.");
-
   }
 
   /**
@@ -804,6 +813,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
               "Mismatch PDBEntry 'Type'");
       Assert.assertNotNull(recov.getFile(),
               "Recovered PDBEntry should have a non-null file entry");
+      Assert.assertEquals(recov.getFile().toLowerCase(Locale.ENGLISH).lastIndexOf("pdb"),recov.getFile().length()-3, "Recovered PDBEntry file should have PDB suffix");
     }
   }
 
@@ -821,7 +831,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
 
-    AlignViewport av = af.getViewport();
+    AlignViewportI av = af.getViewport();
     AlignmentI al = av.getAlignment();
 
     /*
@@ -1067,6 +1077,59 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   }
 
   /**
+   * Load an HMM profile to an alignment, and confirm it is correctly restored
+   * when reloaded from project
+   * 
+   * @throws IOException
+   */
+  @Test(groups = { "Functional" })
+  public void testStoreAndRecoverHmmProfile() throws IOException
+  {
+    Desktop.getInstance().closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+  
+    AlignViewportI av = af.getViewport();
+    AlignmentI al = av.getAlignment();
+
+    /*
+     * mimic drag and drop of hmm file on to alignment
+     */
+    AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.hmm", DataSourceType.FILE);
+    al.insertSequenceAt(0,
+            af2.getViewport().getAlignment().getSequenceAt(0));
+
+    /*
+     * check it loaded in
+     */
+    SequenceI hmmSeq = al.getSequenceAt(0);
+    assertTrue(hmmSeq.hasHMMProfile());
+    HiddenMarkovModel hmm = hmmSeq.getHMM();
+    assertSame(hmm.getConsensusSequence(), hmmSeq);
+
+    /*
+     * save project, close windows, reload project, verify
+     */
+    File tfile = File.createTempFile("testStoreAndRecoverHmmProfile",
+            ".jvp");
+    tfile.deleteOnExit();
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.getInstance().closeAll_actionPerformed(null);
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+    Assert.assertNotNull(af, "Failed to reload project");
+
+    hmmSeq = al.getSequenceAt(0);
+    assertTrue(hmmSeq.hasHMMProfile());
+    assertSame(hmm.getConsensusSequence(), hmmSeq);
+    Mapping mapToHmmConsensus = (Mapping) PA.getValue(hmm,
+            "mapToHmmConsensus");
+    assertNotNull(mapToHmmConsensus);
+    assertSame(mapToHmmConsensus.getTo(), hmmSeq.getDatasetSequence());
+  }
+
+  /**
    * 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
    */