JAL-2629 update spike branch to latest

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

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 41a6b89..3a727b4 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -33,7 +33,9 @@ import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceCollectionI;
@@ -78,6 +80,8 @@ import org.testng.AssertJUnit;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 @Test(singleThreaded = true)
 public class Jalview2xmlTests extends Jalview2xmlBase
 {
@@ -256,6 +260,31 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
   }
 
+  /**
+   * Test for JAL-2223 - multiple mappings in View Mapping report
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" })
+  public void noDuplicatePdbMappingsMade() throws Exception
+  {
+    StructureImportSettings.setProcessSecondaryStructure(true);
+    StructureImportSettings.setVisibleChainAnnotation(true);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/exampleFile_2_7.jar", DataSourceType.FILE);
+    assertNotNull(af, "Didn't read in the example file correctly.");
+
+    // locate Jmol viewer
+    // count number of PDB mappings the structure selection manager holds -
+    String pdbFile = af.getCurrentView().getStructureSelectionManager()
+            .findFileForPDBId("1A70");
+    assertEquals(
+            af.getCurrentView().getStructureSelectionManager()
+                    .getMapping(pdbFile).length,
+            2, "Expected only two mappings for 1A70");
+
+  }
+
   @Test(groups = { "Functional" })
   public void viewRefPdbAnnotation() throws Exception
   {
@@ -857,7 +886,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
    * @throws IOException
    */
   @Test(groups = { "Functional" })
-  public void testSaveLoadFeatureColoursAndFilters() throws IOException
+  public void testStoreAndRecoverFeatureColoursAndFilters()
+          throws IOException
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
@@ -1009,4 +1039,57 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     addFeature(seq, featureType, score++);
     addFeature(seq, featureType, score);
   }
+
+  /**
+   * 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.instance.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.instance.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());
+  }
 }