JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings

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

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index d902fa2..5f1256c 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -34,7 +34,10 @@ import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLocus;
 import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceCollectionI;
@@ -68,6 +71,7 @@ import jalview.schemes.RNAHelicesColour;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.structure.StructureImportSettings;
+import jalview.util.MapList;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -1179,4 +1183,83 @@ public class Jalview2xmlTests extends Jalview2xmlBase
                     .getAlignViewport(),
             "Didn't restore correct view association for the PCA view");
   }
+
+  /**
+   * Test save and reload of DBRefEntry including GeneLocus in project
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" })
+  public void testStoreAndRecoverGeneLocus() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+    String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+            DataSourceType.PASTE);
+    assertNotNull(af, "Didn't read in the example file correctly.");
+  
+    AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0];
+    SequenceI pep = ap.getAlignment().getSequenceAt(0);
+    SequenceI cds = ap.getAlignment().getSequenceAt(1);
+
+    /*
+     * give 'protein' a dbref to self, a dbref with map to CDS,
+     * and a dbref with map to gene 'locus'
+     */
+    DBRefEntry dbref1 = new DBRefEntry("Uniprot", "1", "P30419", null);
+    pep.addDBRef(dbref1);
+    Mapping cdsmap = new Mapping(cds,
+            new MapList(new int[]
+            { 1, 4 }, new int[] { 1, 12 }, 1, 3));
+    DBRefEntry dbref2 = new DBRefEntry("EMBLCDS", "2", "X1235", cdsmap);
+    pep.addDBRef(dbref2);
+    Mapping locusmap = new Mapping(null,
+            new MapList(new int[]
+            { 1, 4 }, new int[] { 2674123, 2674135 }, 1, 3));
+    DBRefEntry dbref3 = new GeneLocus("human", "GRCh38", "5", locusmap);
+    pep.addDBRef(dbref3);
+
+    File tfile = File.createTempFile("testStoreAndRecoverGeneLocus",
+            ".jvp");
+    try
+    {
+      new Jalview2XML(false).saveState(tfile);
+    } catch (Throwable e)
+    {
+      Assert.fail("Didn't save the state", e);
+    }
+    Desktop.instance.closeAll_actionPerformed(null);
+  
+    new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+    AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];
+    SequenceI rpep = rap.getAlignment().getSequenceAt(0);
+    assertEquals(rpep.getName(), "P30419");
+    DBRefEntry[] dbrefs = rpep.getDBRefs();
+    assertEquals(dbrefs.length, 3);
+    DBRefEntry dbRef = dbrefs[0];
+    assertFalse(dbRef instanceof GeneLocus);
+    assertNull(dbRef.getMap());
+    assertEquals(dbRef, dbref1);
+
+    /*
+     * restored dbrefs with mapping have a different 'map to'
+     * sequence but otherwise match the original dbrefs
+     */
+    dbRef = dbrefs[1];
+    assertFalse(dbRef instanceof GeneLocus);
+    assertTrue(dbRef.equalRef(dbref2));
+    assertNotNull(dbRef.getMap());
+    SequenceI rcds = rap.getAlignment().getSequenceAt(1);
+    assertSame(dbRef.getMap().getTo(), rcds);
+    // compare MapList but not map.to
+    assertEquals(dbRef.getMap().getMap(), dbref2.getMap().getMap());
+
+    /*
+     * GeneLocus map.to is null so can compare Mapping objects
+     */
+    dbRef = dbrefs[2];
+    assertTrue(dbRef instanceof GeneLocus);
+    assertEquals(dbRef, dbref3);
+  }
 }