failing test for JAL-2223

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index 6abb7e5..c0eb8c5 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -247,6 +247,31 @@ 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
   {
@@ -413,7 +438,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     String afid = af.getViewport().getSequenceSetId();
 
     // remember reference sequence for each panel
-    Map<String, SequenceI> refseqs = new HashMap<String, SequenceI>();
+    Map<String, SequenceI> refseqs = new HashMap<>();
 
     /*
      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
@@ -551,8 +576,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
      * remember representative and hidden sequences marked 
      * on each panel
      */
-    Map<String, SequenceI> repSeqs = new HashMap<String, SequenceI>();
-    Map<String, List<String>> hiddenSeqNames = new HashMap<String, List<String>>();
+    Map<String, SequenceI> repSeqs = new HashMap<>();
+    Map<String, List<String>> hiddenSeqNames = new HashMap<>();
 
     /*
      * mark sequence 2, 3, 4.. in panels 1, 2, 3...
@@ -568,7 +593,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       repIndex = Math.max(repIndex, 1);
       SequenceI repSeq = alignment.getSequenceAt(repIndex);
       repSeqs.put(ap.getViewName(), repSeq);
-      List<String> hiddenNames = new ArrayList<String>();
+      List<String> hiddenNames = new ArrayList<>();
       hiddenSeqNames.put(ap.getViewName(), hiddenNames);
 
       /*