JAL-3120 preserve feature colour/mincolour/maxcolour while modifying,

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

diff --git a/test/jalview/io/Jalview2xmlTests.java b/test/jalview/io/Jalview2xmlTests.java
index e9e0782..505d1f1 100644 (file)
--- a/test/jalview/io/Jalview2xmlTests.java
+++ b/test/jalview/io/Jalview2xmlTests.java
@@ -257,6 +257,31 @@ 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
   {
@@ -889,8 +914,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     fr.setColour("type2", byLabel);
 
     // type3: by score above threshold
-    FeatureColourI byScore = new FeatureColour(Color.BLACK, Color.BLUE, 1,
-            10);
+    FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
+            Color.BLUE, null, 1, 10);
     byScore.setAboveThreshold(true);
     byScore.setThreshold(2f);
     fr.setColour("type3", byScore);
@@ -902,8 +927,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     fr.setColour("type4", byAF);
 
     // type5: by attribute CSQ:PolyPhen below threshold
-    FeatureColourI byPolyPhen = new FeatureColour(Color.BLACK, Color.BLUE,
-            1, 10);
+    FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
+            Color.BLUE, null, 1, 10);
     byPolyPhen.setBelowThreshold(true);
     byPolyPhen.setThreshold(3f);
     byPolyPhen.setAttributeName("CSQ", "PolyPhen");