JAL-2738 copy to spikes/mungo

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

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 45340d9..152ab84 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -34,7 +34,9 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
+import jalview.structure.StructureSelectionManager;
 
 import java.awt.Color;
 import java.io.File;
@@ -45,11 +47,24 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class FeaturesFileTest
 {
+  private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
+
+  @AfterClass(alwaysRun = true)
+  public void tearDownAfterClass()
+  {
+    /*
+     * remove any sequence mappings created so they don't pollute other tests
+     */
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+    ssm.resetAll();
+  }
 
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
@@ -58,8 +73,6 @@ public class FeaturesFileTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
-
   @Test(groups = { "Functional" })
   public void testParse() throws Exception
   {
@@ -79,9 +92,13 @@ public class FeaturesFileTest
      * updated - JAL-1904), and verify (some) feature group colours
      */
     colours = af.getFeatureRenderer().getFeatureColours();
-    assertEquals("26 feature group colours not found", 26, colours.size());
+    assertEquals("27 feature group colours not found", 27, colours.size());
     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
+    FeatureColourI kdColour = colours.get("kdHydrophobicity");
+    assertTrue(kdColour.isGraduatedColour());
+    assertTrue(kdColour.isAboveThreshold());
+    assertEquals(-2f, kdColour.getThreshold());
 
     /*
      * verify (some) features on sequences