X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=d7b26b0213bf757b057f4ab1a875fab12a43017a;hb=ea3d24d953af89ca95d4480371149b70abbfcc67;hp=2b7291482cc6582378050e29e6f00547024cedeb;hpb=4eb1ed22600411fe5b6e9ac93084b45429ccfad6;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 2b72914..d7b26b0 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -26,15 +26,21 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
 
@@ -55,8 +61,7 @@ public class AlignViewportTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] { "-props",
-        "test/jalview/testProps.jvprops" });
+    Jalview.main(new String[] { "-props", "test/jalview/testProps.jvprops" });
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -74,6 +79,7 @@ public class AlignViewportTest
   @Test(groups = { "Functional" })
   public void testCollateForPdb()
   {
+    // JBP: What behaviour is this supposed to test ?
     /*
      * Set up sequence pdb ids
      */
@@ -296,4 +302,51 @@ public class AlignViewportTest
     assertTrue(ssmMappings.contains(acf2));
     assertFalse(ssmMappings.contains(acf3));
   }
+
+  /**
+   * Test for JAL-1306 - conservation thread should run even when only Quality
+   * (and not Conservation) is enabled in Preferences
+   */
+  @Test(groups = { "Functional" })
+  public void testUpdateConservation_qualityOnly()
+  {
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("SHOW_QUALITY",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.FALSE.toString());
+    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+            Boolean.FALSE.toString());
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", FormatAdapter.FILE);
+    AlignmentAnnotation[] anns = af.viewport.getAlignment()
+            .getAlignmentAnnotation();
+    assertNotNull("No annotations found", anns);
+    assertEquals("More than one annotation found", 1, anns.length);
+    assertTrue("Annotation is not Quality",
+            anns[0].description.startsWith("Alignment Quality"));
+    Annotation[] annotations = anns[0].annotations;
+    assertNotNull("Quality annotations are null", annotations);
+    assertNotNull("Quality in column 1 is null", annotations[0]);
+    assertTrue("No quality value in column 1", annotations[0].value > 10f);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetGlobalColourScheme()
+  {
+    /*
+     * test for JAL-2283 don't inadvertently turn on colour by conservation
+     */
+    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.FALSE.toString());
+    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", FormatAdapter.FILE);
+    ColourSchemeI cs = new PIDColourScheme();
+    af.getViewport().setGlobalColourScheme(cs);
+    assertFalse(cs.conservationApplied());
+  }
 }