JAL-3626 from JAL-3253-applet Cache applicationProperties made private

[jalview.git] / test / jalview / gui / AlignViewportTest.java

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 7801250..76021ce 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -23,9 +23,18 @@ package jalview.gui;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNotSame;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignedCodonFrame;
@@ -33,8 +42,6 @@ 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.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
@@ -42,20 +49,13 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
+import jalview.schemes.ClustalxColourScheme;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MapList;
 import jalview.viewmodel.ViewportRanges;
 
-import java.util.ArrayList;
-import java.util.List;
-
-import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 public class AlignViewportTest
 {
 
@@ -280,15 +280,15 @@ public class AlignViewportTest
   @Test(groups = { "Functional" }, timeOut=2000)
   public void testUpdateConservation_qualityOnly()
   {
-    Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+    Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
             Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("SHOW_QUALITY",
+    Cache.setPropertyNoSave("SHOW_QUALITY",
             Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+    Cache.setPropertyNoSave("SHOW_CONSERVATION",
             Boolean.FALSE.toString());
-    Cache.applicationProperties.setProperty("SHOW_OCCUPANCY",
+    Cache.setPropertyNoSave("SHOW_OCCUPANCY",
             Boolean.FALSE.toString());
-    Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+    Cache.setPropertyNoSave("SHOW_IDENTITY",
             Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
@@ -297,9 +297,29 @@ public class AlignViewportTest
      * wait for Conservation thread to complete
      */
     AlignViewport viewport = af.getViewport();
+    waitForCalculations(viewport);
+    AlignmentAnnotation[] anns = 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);
+  }
+
+  /**
+   * Wait for consensus etc calculation threads to complete
+   * 
+   * @param viewport
+   */
+  protected void waitForCalculations(AlignViewport viewport)
+  {
     synchronized (this)
     {
-      while (viewport.getAlignmentConservationAnnotation() != null)
+      while (viewport.getCalcManager().isWorking())
       {
         try
         {
@@ -309,16 +329,6 @@ public class AlignViewportTest
         }
       }
     }
-    AlignmentAnnotation[] anns = 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" })
@@ -327,15 +337,40 @@ public class AlignViewportTest
     /*
      * test for JAL-2283: don't inadvertently turn on colour by conservation
      */
-    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
-    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+    Cache.setPropertyNoSave("DEFAULT_COLOUR_PROT", "None");
+    Cache.setPropertyNoSave("SHOW_CONSERVATION",
             Boolean.TRUE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     ColourSchemeI cs = new PIDColourScheme();
-    af.getViewport().setGlobalColourScheme(cs);
-    assertFalse(af.getViewport().getResidueShading()
+    AlignViewport viewport = af.getViewport();
+    viewport.setGlobalColourScheme(cs);
+    assertFalse(viewport.getResidueShading()
             .conservationApplied());
+
+    /*
+     * JAL-3201 groups have their own ColourSchemeI instances
+     */
+    AlignmentI aln = viewport.getAlignment();
+    SequenceGroup sg1 = new SequenceGroup();
+    sg1.addSequence(aln.getSequenceAt(0), false);
+    sg1.addSequence(aln.getSequenceAt(2), false);
+    SequenceGroup sg2 = new SequenceGroup();
+    sg2.addSequence(aln.getSequenceAt(1), false);
+    sg2.addSequence(aln.getSequenceAt(3), false);
+    aln.addGroup(sg1);
+    aln.addGroup(sg2);
+    viewport.setColourAppliesToAllGroups(true);
+    viewport.setGlobalColourScheme(new ClustalxColourScheme());
+    ColourSchemeI cs0 = viewport.getGlobalColourScheme();
+    ColourSchemeI cs1 = sg1.getColourScheme();
+    ColourSchemeI cs2 = sg2.getColourScheme();
+    assertTrue(cs0 instanceof ClustalxColourScheme);
+    assertTrue(cs1 instanceof ClustalxColourScheme);
+    assertTrue(cs2 instanceof ClustalxColourScheme);
+    assertNotSame(cs0, cs1);
+    assertNotSame(cs0, cs2);
+    assertNotSame(cs1, cs2);
   }
 
   @Test(groups = { "Functional" })
@@ -441,6 +476,7 @@ public class AlignViewportTest
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
             DataSourceType.PASTE);
     AlignViewport testme = af.getViewport();
+    waitForCalculations(testme);
     SequenceI cons = testme.getConsensusSeq();
     assertEquals("A-C", cons.getSequenceAsString());
   }