X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=ff8b19cc34da5ae64564ca3c29ab9e71befd224c;hb=418006c3714eb8da78234660698231597eb90fb1;hp=75e8065d000333fa8eefd6d8b6430c2f4a09af29;hpb=87256ba36fb105a1115067ffe2563412e9281d2d;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 75e8065..ff8b19c 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -79,9 +79,7 @@ public class AlignViewportTest
     /*
      * remove any sequence mappings left lying around by other tests
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.getInstance());
-    ssm.resetAll();
+    Desktop.getInstance().getStructureSelectionManager().resetAll();
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -127,9 +125,8 @@ public class AlignViewportTest
      * Verify that creating the alignment for the new View has registered the
      * mappings
      */
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.getInstance());
-    List<AlignedCodonFrame> sequenceMappings = ssm.getSequenceMappings();
+    List<AlignedCodonFrame> sequenceMappings = Desktop.getInstance()
+            .getStructureSelectionManager().getSequenceMappings();
     assertEquals(2, sequenceMappings.size());
     assertTrue(sequenceMappings.contains(acf1));
     assertTrue(sequenceMappings.contains(acf2));
@@ -152,8 +149,8 @@ public class AlignViewportTest
   {
     Desktop d = Desktop.getInstance();
     assertNotNull(d);
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.getInstance());
+    StructureSelectionManager ssm = Desktop.getInstance()
+            .getStructureSelectionManager();
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@@ -215,8 +212,8 @@ public class AlignViewportTest
   {
     Desktop d = Desktop.getInstance();
     assertNotNull(d);
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.getInstance());
+    StructureSelectionManager ssm = Desktop.getInstance()
+            .getStructureSelectionManager();
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
@@ -280,15 +277,15 @@ 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);
@@ -327,8 +324,8 @@ 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);
@@ -448,7 +445,6 @@ public class AlignViewportTest
     {
       c++;
     }
-    ;
     Assert.assertEquals(c, 1, "Expected to find one occupancy row.");
   }