X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=fa71b2eaa35b75ac48806965d2d1d9b615485494;hb=8e1be43e250107a4d86898bd554cf03098fa5957;hp=8a550a7134f2294a6e998d10628f7a4c2ce6ebed;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 8a550a7..fa71b2e 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -39,8 +39,8 @@ import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
@@ -147,7 +147,7 @@ public class AlignViewportTest
      * alignment with reference to mappings
      */
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq1\nCAGT\n", FormatAdapter.PASTE);
+            ">Seq1\nCAGT\n", DataSourceType.PASTE);
 
     SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
@@ -196,9 +196,9 @@ public class AlignViewportTest
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
+            ">Seq1\nRSVQ\n", DataSourceType.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq2\nDGEL\n", FormatAdapter.PASTE);
+            ">Seq2\nDGEL\n", DataSourceType.PASTE);
     SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
     SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
     SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
@@ -259,9 +259,9 @@ public class AlignViewportTest
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
+            ">Seq1\nRSVQ\n", DataSourceType.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq2\nDGEL\n", FormatAdapter.PASTE);
+            ">Seq2\nDGEL\n", DataSourceType.PASTE);
     SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
     SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
     SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
@@ -328,7 +328,7 @@ public class AlignViewportTest
     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
             Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", FormatAdapter.FILE);
+            "examples/uniref50.fa", DataSourceType.FILE);
     AlignmentAnnotation[] anns = af.viewport.getAlignment()
             .getAlignmentAnnotation();
     assertNotNull("No annotations found", anns);
@@ -345,23 +345,24 @@ public class AlignViewportTest
   public void testSetGlobalColourScheme()
   {
     /*
-     * test for JAL-2283 don't inadvertently turn on colour by conservation
+     * test for JAL-2283: don't inadvertently turn on colour by conservation
      */
-    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
             Boolean.TRUE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", FormatAdapter.FILE);
+            "examples/uniref50.fa", DataSourceType.FILE);
     ColourSchemeI cs = new PIDColourScheme();
     af.getViewport().setGlobalColourScheme(cs);
-    assertFalse(cs.conservationApplied());
+    assertFalse(af.getViewport().getViewportColourScheme()
+            .conservationApplied());
   }
 
   @Test(groups = { "Functional" })
   public void testSetGetHasSearchResults()
   {
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", FormatAdapter.FILE);
+            "examples/uniref50.fa", DataSourceType.FILE);
     SearchResultsI sr = new SearchResults();
     SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);