Merge branch 'develop' into trialMerge

[jalview.git] / test / MCview / PDBfileTest.java

diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index 551e805..c07c62e 100644 (file)
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -34,7 +34,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureImportSettings;
 
 import java.io.IOException;
@@ -83,7 +83,7 @@ public class PDBfileTest
      * Constructor with file path performs parse()
      */
     PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     assertEquals("3W5V", pf.getId());
     // verify no alignment annotations created
@@ -159,7 +159,7 @@ public class PDBfileTest
   public void testParse_withAnnotations_noSS() throws IOException
   {
     PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
     assertEquals(4, anns.length);
@@ -217,7 +217,7 @@ public class PDBfileTest
   public void testParse_withJmol_noAnnotations() throws IOException
   {
     PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     /*
      * alignment annotations _are_ created anyway (in
@@ -247,7 +247,7 @@ public class PDBfileTest
           throws IOException
   {
     PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     /*
      * Alignment annotations for TempFactor, SecStruct, per sequence (chain)
@@ -305,7 +305,7 @@ public class PDBfileTest
     // TODO requires a mock for Annotate3D processing
     // and/or run as an integration test
     PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
   }
 
   /**
@@ -321,8 +321,6 @@ public class PDBfileTest
     return al.getAlignmentAnnotation();
   }
 
-  // @formatter:on
-
   @BeforeMethod(alwaysRun = true)
   public void setUp()
   {