X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fparadise%2FTestAnnotate3D.java;h=a7c439f7cbdc3d7736d2d9afafb49cf66753670f;hb=71fc0e8716067e0d1100f82cced73c38bfb8d7f6;hp=dca7bf8e7f47b3a4dd05bdf37e3ad66a9674343f;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index dca7bf8..a7c439f 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -21,10 +21,8 @@
 package jalview.ext.paradise;
 
 import static org.junit.Assert.assertTrue;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
-import jalview.ext.paradise.Annotate3D;
 import jalview.io.FastaFile;
 import jalview.io.FormatAdapter;
 
@@ -46,10 +44,11 @@ public class TestAnnotate3D
   @Test
   public void test1GIDbyId() throws Exception
   {
-    // use same ID as standard tests given at https://bitbucket.org/fjossinet/pyrna-rest-clients
+    // use same ID as standard tests given at
+    // https://bitbucket.org/fjossinet/pyrna-rest-clients
     Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
     assertTrue("Didn't retrieve 1GID by id.", ids != null);
-    testRNAMLcontent(ids,null);
+    testRNAMLcontent(ids, null);
   }
 
   @Test
@@ -71,9 +70,13 @@ public class TestAnnotate3D
         iline = id.readLine();
         fline = file.readLine();
         if (iline != null)
+        {
           System.out.println(iline);
+        }
         if (fline != null)
+        {
           System.out.println(fline);
+        }
         // next assert fails for latest RNAview - because the XMLID entries
         // change between file and ID based RNAML generation.
         assertTrue(
@@ -95,7 +98,8 @@ public class TestAnnotate3D
   @Test
   public void testPDBfileVsRNAML() throws Exception
   {
-    PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
+    PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
+            FormatAdapter.FILE);
     Assert.assertTrue(pdbf.isValid());
     // Comment - should add new FileParse constructor like new FileParse(Reader
     // ..). for direct reading
@@ -122,7 +126,8 @@ public class TestAnnotate3D
       assertTrue("No data returned by Annotate3D", sb.length() > 0);
       AlignmentI al = new FormatAdapter().readFile(sb.toString(),
               FormatAdapter.PASTE, "RNAML");
-      if (al==null || al.getHeight()==0) {
+      if (al == null || al.getHeight() == 0)
+      {
         System.out.println(sb.toString());
       }
       assertTrue("No alignment returned.", al != null);