X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fparadise%2FTestAnnotate3D.java;h=7d0916bd6967ebb229b786415ca24c00c9d8ccd3;hb=55ebdfcc6bd979605c9bb2b4092a422b035bc27e;hp=1b70e8de026f7fa100528ce7b4b0e1a7572b8248;hpb=5f4e1e4c330b045e9c8bce28ee132a0fca3834d8;p=jalview.git

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index 1b70e8d..7d0916b 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -25,7 +25,9 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.FastaFile;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.BufferedReader;
@@ -38,9 +40,8 @@ import org.testng.AssertJUnit;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import MCview.PDBfile;
-
 import compbio.util.FileUtil;
+import mc_view.PDBfile;
 
 public class TestAnnotate3D
 {
@@ -110,7 +111,7 @@ public class TestAnnotate3D
   public void testPDBfileVsRNAML() throws Exception
   {
     PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     Assert.assertTrue(pdbf.isValid());
     // Comment - should add new FileParse constructor like new FileParse(Reader
     // ..). for direct reading
@@ -137,7 +138,7 @@ public class TestAnnotate3D
       assertTrue("No data returned by Annotate3D", sb.length() > 0);
       final String lines = sb.toString();
       AlignmentI al = new FormatAdapter().readFile(lines,
-              FormatAdapter.PASTE, "RNAML");
+              DataSourceType.PASTE, FileFormat.Rnaml);
       if (al == null || al.getHeight() == 0)
       {
         System.out.println(lines);
@@ -150,10 +151,10 @@ public class TestAnnotate3D
         {
           {
             SequenceI struseq = null;
-            String sq_ = new String(sq.getSequence()).toLowerCase();
+            String sq_ = sq.getSequenceAsString().toLowerCase();
             for (SequenceI _struseq : pdbf.getSeqsAsArray())
             {
-              final String lowerCase = new String(_struseq.getSequence())
+              final String lowerCase = _struseq.getSequenceAsString()
                       .toLowerCase();
               if (lowerCase.equals(sq_))
               {
@@ -165,11 +166,11 @@ public class TestAnnotate3D
             {
               AssertJUnit
                       .fail("Couldn't find this sequence in original input:\n"
-                              + new FastaFile()
-                                      .print(new SequenceI[] { sq })
+                              + new FastaFile().print(
+                                      new SequenceI[] { sq }, true)
                               + "\n\nOriginal input:\n"
-                              + new FastaFile().print(pdbf.getSeqsAsArray())
-                              + "\n");
+                              + new FastaFile().print(
+                                      pdbf.getSeqsAsArray(), true) + "\n");
             }
           }
         }