X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fparadise%2FTestAnnotate3D.java;h=c2be67ec89f89c7b83eed2d1444c7dfea7d1b0a2;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=6635f0d441a6c6fcaed3038b8183ed15c4f08fb7;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index 6635f0d..c2be67e 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,12 +20,13 @@
  */
 package jalview.ext.paradise;
 
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
-import jalview.ext.paradise.Annotate3D;
+import jalview.io.DataSourceType;
 import jalview.io.FastaFile;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.BufferedReader;
@@ -33,8 +34,9 @@ import java.io.File;
 import java.io.Reader;
 import java.util.Iterator;
 
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
 
 import MCview.PDBfile;
 
@@ -43,7 +45,7 @@ import compbio.util.FileUtil;
 public class TestAnnotate3D
 {
 
-  @Test
+  @Test(groups = { "Network" }, enabled = true)
   public void test1GIDbyId() throws Exception
   {
     // use same ID as standard tests given at
@@ -53,7 +55,7 @@ public class TestAnnotate3D
     testRNAMLcontent(ids, null);
   }
 
-  @Test
+  @Test(groups = { "Network" }, enabled = true)
   public void testIdVsContent2GIS() throws Exception
   {
     Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
@@ -72,9 +74,13 @@ 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(
@@ -93,10 +99,11 @@ public class TestAnnotate3D
    * 
    * @throws Exception
    */
-  @Test
+  @Test(groups = { "Network" }, enabled = true)
   public void testPDBfileVsRNAML() throws Exception
   {
-    PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
+    PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
+            DataSourceType.FILE);
     Assert.assertTrue(pdbf.isValid());
     // Comment - should add new FileParse constructor like new FileParse(Reader
     // ..). for direct reading
@@ -121,11 +128,12 @@ public class TestAnnotate3D
         sb.append(line + "\n");
       }
       assertTrue("No data returned by Annotate3D", sb.length() > 0);
-      AlignmentI al = new FormatAdapter().readFile(sb.toString(),
-              FormatAdapter.PASTE, "RNAML");
+      final String lines = sb.toString();
+      AlignmentI al = new FormatAdapter().readFile(lines,
+              DataSourceType.PASTE, FileFormat.Rnaml);
       if (al == null || al.getHeight() == 0)
       {
-        System.out.println(sb.toString());
+        System.out.println(lines);
       }
       assertTrue("No alignment returned.", al != null);
       assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
@@ -138,8 +146,9 @@ public class TestAnnotate3D
             String sq_ = new String(sq.getSequence()).toLowerCase();
             for (SequenceI _struseq : pdbf.getSeqsAsArray())
             {
-              if (new String(_struseq.getSequence()).toLowerCase().equals(
-                      sq_))
+              final String lowerCase = new String(_struseq.getSequence())
+                      .toLowerCase();
+              if (lowerCase.equals(sq_))
               {
                 struseq = _struseq;
                 break;
@@ -147,11 +156,13 @@ public class TestAnnotate3D
             }
             if (struseq == null)
             {
-              Assert.fail("Couldn't find this sequence in original input:\n"
-                      + new FastaFile().print(new SequenceI[]
-                      { sq })
-                      + "\n\nOriginal input:\n"
-                      + new FastaFile().print(pdbf.getSeqsAsArray()) + "\n");
+              AssertJUnit
+                      .fail("Couldn't find this sequence in original input:\n"
+                              + new FastaFile()
+                                      .print(new SequenceI[] { sq })
+                              + "\n\nOriginal input:\n"
+                              + new FastaFile().print(pdbf.getSeqsAsArray())
+                              + "\n");
             }
           }
         }