X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fparadise%2FTestAnnotate3D.java;h=702d9ad42a0586d9a49a0def341cfacf150390c3;hb=9d75efeeb9a6e51bd328f56e376dca4e007b635c;hp=1ed46f4e5669efd773f00a053d7ee982a0293d43;hpb=89b54c4138d9fcf60324227b4b64e92447793d3f;p=jalview.git

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index 1ed46f4..702d9ad 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -10,6 +10,8 @@ import jalview.io.FormatAdapter;
 
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.Reader;
+import java.util.Iterator;
 
 import org.junit.Assert;
 import org.junit.Test;
@@ -24,13 +26,17 @@ public class TestAnnotate3D
   @Test
   public void testIdVsContent() throws Exception
   {
-    BufferedReader id = (BufferedReader) Annotate3D
+    Iterator<Reader> ids = Annotate3D
             .getRNAMLForPDBId("2GIS");
-    assertTrue("Didn't retrieve 2GIS by id.", id != null);
-    BufferedReader file = (BufferedReader) Annotate3D
+    assertTrue("Didn't retrieve 2GIS by id.", ids != null);
+    Iterator<Reader> files = Annotate3D
             .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
                     "examples/2GIS.pdb")));
-    assertTrue("Didn't retrieve using examples/2GIS.pdb.", file != null);
+    assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
+    int i=0;
+    while (ids.hasNext() && files.hasNext())
+    {
+      BufferedReader file=new BufferedReader(files.next()), id=new BufferedReader(ids.next());
     String iline, fline;
     do
     {
@@ -40,12 +46,13 @@ public class TestAnnotate3D
         System.out.println(iline);
       if (fline != null)
         System.out.println(fline);
-
-      assertTrue("Results differ for ID and file upload based retrieval",
+      // next assert fails for latest RNAview - because the XMLID entries change between file and ID based RNAML generation.
+      assertTrue("Results differ for ID and file upload based retrieval (chain entry "+(++i)+")",
               ((iline == fline && iline == null) || (iline != null
                       && fline != null && iline.equals(fline))));
 
     } while (iline != null);
+    }
   }
 
   /**
@@ -62,39 +69,46 @@ public class TestAnnotate3D
     StringBuffer sb = new StringBuffer();
     // Comment - should add new FileParse constructor like new FileParse(Reader
     // ..). for direct reading
-    BufferedReader br = new BufferedReader(
-            Annotate3D.getRNAMLForPDBFileAsString(FileUtil
-                    .readFileToString(new File("examples/2GIS.pdb"))));
-    String line;
-    while ((line = br.readLine()) != null)
+    Iterator<Reader> readers = Annotate3D
+            .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
+                    "examples/2GIS.pdb")));
+    int r=0;
+    while (readers.hasNext())
     {
-      sb.append(line + "\n");
-    }
-    assertTrue("No data returned by Annotate3D", sb.length() > 0);
-    AlignmentI al = new FormatAdapter().readFile(sb.toString(),
-            FormatAdapter.PASTE, "RNAML");
+      System.out.println("Testing RNAML input number "+(++r));
+      BufferedReader br = new BufferedReader(readers.next());
+      String line;
+      while ((line = br.readLine()) != null)
+      {
+        sb.append(line + "\n");
+      }
+      assertTrue("No data returned by Annotate3D", sb.length() > 0);
+      AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+              FormatAdapter.PASTE, "RNAML");
 
-    assertTrue("No alignment returned.", al != null);
-    assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
-    for (SequenceI sq : al.getSequences())
-    {
+      assertTrue("No alignment returned.", al != null);
+      assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
+      for (SequenceI sq : al.getSequences())
       {
-        SequenceI struseq = null;
-        String sq_ = new String(sq.getSequence()).toLowerCase();
-        for (SequenceI _struseq : pdbf.getSeqsAsArray())
         {
-          if (new String(_struseq.getSequence()).toLowerCase().equals(sq_))
+          SequenceI struseq = null;
+          String sq_ = new String(sq.getSequence()).toLowerCase();
+          for (SequenceI _struseq : pdbf.getSeqsAsArray())
           {
-            struseq = _struseq;
-            break;
+            if (new String(_struseq.getSequence()).toLowerCase()
+                    .equals(sq_))
+            {
+              struseq = _struseq;
+              break;
+            }
+          }
+          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");
           }
-        }
-        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");
         }
       }
     }