upgrade to latest paradise services model using JSon response.

[jalview.git] / test / jalview / ext / paradise / TestAnnotate3D.java

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index d358c44..702d9ad 100644 (file)
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -2,13 +2,22 @@ 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;
 
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.Reader;
+import java.util.Iterator;
 
+import org.junit.Assert;
 import org.junit.Test;
 
+import MCview.PDBfile;
+
 import compbio.util.FileUtil;
 
 public class TestAnnotate3D
@@ -17,11 +26,17 @@ public class TestAnnotate3D
   @Test
   public void testIdVsContent() throws Exception
   {
-    BufferedReader id = (BufferedReader) Annotate3D.getRNAMLForPDBId("2GIS");
-    assertTrue("Didn't retrieve 2GIS by id.", id != null);
-    BufferedReader file = (BufferedReader) Annotate3D.getRNAMLForPDBFileAsString(FileUtil
-            .readFileToString(new File("examples/2GIS.pdb")));
-    assertTrue("Didn't retrieve using examples/2GIS.pdb.", file != null);
+    Iterator<Reader> ids = Annotate3D
+            .getRNAMLForPDBId("2GIS");
+    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.", 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
     {
@@ -31,12 +46,71 @@ 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);
+    }
   }
 
+  /**
+   * test to demonstrate JAL-1142 - compare sequences in RNAML returned from
+   * Annotate3d vs those extracted by Jalview from the originl PDB file
+   * 
+   * @throws Exception
+   */
+  @Test
+  public void testPDBfileVsRNAML() throws Exception
+  {
+    PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
+    Assert.assertTrue(pdbf.isValid());
+    StringBuffer sb = new StringBuffer();
+    // Comment - should add new FileParse constructor like new FileParse(Reader
+    // ..). for direct reading
+    Iterator<Reader> readers = Annotate3D
+            .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
+                    "examples/2GIS.pdb")));
+    int r=0;
+    while (readers.hasNext())
+    {
+      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())
+      {
+        {
+          SequenceI struseq = null;
+          String sq_ = new String(sq.getSequence()).toLowerCase();
+          for (SequenceI _struseq : pdbf.getSeqsAsArray())
+          {
+            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");
+          }
+        }
+      }
+    }
+  }
 }