From 89b54c4138d9fcf60324227b4b64e92447793d3f Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 21 Aug 2012 11:29:58 +0100
Subject: [PATCH] JAL-1142 - test to demonstrate mismatch between rnaview and
 Jalview PDB parsing with 2GIS

---
 test/jalview/ext/paradise/TestAnnotate3D.java |   66 +++++++++++++++++++++++--
 1 file changed, 63 insertions(+), 3 deletions(-)

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index d358c44..1ed46f4 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -2,13 +2,20 @@ 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 org.junit.Assert;
 import org.junit.Test;
 
+import MCview.PDBfile;
+
 import compbio.util.FileUtil;
 
 public class TestAnnotate3D
@@ -17,10 +24,12 @@ public class TestAnnotate3D
   @Test
   public void testIdVsContent() throws Exception
   {
-    BufferedReader id = (BufferedReader) Annotate3D.getRNAMLForPDBId("2GIS");
+    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")));
+    BufferedReader file = (BufferedReader) Annotate3D
+            .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
+                    "examples/2GIS.pdb")));
     assertTrue("Didn't retrieve using examples/2GIS.pdb.", file != null);
     String iline, fline;
     do
@@ -39,4 +48,55 @@ public class TestAnnotate3D
     } 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
+    BufferedReader br = new BufferedReader(
+            Annotate3D.getRNAMLForPDBFileAsString(FileUtil
+                    .readFileToString(new File("examples/2GIS.pdb"))));
+    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");
+        }
+      }
+    }
+  }
 }
-- 
1.7.10.2