From 09da3ad08ff2e25e67e3f4a08ae4644660eebd72 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 6 Oct 2014 12:24:14 +0100
Subject: [PATCH] JAL-654 format and refactor test demonstrating PDB secondary
 structure on alignment not properly linked to alignment
 sequence

---
 test/jalview/ext/jmol/PDBFileWithJmolTest.java |   52 ++++++++++++++++--------
 1 file changed, 34 insertions(+), 18 deletions(-)

diff --git a/test/jalview/ext/jmol/PDBFileWithJmolTest.java b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
index ef14287..d561acb 100644
--- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java
+++ b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
@@ -40,17 +40,23 @@ import org.junit.Test;
 public class PDBFileWithJmolTest
 {
   String[] testFile = new String[]
-  { "./examples/1GAQ.txt" }; // , "./examples/DNMT1_MOUSE.pdb" };
+  { "./examples/1GAQ.txt" }; // ,
+
+  // "./examples/DNMT1_MOUSE.pdb"
+  // };
 
   @Test
-   public void testAlignmentLoader() throws Exception
-   {
-    for (String f:testFile) {
+  public void testAlignmentLoader() throws Exception
+  {
+    for (String f : testFile)
+    {
       FileLoader fl = new jalview.io.FileLoader(false);
-      AlignFrame af = fl.LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
+      AlignFrame af = fl
+              .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
       validateSecStrRows(af.getViewport().getAlignment());
     }
-   }
+  }
+
   @Test
   public void testFileParser() throws Exception
   {
@@ -76,26 +82,36 @@ public class PDBFileWithJmolTest
 
   private void validateSecStrRows(AlignmentI al)
   {
-
     if (!al.isNucleotide())
     {
       for (SequenceI asq : al.getSequences())
       {
         SequenceI sq = asq;
-        while (sq.getDatasetSequence()!=null && sq.getAnnotation()==null)
+        boolean hasDs = false;
+        while (sq.getDatasetSequence() != null
+                && sq.getAnnotation() == null)
         {
-          sq = asq.getDatasetSequence();
+          sq = sq.getDatasetSequence();
+          hasDs = true;
+        }
+        checkFirstAAIsAssoc(sq);
+        if (hasDs)
+        {
+          // also verify if alignment sequence has annotation on it
+          // that is correctly mapped
+          checkFirstAAIsAssoc(asq);
         }
-        assertTrue(
-                "No secondary structure assigned for protein sequence.",
-                sq.getAnnotation() != null
-                        && sq.getAnnotation().length >= 1
-                        && sq.getAnnotation()[0].hasIcons);
-        assertTrue(
-                "Secondary structure not associated for sequence "
-                        + sq.getName(),
-                sq.getAnnotation()[0].sequenceRef == sq);
       }
     }
   }
+
+  private void checkFirstAAIsAssoc(SequenceI sq)
+  {
+    assertTrue("No secondary structure assigned for protein sequence.",
+            sq.getAnnotation() != null && sq.getAnnotation().length >= 1
+                    && sq.getAnnotation()[0].hasIcons);
+    assertTrue(
+            "Secondary structure not associated for sequence "
+                    + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
+  }
 }
-- 
1.7.10.2