From 8d4567f28f3fce1e763beefeed625b35b3d6e8fe Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 29 Oct 2014 10:47:13 +0000
Subject: [PATCH] JAL-1264 JAL-674 test to exercise the
 AlignmentAnnotation.remap method via the
 jalview.structure.StructureMapping.transfer method

---
 test/jalview/structure/Mapping.java |  103 +++++++++++++++++++++++++++++++++++
 1 file changed, 103 insertions(+)
 create mode 100644 test/jalview/structure/Mapping.java

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
new file mode 100644
index 0000000..cd7fafe
--- /dev/null
+++ b/test/jalview/structure/Mapping.java
@@ -0,0 +1,103 @@
+package jalview.structure;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import org.junit.Test;
+
+import MCview.PDBfile;
+
+public class Mapping
+{
+
+  @Test
+  public void testPDBentryMapping() throws Exception
+  {
+    Sequence sq = new Sequence(
+            "1GAQ A subseq 126 to 219",
+            "EIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPNATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKM");
+    Sequence sq1 = new Sequence(sq);
+    String inFile;
+    StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+    // Associate the 1GAQ pdb file with the subsequence 'imported' from another
+    // source
+    PDBfile pde = ssm.setMapping(new SequenceI[]
+    { sq }, new String[]
+    { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
+    assertTrue("PDB File couldn't be found", pde != null);
+    StructureMapping[] mp = ssm.getMapping(inFile);
+    assertTrue("No mappings made.", mp != null && mp.length > 0);
+    boolean hasSecStr=false,hasTemp=false;
+    for (StructureMapping origMap:mp)
+    {
+      if (origMap.getSequence()==sq)
+      {
+        assertEquals("Mapping was incomplete.", sq.getLength() - 1,
+                (origMap.getPDBResNum(sq.getEnd()) - origMap
+                        .getPDBResNum(sq.getStart())));
+        // sanity check - if this fails, mapping from first position in sequence
+        // we want to transfer to is not where we expect
+        assertEquals(1, origMap.getSeqPos(126));
+        SequenceI firstChain = pde.getSeqs().get(0);
+        // Compare the annotated positions on the PDB chain sequence with the
+        // annotation on the associated sequence
+        for (AlignmentAnnotation alan : firstChain.getAnnotation())
+        {
+          if (alan.hasIcons)
+          {
+            hasSecStr = true;
+          }
+          if (alan.graph == alan.LINE_GRAPH)
+          {
+            hasTemp = true;
+          }
+
+          AlignmentAnnotation transfer = origMap.transfer(alan);
+          System.out.println("pdb:" + firstChain.getSequenceAsString());
+          System.out.println("ann:" + alan.toString());
+          System.out.println("pdb:" + sq.getSequenceAsString());
+          System.out.println("ann:" + transfer.toString());
+
+          for (int p = 0, pSize = firstChain.getLength() - 1; p < pSize; p++)
+          {
+            // walk along the pdb chain's jalview sequence
+            int rseqpos;
+            int fpos = origMap.getSeqPos(rseqpos = firstChain
+                    .findPosition(p));
+            // only look at positions where there is a corresponding position in
+            // mapping
+            if (fpos < 1)
+            {
+              continue;
+            }
+            // p is index into PDB residue entries
+            // rseqpos is pdb sequence position for position p
+            // fpos is sequence position for associated position for rseqpos
+            int tanpos = sq.findIndex(fpos);
+            if (transfer.annotations.length <= tanpos)
+            {
+              // gone beyond mapping to the sequence
+              break;
+            }
+            Annotation a = transfer.annotations[sq.findIndex(fpos)], b = alan.annotations[p];
+            assertEquals("Non-equivalent annotation element at " + p + "("
+                    + rseqpos + ")"
+                            + " expected at " + fpos + " (alIndex "
+                            + sq.findIndex(fpos) + ")",
+                    a == null ? a : a.toString(),
+                    b == null ? b : b.toString());
+            System.out.print("(" + a + "|" + b + ")");
+          }
+
+        }
+      }
+    }
+    assertTrue("No secondary structure transferred to associated sequence.",hasSecStr);
+    assertTrue("No temperature factor transferred to associated sequence.",hasTemp);
+  }
+
+}
-- 
1.7.10.2