From 02064f049e4309bc24792e99a133f56fb9c114d0 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Thu, 30 Oct 2014 16:51:10 +0000
Subject: [PATCH] JAL-674 count number of annotation transferred in test

---
 test/jalview/structure/Mapping.java |   39 +++++++++++++++++++----------------
 1 file changed, 21 insertions(+), 18 deletions(-)

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index 4dfd1af..8cf005b 100644
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -25,13 +25,32 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     // Associate the 1GAQ pdb file with the subsequence 'imported' from another
     // source
-    PDBfile pde = ssm.setMapping(new SequenceI[]
+    PDBfile pde = ssm.setMapping(true, 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;
+    int nsecStr = 0, nsTemp = 0;
+    // test for presence of transferred annotation on sequence
+    for (AlignmentAnnotation alan : sq.getAnnotation())
+    {
+      if (alan.hasIcons)
+      {
+        nsecStr++;
+      }
+      if (alan.graph == alan.LINE_GRAPH)
+      {
+        nsTemp++;
+      }
+    }
+    assertEquals(
+            "Only one secondary structure should be transferred to associated sequence.",
+            1, nsecStr);
+    assertEquals(
+            "Only two line graphs should be transferred to associated sequence.",
+            2, nsTemp);
+    // Now test the transfer function and compare annotated positions
     for (StructureMapping origMap:mp)
     {
       if (origMap.getSequence()==sq)
@@ -87,22 +106,6 @@ public class Mapping
         }
       }
     }
-    hasSecStr = false;
-    hasTemp = false;
-    // test for presence of transferred annotation on sequence
-    for (AlignmentAnnotation alan : sq.getAnnotation())
-    {
-      if (alan.hasIcons)
-      {
-        hasSecStr = true;
-      }
-      if (alan.graph == alan.LINE_GRAPH)
-      {
-        hasTemp = true;
-      }
-    }
-    assertTrue("No secondary structure transferred to associated sequence.",hasSecStr);
-    assertTrue("No temperature factor transferred to associated sequence.",hasTemp);
   }
 
 }
-- 
1.7.10.2