X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2FPDBSequenceFetcherTest.java;h=e7f9ff1288b2332899d670f3c61d0f24a6da93ae;hb=4ea2f7c6e700c5137c62a09a93d0127f8d58158b;hp=78ab67e0353925c0579f5775a7d9f1efd5795bc8;hpb=8ae616ebad21429f5c58a9190b9919e873806c3c;p=jalview.git

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index 78ab67e..e7f9ff1 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -35,6 +35,7 @@ import jalview.ws.seqfetcher.DbSourceProxy;
 import java.util.Arrays;
 import java.util.List;
 
+import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
@@ -61,7 +62,7 @@ public class PDBSequenceFetcherTest
     Cache.applicationProperties.setProperty("ADD_SS_ANN",
             Boolean.TRUE.toString());
 
-    sf = new SequenceFetcher(false);
+    sf = new SequenceFetcher();
   }
 
   /**
@@ -131,6 +132,7 @@ public class PDBSequenceFetcherTest
   private void testRetrieveProteinSeqFromPDB() throws Exception
   {
     List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
+    StringBuilder errors = new StringBuilder();
     for (TestRetrieveObject str : toRetrieve)
     {
       AlignmentI response = sps.get(0).getSequenceRecords(str.id);
@@ -145,14 +147,36 @@ public class PDBSequenceFetcherTest
                 sq.getAllPDBEntries().size() > 0);
         // FIXME: should test that all residues extracted as sequences from
         // chains in structure have a mapping to data in the structure
-
-        for (int rs = sq.getStart(); rs < sq.getStart()
-                + sq.getLength(); rs++)
+        List<SequenceFeature> prev = null;
+        int lastp = -1;
+        for (int col = 1; col <= sq.getLength(); col++)
         {
-          List<SequenceFeature> sf = sq.findFeatures(rs, rs, "RESNUM");
-          assertEquals(sf.size(), 1);
+          List<SequenceFeature> sf = sq.findFeatures(col, col, "RESNUM");
+          if (sf.size() != 1)
+          {
+            errors.append(str.id + ": "
+                    + "Expected one feature at column (position): "
+                    + (col - 1) + " (" + sq.findPosition(col - 1) + ")"
+                    + ": saw " + sf.size());
+            errors.append("\n");
+            if (prev != null)
+            {
+              errors.append("Last Feature was at position " + lastp + ": "
+                      + prev.get(0).toString());
+              errors.append("\n");
+            }
+          }
+          else
+          {
+            prev = sf;
+            lastp = sq.findPosition(col - 1);
+          }
         }
       }
     }
+    if (errors.length() > 0)
+    {
+      Assert.fail(errors.toString());
+    }
   }
 }