JAL-1941 added test URL and notes about PyRNA restclient

[jalview.git] / test / MCview / PDBfileTest.java

diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index 31c3beb..a6a1de4 100644 (file)
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -83,6 +83,8 @@ public class PDBfileTest
     assertEquals("D", pf.getChains().get(3).id);
 
     PDBChain chainA = pf.getChains().get(0);
+    SequenceI seqA = pf.getSeqs().get(0);
+
     assertEquals(0, chainA.seqstart); // not set
     assertEquals(0, chainA.seqend); // not set
     assertEquals(18, chainA.sequence.getStart());
@@ -91,8 +93,8 @@ public class PDBfileTest
     assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
     assertEquals("3W5V|A", chainA.sequence.getName());
     assertNull(chainA.sequence.getAnnotation());
-    assertEquals(1, chainA.sequence.getAllPDBEntries().size());
-    PDBEntry pdb = chainA.sequence.getAllPDBEntries().get(0);
+    assertEquals(1, seqA.getAllPDBEntries().size());
+    PDBEntry pdb = seqA.getAllPDBEntries().get(0);
     assertEquals("A", pdb.getChainCode());
     assertEquals("PDB", pdb.getType());
     assertEquals("3W5V", pdb.getId());
@@ -251,10 +253,10 @@ public class PDBfileTest
     /*
      * PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case
      */
-    assertEquals("Secondary Structure for 3W5VA", anns[0].description);
-    assertEquals("Secondary Structure for 3W5VB", anns[2].description);
-    assertEquals("Secondary Structure for 3W5VC", anns[4].description);
-    assertEquals("Secondary Structure for 3W5VD", anns[6].description);
+    assertEquals("Secondary Structure for 3w5vA", anns[0].description);
+    assertEquals("Secondary Structure for 3w5vB", anns[2].description);
+    assertEquals("Secondary Structure for 3w5vC", anns[4].description);
+    assertEquals("Secondary Structure for 3w5vD", anns[6].description);
 
     /*
      * Verify SS annotations are linked to respective sequences (chains)