adds AltLoc NullPointerException test

Sebastian Bittrich · Sebastian Bittrich · commit 7c036221db18 · 2019-05-01T17:16:39.000-07:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileConsumerImplTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/cif/CifFileConsumerImplTest.java
@@ -21,6 +21,18 @@
 import static org.junit.Assert.*;
 
 public class CifFileConsumerImplTest {
+    /**
+     * java.lang.NullPointerException - failed for /var/bcif/hm/2hmz.bcif
+     */
+    @Test
+    @Ignore("ignored for now as Bcif file source may change - currently using local files")
+    public void testAltLocCleanup() throws IOException, StructureException {
+        StructureIO.getAtomCache().setUseMmCif(true);
+        StructureIO.getStructure("2hmz");
+        Structure cif = loadLocalCif("2hmz");
+        Structure bcif = loadLocalBcif("2hmz");
+    }
+
     /**
      * java.lang.NumberFormatException: multiple points have been thrown.
      */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifFileConsumerImpl.java
@@ -1112,7 +1112,6 @@ public void finish() {
             SeqRes2AtomAligner.storeUnAlignedSeqRes(structure, seqResChains, params.isHeaderOnly());
         }
 
-        // TODO java.lang.NullPointerException - failed for /var/bcif/hm/2hmz.bcif
         // Now make sure all altlocgroups have all the atoms in all the groups
         StructureTools.cleanUpAltLocs(structure);
 

Original file line number	Diff line number	Diff line change
`@@ -1112,7 +1112,6 @@ public void finish() {`
`1112`	`1112`	`SeqRes2AtomAligner.storeUnAlignedSeqRes(structure, seqResChains, params.isHeaderOnly());`
`1113`	`1113`	`}`
`1114`	`1114`
`1115`		`- // TODO java.lang.NullPointerException - failed for /var/bcif/hm/2hmz.bcif`
`1116`	`1115`	`// Now make sure all altlocgroups have all the atoms in all the groups`
`1117`	`1116`	`StructureTools.cleanUpAltLocs(structure);`
`1118`	`1117`