Better logging and removing some warnings

josemduarte · josemduarte · commit a6b34a4bf941 · 2016-01-06T12:10:37.000-08:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/MMcifTest.java
@@ -226,8 +226,8 @@ protected void comparePDB2cif(String id, String chainId){
 	private void checkGroups(Group g1, Group g2){
 
 		//System.out.print("comparing " +g1 + " " + g2);
-		String pdbId1 = g1.getChain().getParent().getPDBCode();
-		String pdbId2 = g1.getChain().getParent().getPDBCode();
+		String pdbId1 = g1.getChain().getStructure().getPDBCode();
+		String pdbId2 = g1.getChain().getStructure().getPDBCode();
 		assertEquals(pdbId1, pdbId2);
 
 		assertEquals(g1.getType(),g2.getType());
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/TestLongPdbVsMmCifParsing.java
@@ -418,8 +418,8 @@ private void testSingleChain(Chain cPdb, Chain cCif) {
 		}
 
 		
-		assertNotNull("getParent is null in pdb (chain "+chainId+")",cPdb.getParent());
-		assertNotNull("getParent is null in cif (chain "+chainId+")",cCif.getParent());
+		assertNotNull("getParent is null in pdb (chain "+chainId+")",cPdb.getStructure());
+		assertNotNull("getParent is null in cif (chain "+chainId+")",cCif.getStructure());
 
 			
 		assertEquals("failed for getAtomLength (chain "+chainId+"):",cPdb.getAtomLength(),cCif.getAtomLength());
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.java
@@ -492,7 +492,9 @@ private Atom convertAtom(AtomSite atom){
 		Element element = Element.R;
 		try {
 			element = Element.valueOfIgnoreCase(atom.getType_symbol());
-		}  catch (IllegalArgumentException e){}
+		}  catch (IllegalArgumentException e) {
+			logger.warn("Element {} was not recognised as a BioJava-known element, the element will be represented as the generic element {}", atom.getType_symbol(), Element.R.name());
+		}
 		a.setElement(element);
 
 		return a;
@@ -1690,7 +1692,7 @@ public void newPdbxPolySeqScheme(PdbxPolySeqScheme ppss) {
 		if (asymStrandId.containsKey(ppss.getAsym_id()))
 			return;
 
-		// this is one of the interal mmcif rules it seems...
+		// this is one of the internal mmcif rules it seems...
 		if ( ppss.getPdb_strand_id() == null) {
 			asymStrandId.put(ppss.getAsym_id(), ppss.getAuth_mon_id());
 			return;

Original file line number	Diff line number	Diff line change
`@@ -418,8 +418,8 @@ private void testSingleChain(Chain cPdb, Chain cCif) {`
`418`	`418`	`}`
`419`	`419`
`420`	`420`
`421`		`- assertNotNull("getParent is null in pdb (chain "+chainId+")",cPdb.getParent());`
`422`		`- assertNotNull("getParent is null in cif (chain "+chainId+")",cCif.getParent());`
	`421`	`+ assertNotNull("getParent is null in pdb (chain "+chainId+")",cPdb.getStructure());`
	`422`	`+ assertNotNull("getParent is null in cif (chain "+chainId+")",cCif.getStructure());`
`423`	`423`
`424`	`424`
`425`	`425`	`assertEquals("failed for getAtomLength (chain "+chainId+"):",cPdb.getAtomLength(),cCif.getAtomLength());`