Avoiding an NPE in mmtf reader

josemduarte · josemduarte · commit e4adfa1a587b · 2017-07-16T13:48:30.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -129,6 +129,10 @@ public void finalizeStructure() {
 			for(Chain modelChain : modelChainMap.values()){
 				structure.addChain(modelChain, i);
 				String sequence = chainSequenceMap.get(modelChain.getId());
+				if (sequence == null) {
+					logger.warn("Sequence is null for chain with asym_id {}. Most likely the chain is non-polymeric. Will not add seqres groups for it.", modelChain.getId());
+					continue;
+				}
 				MmtfUtils.addSeqRes(modelChain, sequence);
 			}
 		}

Original file line number	Diff line number	Diff line change
`@@ -129,6 +129,10 @@ public void finalizeStructure() {`
`129`	`129`	`for(Chain modelChain : modelChainMap.values()){`
`130`	`130`	`structure.addChain(modelChain, i);`
`131`	`131`	`String sequence = chainSequenceMap.get(modelChain.getId());`
	`132`	`+ if (sequence == null) {`
	`133`	`+ logger.warn("Sequence is null for chain with asym_id {}. Most likely the chain is non-polymeric. Will not add seqres groups for it.", modelChain.getId());`
	`134`	`+ continue;`
	`135`	`+ }`
`132`	`136`	`MmtfUtils.addSeqRes(modelChain, sequence);`
`133`	`137`	`}`
`134`	`138`	`}`