Deal with missing strand_id

josemduarte · josemduarte · commit 2841770e7946 · 2025-02-28T13:24:40.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConsumerImpl.java
@@ -1311,7 +1311,8 @@ public void finish() {
             seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null);
             seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex));
 
-            String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex);
+            String strandId = structRefSeqDif.getPdbxPdbStrandId().isDefined()? structRefSeqDif.getPdbxPdbStrandId().get(rowIndex) : null;
+            if (strandId == null) continue;
             List<SeqMisMatch> seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>());
             seqMisMatches.add(seqMisMatch);
         }

Original file line number	Diff line number	Diff line change
`@@ -1311,7 +1311,8 @@ public void finish() {`
`1311`	`1311`	`seqMisMatch.setUniProtId(structRefSeqDif.getPdbxSeqDbAccessionCode().isDefined()? structRefSeqDif.getPdbxSeqDbAccessionCode().get(rowIndex):null);`
`1312`	`1312`	`seqMisMatch.setSeqNum(structRefSeqDif.getSeqNum().get(rowIndex));`
`1313`	`1313`
`1314`		`- String strandId = structRefSeqDif.getPdbxPdbStrandId().get(rowIndex);`
	`1314`	`+ String strandId = structRefSeqDif.getPdbxPdbStrandId().isDefined()? structRefSeqDif.getPdbxPdbStrandId().get(rowIndex) : null;`
	`1315`	`+ if (strandId == null) continue;`
`1315`	`1316`	`List<SeqMisMatch> seqMisMatches = misMatchMap.computeIfAbsent(strandId, k -> new ArrayList<>());`
`1316`	`1317`	`seqMisMatches.add(seqMisMatch);`
`1317`	`1318`	`}`