Better logging

josemduarte · josemduarte · commit 2898281a7116 · 2017-11-16T09:12:30.000-08:00
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
@@ -1752,8 +1752,8 @@ public void newStructRefSeq(StructRefSeq sref) {
 			seqend   = Integer.parseInt(sref.getPdbx_auth_seq_align_end());
 		}
 		catch(NumberFormatException e){
-			logger.info("Couldn't parse sequence alignment positions.");
-			logger.debug(e.toString());
+			// this happens in a few entries, annotation error? e.g. 6eoj
+			logger.warn("Couldn't parse pdbx_auth_seq_align_beg/end in _struct_ref_seq. Will not store dbref alignment info for accession {}. Error: {}", r.getDbAccession(), e.getMessage());
 			return;
 		}
 		Character begin_ins_code = new Character(sref.getPdbx_seq_align_beg_ins_code().charAt(0));

Original file line number	Diff line number	Diff line change
`@@ -1752,8 +1752,8 @@ public void newStructRefSeq(StructRefSeq sref) {`
`1752`	`1752`	`seqend = Integer.parseInt(sref.getPdbx_auth_seq_align_end());`
`1753`	`1753`	`}`
`1754`	`1754`	`catch(NumberFormatException e){`
`1755`		`- logger.info("Couldn't parse sequence alignment positions.");`
`1756`		`- logger.debug(e.toString());`
	`1755`	`+ // this happens in a few entries, annotation error? e.g. 6eoj`
	`1756`	`+ logger.warn("Couldn't parse pdbx_auth_seq_align_beg/end in _struct_ref_seq. Will not store dbref alignment info for accession {}. Error: {}", r.getDbAccession(), e.getMessage());`
`1757`	`1757`	`return;`
`1758`	`1758`	`}`
`1759`	`1759`	`Character begin_ins_code = new Character(sref.getPdbx_seq_align_beg_ins_code().charAt(0));`