fix logging in CifStructureConsumerImpl if type symbol is unknown

sbittrich · sbittrich · commit 687e0290af99 · 2021-04-13T12:17:30.000-07:00
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
@@ -332,7 +332,7 @@ public void consumeAtomSite(AtomSite atomSite) {
                 atom.setElement(element);
             }  catch (IllegalArgumentException e) {
                 logger.info("Element {} was not recognised as a BioJava-known element, the element will be " +
-                        "represented as the generic element {}", typeSymbol, Element.R.name());
+                        "represented as the generic element {}", ts, Element.R.name());
                 atom.setElement(Element.R);
             }
 

Original file line number	Diff line number	Diff line change
`@@ -332,7 +332,7 @@ public void consumeAtomSite(AtomSite atomSite) {`
`332`	`332`	`atom.setElement(element);`
`333`	`333`	`} catch (IllegalArgumentException e) {`
`334`	`334`	`logger.info("Element {} was not recognised as a BioJava-known element, the element will be " +`
`335`		`- "represented as the generic element {}", typeSymbol, Element.R.name());`
	`335`	`+ "represented as the generic element {}", ts, Element.R.name());`
`336`	`336`	`atom.setElement(Element.R);`
`337`	`337`	`}`
`338`	`338`