Update UniprotProxySequenceReader.java

emckee2006 · emckee2006 · commit b5425aff6fc1 · 2019-06-05T12:34:34.000-04:00
Uniprot has begun adding spaces into the sequence string. We simply strip them out again so we don't get a compound noot found error.
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
@@ -149,7 +149,7 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
 	public void setContents(String sequence) throws CompoundNotFoundException {
 		// Horrendously inefficient - pretty much the way the old BJ did things.
 		// TODO Should be optimised.
-		this.sequence = sequence;
+		this.sequence = sequence.replaceAll(" ", "");
 		this.parsedCompounds.clear();
 		for (int i = 0; i < sequence.length();) {
 			String compoundStr = null;
