We noticed that you have 90 violations of the Sonar rule RSPEC-1940 "Boolean checks should not be inverted". When you call isEmpty(), it clearly communicates the code’s intention, which is to check if the collection is empty. Using size() == 0 for this purpose is less direct and makes the code slightly more complex.

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org\biojava\nbio\core\alignment\SimpleAlignedSequence.java
@@ -411,5  +411,5 @@

	// combine sublocations into 1 Location
\-		if (sublocations.size() == 0) {
\+		if (sublocations.isEmpty()) {
		location = null;