BioJava

Annoying code change because the SequenceMixin.reverse() did not keep up with the rename in the Sequence interface

Sequence.getReverse() has been changed to getInverse() to avoid confusion.

Modified in line with latest version of biojava3-core's Sequence interface

Modified in line with latest version of biojava3-core's Sequence interface

Change to the sequence & compoundset interfaces. We have removed getSequenceAsString with reference to positions in favor for one which is based on asking for subsequences and then requesting the String from that subsequence. All tests pass & badly named tests renamed to make sure Maven picks up on them

Parser was broken when faced with points greater than a single integer. Regular expression is no long as greedy and seems to have fixed the problem. Circular detection has also been fixed so it cannot happen if a location skips between accessions.

[maven-release-plugin] prepare for next development iteration

[maven-release-plugin] prepare release biojava-3.0-alpha4

Had to edit these to avoid delegation onto the backing store when we ask for the sequence at a given position. The code passes through a location which may decrease speed but it I'm sure it'll work.

Bug found where the sequence exceeded the size of the k-mer. Infinite loop added & now breaking when we no longer have any more k-mers to process