BioJava

updating dependencies

renaming class to avoid maven conflict

Corrected a bug in the NeedlemanWunsch algorithm class that lead to the situation that the alignments were not always displayed correctly: The end of sequences was cut because instead of telling the formatter that the complete sequence is to be ... [More] displayed, only the number of columns/rows in the cost matrix was used. But these numbers represent the length of the original sequence, not the length after insertion of gaps. The alignment itself was not affected by the bug, it was only the way how the algorithm displayed its results. [Less]

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

[maven-release-plugin] prepare release biojava-3.0-alpha2

making test less verbose

Added methods to see what the state of a compound set is before using it (such as how big are the string repsentations of compounds). The location list parsing code was also moved from the INCSDCParser to the LocationHelper class. All tests pass

some minor improvement for SITE parsing..

now with correct artifact version nr

now with correct artifact version nr