Twine uses the Java
Simple Plugin Framework (JSPF) to organize and launch
user-written Java programs to analyze and modify sequences.
Plugins follow a skeletal structure, overriding one method to
accept an array of all open AlignedSequence
objects.
One or more of these AlignedSequence objects can be
analyzed/modified, and optionally returned to Twine.
Once modified, the new AlignedSequence can be initialized with a
name, FASTA sequence string, and the HashMap of all Motifs,
borrowed from any of the other AlignedSequence Objects by
getMotifs().