A B C D E F G H I J K L M N O P R S T V _

F

FASTAParser - class edu.uconn.mcb.lineageevolver.parsing.FASTAParser.

Class used for parsing FASTA-formatted files.

FASTAParser() - Constructor for class edu.uconn.mcb.lineageevolver.parsing.FASTAParser

findEnd(int) - Method in class edu.uconn.mcb.lineageevolver.DiagonalRecombiner

Searches for matching regions between source and destination genes within a reasonable distance of the provided target region.

findStart(int, int) - Method in class edu.uconn.mcb.lineageevolver.DiagonalRecombiner

Searches the source and destination genes between given start and end points for a matching region of length 6.

fork(ArrayList, GraphTopology) - Method in class edu.uconn.mcb.lineageevolver.LineageFork

Processes an n-furcation in the tree.