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

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parseFile(String) - Static method in class edu.uconn.mcb.lineageevolver.parsing.FASTAParser

Returns an array of sequences, as obtained by parsing the given file.

parseFile(String) - Method in class edu.uconn.mcb.lineageevolver.parsing.LECParser

Parses an ELECT-generated XML file, yeilding a filled Configuration object.

printString() - Method in class edu.uconn.mcb.lineageevolver.Genome

Similar to toString(), but also details each gene recursively, all printing to System.out as oppose to returning a string.

processTree() - Method in class edu.uconn.mcb.lineageevolver.Lineage

Processes evolution and hgt according to the configured tree.