includeAdditionalCharacters
public static Scores includeAdditionalCharacters(Scores scores,
java.lang.String characters)
includes additional characters in the score matrix which will all have scored zero when compared to other
characters.
Current system does not handle special characters well, such as ? Or "R" for NucleotideSequences,
which represents a "A" or "G".
Currently, we just add all characters to the allowed set of characters, and they are scored as
zero cost when comparing to other characters, including themselves. One-day, we should probably
introduce better scoring system so that "R" is a positive score compared to "A" or "G",
but a negative score compared to "C" or "T".
example usage:
scores = Scores.includeAdditionalCharacters(scores, "?ABCDEFGHIJKLMNOPQRSTUVWXYZ");
- Parameters:
scores
- characters
-
- Returns:
- a new score matrix.