- public static ProfilesI calculateInformation(final HiddenMarkovModel hmm,
- int width, int start, int end, boolean saveFullProfile,
- boolean removeBelowBackground)
+ /**
+ * Returns the full set of profiles for a hidden Markov model. The underlying
+ * data is the raw probabilities of a residue being emitted at each node,
+ * however the profiles returned by this function contain the percentage
+ * chance of a residue emission.
+ *
+ * @param hmm
+ * @param width
+ * The width of the Profile array (Profiles) to be returned.
+ * @param start
+ * The alignment column on which the first profile is based.
+ * @param end
+ * The alignment column on which the last profile is based.
+ * @param removeBelowBackground
+ * if true, symbols with a match emission probability less than
+ * background frequency are ignored
+ * @return
+ */
+ public static ProfilesI calculateHMMProfiles(final HiddenMarkovModel hmm,
+ int width, int start, int end, boolean removeBelowBackground,
+ boolean infoLetterHeight)