- * @param column
- * Index of the column, starting from 0.
- * @return
- */
- public static float getInformationContent(int column,
- HiddenMarkovModel hmm)
- {
- float informationContent = 0f;
-
- for (char symbol : hmm.getSymbols())
- {
- float freq = 0f;
- freq = ResidueProperties.backgroundFrequencies
- .get(hmm.getAlphabetType()).get(symbol);
- Double hmmProb = hmm.getMatchEmissionProbability(column, symbol);
- float prob = hmmProb.floatValue();
- informationContent += prob * (Math.log(prob / freq) / Math.log(2));
-
- }
-
- return informationContent;
- }
-
- /**
- * Produces a HMM profile for a column in an alignment
+ * <pre>
+ * [profileType=0, numberOfValues, 100, charValue1, percentage1, charValue2, percentage2, ...]
+ * in descending order of percentage value
+ * </pre>