- private static final double LOG2 = Math.log(2);
-
- // Stores file properties. Do not directly access this field as it contains
- // only string value - use the getter methods. For example, to find the length
- // of theHMM, use getModelLength()to return an int value
- Map<String, String> fileProperties = new HashMap<>();
-
- // contains all of the symbols used in this model. The index of each symbol
- // represents its lookup value
- List<Character> symbols = new ArrayList<>();
-
- // contains information for each node in the model. The begin node is at index
- // 0. Node 0 contains average emission probabilities for each symbol
- List<HMMNode> nodes = new ArrayList<>();
-
- // contains the HMM node for each alignment column, alignment columns start at
- // index 0;
- Map<Integer, HMMNode> nodeLookup = new HashMap<>();
-
- // contains the symbol index for each symbol
- Map<Character, Integer> symbolIndexLookup = new HashMap<>();
-
- final static String YES = "yes";
-
- final static String NO = "no";
-
- // keys for file properties hashmap
- private static final String NAME = "NAME";
-
- private static final String ACCESSION_NUMBER = "ACC";
-
- private static final String DESCRIPTION = "DESC";
-
- private static final String LENGTH = "LENG";