- // 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<>();
-
- final String YES = "yes";
-
- final String NO = "no";
-
- int numberOfSymbols;
-
- //keys for file properties hashmap
- private final String NAME = "NAME";
-
- private final String ACCESSION_NUMBER = "ACC";
-
- private final String DESCRIPTION = "DESC";
-
- private final String LENGTH = "LENG";
-
- private final String MAX_LENGTH = "MAXL";
-
- private final String ALPHABET = "ALPH";
-
- private final String DATE = "DATE";
-
- private final String COMMAND_LOG = "COM";
-
- private final String NUMBER_OF_SEQUENCES = "NSEQ";
-
- private final String EFF_NUMBER_OF_SEQUENCES = "EFFN";
-
- private final String CHECK_SUM = "CKSUM";
-
- private final String GATHERING_THRESHOLDS = "GA";
-
- private final String TRUSTED_CUTOFFS = "TC";
-
- private final String NOISE_CUTOFFS = "NC";