Class SequenceDatabaseRule


  • public class SequenceDatabaseRule
    extends java.lang.Object
    Implementation of a sequence database, where each sequence is implemented as a list of integers and should have a unique id.
    Author:
    Philipe-Fournier-Viger
    See Also:
    Sequence
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addSequence​(Sequence sequence)
      Method to add a sequence to this sequence database
      java.util.Set<java.lang.Integer> getSequenceIDs()
      Get the list of sequence IDs for this database.
      java.util.List<Sequence> getSequences()
      Get the sequences from this sequence database.
      void loadFile​(java.lang.String path)
      Method to load a sequence database from a text file in SPMF format.
      void print()
      Print this sequence database to System.out.
      void printDatabaseStats()
      Print statistics about this database.
      int size()
      Get the sequence count in this database.
      java.lang.String toString()
      Return a string representation of this sequence database.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
    • Constructor Detail

      • SequenceDatabaseRule

        public SequenceDatabaseRule()
    • Method Detail

      • loadFile

        public void loadFile​(java.lang.String path)
                      throws java.io.IOException
        Method to load a sequence database from a text file in SPMF format.
        Parameters:
        path - the input file path.
        Throws:
        java.io.IOException - exception if error while reading the file.
      • addSequence

        public void addSequence​(Sequence sequence)
        Method to add a sequence to this sequence database
        Parameters:
        sequence - A sequence of type "Sequence".
      • print

        public void print()
        Print this sequence database to System.out.
      • printDatabaseStats

        public void printDatabaseStats()
        Print statistics about this database.
      • toString

        public java.lang.String toString()
        Return a string representation of this sequence database.
        Overrides:
        toString in class java.lang.Object
      • size

        public int size()
        Get the sequence count in this database.
        Returns:
        the sequence count.
      • getSequences

        public java.util.List<Sequence> getSequences()
        Get the sequences from this sequence database.
        Returns:
        A list of sequences (Sequence).
      • getSequenceIDs

        public java.util.Set<java.lang.Integer> getSequenceIDs()
        Get the list of sequence IDs for this database.
        Returns:
        A set containing the sequence IDs of sequence in this database.