Class IntervalTreeIndex

    • Field Detail

      • INDEX_TYPE

        public static final int INDEX_TYPE
    • Constructor Detail

      • IntervalTreeIndex

        public IntervalTreeIndex​(InputStream inputStream)
                          throws IOException
        Load from file.
        Parameters:
        inputStream - This method assumes that the input stream is already buffered as appropriate. Caller should close after this object is constructed.
        Throws:
        IOException
      • IntervalTreeIndex

        public IntervalTreeIndex​(Path featureFile)
        Prepare to build an index.
        Parameters:
        featureFile - File which we are indexing
      • IntervalTreeIndex

        public IntervalTreeIndex​(String featureFile)
        Prepare to build an index.
        Parameters:
        featureFile - File which we are indexing
    • Method Detail

      • getChrIndexClass

        public Class getChrIndexClass()
        Description copied from class: AbstractIndex
        returns the class for the index type
        Specified by:
        getChrIndexClass in class AbstractIndex
        Returns:
        a Class, from which a new instance can be created
      • getType

        protected int getType()
        Description copied from class: AbstractIndex
        get the index type
        Specified by:
        getType in class AbstractIndex
        Returns:
        The index type
      • insert

        public void insert​(String chr,
                           Interval interval)
        Add a new interval to this index
        Parameters:
        chr - Chromosome
        interval -
      • printTree

        public void printTree()