#
# Licensed to Big Data Genomics (BDG) under one
# or more contributor license agreements.  See the NOTICE file
# distributed with this work for additional information
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License.  You may obtain a copy of the License at
#
#
# Unless required by applicable law or agreed to in writing, software
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
#
r"""
======
models
======
.. autosummary::
:toctree: _generate/

ReferenceRegion
"""

[docs]class ReferenceRegion:
"""
Represents a contiguous region of the reference genome.
"""

[docs]    def __init__(self, referenceName, start, end):
"""
Represents a contiguous region of the reference genome.

:param referenceName The name of the sequence (chromosome) in the reference genome
:param start The 0-based residue-coordinate for the start of the region
:param end The 0-based residue-coordinate for the first residue <i>after</i> the start
which is <i>not</i> in the region -- i.e. [start, end) define a 0-based
half-open interval.
"""

self.referenceName = referenceName
self.start = start
self.end = end

def _toJava(self, jvm):
"""