// Copyright (c) 2014 - 2019, The Trustees of Indiana University.
//
// Licensed 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
//
//    http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.

#ifndef TOPPIC_SEQ_FASTA_SUB_SEQ_HPP_
#define TOPPIC_SEQ_FASTA_SUB_SEQ_HPP_

#include "seq/fasta_seq.hpp"

namespace toppic {

class FastaSubSeq : public FastaSeq {
 public:
  FastaSubSeq(FastaSeqPtr seq_ptr, int sub_seq_start, int sub_seq_len);

  int getSubSeqStart() {return sub_seq_start_;}

  int getSubSeqEnd() {return sub_seq_end_;}

  bool isNTerm() {return sub_seq_start_ == 0;}

  int getLen() {return length_;}

 private:
  int sub_seq_start_;

  int sub_seq_end_;

  int length_;
};

typedef std::shared_ptr<FastaSubSeq> FastaSubSeqPtr;
typedef std::vector<FastaSubSeqPtr> FastaSubSeqPtrVec;

}  // namespace toppic

#endif
