// Copyright 2018 Google LLC.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions
// are met:
//
// 1. Redistributions of source code must retain the above copyright notice,
//    this list of conditions and the following disclaimer.
//
// 2. Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//
// 3. Neither the name of the copyright holder nor the names of its
//    contributors may be used to endorse or promote products derived from this
//    software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
syntax = "proto3";

import "third_party/nucleus/protos/range.proto";
import "third_party/nucleus/protos/reference.proto";

package nucleus.genomics.v1;

// This message represents a single FASTA record. This can be any FASTA file,
// representing DNA, RNA, protein, or other sequence.
message FastaRecord {
  // If the FastaReaderOptions.parse_header field is false, this field is
  // populated with the raw text of the description line, stripping the leading
  // '>' and any trailing whitespace and the newline. Otherwise this field is
  // empty.
  string defline = 1;

  // If the FastaReaderOptions.parse_header field is true, this message is
  // populated based on the contents of the description and sequence lines.
  // Otherwise this field is empty.
  // NOTE: the "contig" info provided here is solely based on the record itself,
  // and provides a mechanism to separate the sequence name from its description
  // and includes the number of basepairs in the sequence.
  ContigInfo contig = 2;

  // Iff the FastaReaderOptions.include_range field is true, this message is
  // populated with the location of the sequence within the contig.
  // `region.end - region.start` should thus equal the length of the sequence.
  // This could differ from the range [0, len(sequence)) in the case of a
  // query operation for a particular region of a FASTA sequence.
  Range region = 3;

  // The raw sequence letters. Depending on the
  // `FastaReaderOptions.keep_true_case` field, these may be uppercased or
  // keeping the original true case.
  string sequence = 4;
}

message FastaReaderOptions {
  // If false, casts all bases to uppercase before returning them.
  bool keep_true_case = 1;

  // If set, all sequences are verified to contain only characters present in
  // the input alphabet defined here.
  string alphabet = 2;

  enum DeflineParsing {
    // No parsing is performed, and the `defline` field holds the raw string of
    // the line.
    NONE = 0;

    // Parses the description line of each record into a ContigInfo object in
    // the `contig` field.
    CONTIG_INFO = 1;
  }
  DeflineParsing defline_parsing = 3;

  // If true, the `region` field is populated in each FastaRecord.
  bool include_range_in_records = 4;
}

// Options for writing FASTA files.
// Currently this is a placeholder message but could be used to support
// different choices on output like the number of columns per line.
message FastaWriterOptions {
}