/// <summary>
/// Parses the provided FASTA sequence data for a single sequence.
/// </summary>
/// <param name="data">The string to parse.</param>
/// <returns>
/// A new <see cref="IActualSequence"/> object parsed from the provided
/// data string. Depending on the data passed in, this could either be
/// an <see cref="AminoAcidSequence"/> object or a
/// <see cref="NucleicAcidSequence"/> object. If the sequence is
/// ambiguous, the latter type is assumed and returned.
/// </returns>
/// <exception cref="ArgumentNullException">
/// <paramref name="data"/> is <see langword="null"/>.
/// </exception>
/// <exception cref="FormatException">
/// <paramref name="data"/> is empty or all whitespace.
/// -or-
/// <paramref name="data"/> is in an incorrect format.
/// </exception>
public static IActualSequence Parse(string data)
{
if (data == null)
{
throw new ArgumentNullException(nameof(data), "The sequence data to parse cannot be null.");
}
if (string.IsNullOrWhiteSpace(data))
{
throw new FormatException("The sequence data to parse cannot be empty or all whitespace.");
}
if (NucleicAcidSequence.TryParse(data, out NucleicAcidSequence nucleicAcidSequenceData))
{
return(nucleicAcidSequenceData);
}
else if (AminoAcidSequence.TryParse(data, out AminoAcidSequence aminoAcidSequenceData))
{
return(aminoAcidSequenceData);
}
else
{
throw new FormatException("The provided string is not a valid FASTA amino or nucleic acid sequence.");
}
}
/// <summary>
/// Converts a string representation of a FASTA file nucelic acid
/// sequence to its <see cref="AminoAcidSequence"/> equivalent.
/// A return value indicates whether the conversion succeeded.
/// </summary>
/// <param name="s">A string containing the sequence to convert.</param>
/// <param name="result">
/// When this method returns, contains the
/// <see cref="AminoAcidSequence"/> value equivalent of the
/// sequence contained in <paramref name="s"/>, if the conversion
/// succeeded, or an empty sequence if the conversion failed. The
/// conversion fails if the <paramref name="s"/> parameter is
/// <see langword="null"/>, empty, all whitespace, or is not of the
/// correct format. This parameter is passed uninitialized; any value
/// originally supplied in result will be overwritten.
/// </param>
/// <returns>
/// <see langword="true"/> if <paramref name="s"/> was converted
/// successfully; otherwise, <see langword="false"/>.
/// </returns>
/// <seealso cref="Parse(string)"/>
public static bool TryParse(string s, out AminoAcidSequence result)
{
if (s == null)
{
result = default;
return(false);
}
string cleanedUpCharacters = s.RemoveAllWhitespace();
if (!IsValidSequence(cleanedUpCharacters))
{
result = default;
return(false);
}
result = new AminoAcidSequence(cleanedUpCharacters.ToUpperInvariant());
return(true);
}
