/// <summary>
/// Parses a single biological sequence text from a file.
/// </summary>
/// <param name="filename">The name of a biological sequence file.</param>
/// <param name="isReadOnly">
/// Flag to indicate whether the resulting sequence should be in readonly mode or not.
/// If this flag is set to true then the resulting sequence's isReadOnly property
/// will be set to true, otherwise it will be set to false.
/// </param>
/// <returns>The parsed ISequence object.</returns>
public ISequence ParseOne(string filename, bool isReadOnly)
{
using (MBFTextReader mbfReader = new MBFTextReader(filename))
{
return(ParseOne(mbfReader, isReadOnly));
}
}
/// <summary>
/// Parses a list of biological sequence texts from a reader.
/// </summary>
/// <param name="reader">A reader for a biological sequence text.</param>
/// <param name="isReadOnly">
/// Flag to indicate whether the resulting sequences should be in readonly mode or not.
/// If this flag is set to true then the resulting sequences's isReadOnly property
/// will be set to true, otherwise it will be set to false.
/// </param>
/// <returns>The list of parsed ISequence objects.</returns>
public IList <ISequence> Parse(TextReader reader, bool isReadOnly)
{
using (MBFTextReader mbfReader = new MBFTextReader(reader))
{
return(Parse(mbfReader, isReadOnly));
}
}
/// <summary>
/// Parses a list of biological sequence texts from a reader.
/// </summary>
/// <param name="reader">A reader for a biological sequence text.</param>
/// <param name="isReadOnly">
/// Flag to indicate whether the resulting sequences should be in readonly mode or not.
/// If this flag is set to true then the resulting sequences's isReadOnly property
/// will be set to true, otherwise it will be set to false.
/// </param>
/// <returns>The iterator of parsed ISequence objects.</returns>
public IEnumerable <ISequence> ParseStream(TextReader reader, bool isReadOnly)
{
using (MBFTextReader mbfReader = new MBFTextReader(reader))
{
return(ParseStream(mbfReader, isReadOnly));
}
}
/// <summary>
/// Parses a list of sequences using a MBFTextReader.
/// </summary>
/// <remarks>
/// This method should be overridden by any parsers that need to process file-scope
/// metadata that applies to all of the sequences in the file.
/// </remarks>
/// <param name="mbfReader">A reader for a biological sequence text.</param>
/// <param name="isReadOnly">
/// Flag to indicate whether the resulting sequences should be in readonly mode or not.
/// If this flag is set to true then the resulting sequences's isReadOnly property
/// will be set to true, otherwise it will be set to false.
/// </param>
/// <returns>The list of parsed ISequence objects.</returns>
protected virtual IList <ISequence> Parse(MBFTextReader mbfReader, bool isReadOnly)
{
if (mbfReader == null)
{
throw new ArgumentNullException("mbfReader");
}
List <ISequence> sequences = new List <ISequence>();
sequences.AddRange(ParseStream(mbfReader, isReadOnly));
return(sequences);
}
/// <summary>
/// Parses a list of sequences using a MBFTextReader.
/// </summary>
/// <remarks>
/// This method should be overridden by any parsers that need to process file-scope
/// metadata that applies to all of the sequences in the file.
/// </remarks>
/// <param name="mbfReader">A reader for a biological sequence text.</param>
/// <param name="isReadOnly">
/// Flag to indicate whether the resulting sequences should be in readonly mode or not.
/// If this flag is set to true then the resulting sequences's isReadOnly property
/// will be set to true, otherwise it will be set to false.
/// </param>
/// <returns>The iterator of parsed ISequence objects.</returns>
protected virtual IEnumerable <ISequence> ParseStream(MBFTextReader mbfReader, bool isReadOnly)
{
if (mbfReader == null)
{
throw new ArgumentNullException("mbfReader");
}
// no empty files allowed
if (!mbfReader.HasLines)
{
Trace.Report(Properties.Resource.IONoTextToParse);
throw new InvalidDataException(Properties.Resource.IONoTextToParse);
}
while (mbfReader.HasLines)
{
yield return(ParseOne(mbfReader, isReadOnly));
}
}
// Parses a single sequences using a MBFTextReader.
private ISequence ParseOne(MBFTextReader mbfReader, bool isReadOnly)
{
if (mbfReader == null)
{
throw new ArgumentNullException("mbfReader");
}
// no empty files allowed
if (!mbfReader.HasLines)
{
string message = Properties.Resource.IONoTextToParse;
Trace.Report(message);
throw new InvalidDataException(message);
}
_distinctSymbols = new List <char>();
// do the actual parsing
ISequence sequence = ParseOneWithSpecificFormat(mbfReader, isReadOnly);
_distinctSymbols = null;
return(sequence);
}
/// <summary> /// Parses a single biological sequence text from a reader into a sequence. /// </summary> /// <param name="mbfReader">A reader for a biological sequence text.</param> /// <param name="isReadOnly"> /// Flag to indicate whether the resulting sequence should be in readonly mode or not. /// If this flag is set to true then the resulting sequence's isReadOnly property /// will be set to true, otherwise it will be set to false. /// </param> /// <returns>Sequence instance.</returns> protected abstract ISequence ParseOneWithSpecificFormat(MBFTextReader mbfReader, bool isReadOnly);
