/// <summary>
/// Parses a list of biological sequence data from a BioTextReader.
/// </summary>
/// <param name="bioReader">BioTextReader instance for a biological sequence data.</param>
/// <param name="isReadOnly">
/// Flag to indicate whether the resulting QualitativeSequences should be in readonly mode or not.
/// If this flag is set to true then the resulting QualitativeSequences's isReadOnly property
/// will be set to true, otherwise it will be set to false.
/// </param>
/// <returns>The list of parsed IQualitativeSequence objects.</returns>
new protected IList <IQualitativeSequence> Parse(BioTextReader bioReader, bool isReadOnly)
{
if (bioReader == null)
{
throw new ArgumentNullException("bioReader");
}
// no empty files allowed
if (!bioReader.HasLines)
{
string message = string.Format(CultureInfo.CurrentCulture, Resource.IOFormatErrorMessage, Name, Resource.IONoTextToParse);
Trace.Report(message);
throw new FileFormatException(message);
}
if (!string.IsNullOrEmpty(bioReader.FileName) &&
IsDataVirtualizationEnabled && SidecarFileProvider.IsIndexFileExists(bioReader.FileName))
{
while (bioReader.HasLines)
{
ParseOne(bioReader, isReadOnly);
}
// Create sidecar
SidecarFileProvider provider = SidecarFileProvider.CreateIndexFile(bioReader.FileName, _sequencePointers);
VirtualQualitativeSequenceList virtualSequences =
new VirtualQualitativeSequenceList(provider, this, _sequencePointers.Count)
{
CreateSequenceAsReadOnly = isReadOnly
};
_sequencePointers.Clear();
return(virtualSequences);
}
else
{
List <IQualitativeSequence> qualSequences = new List <IQualitativeSequence>();
while (bioReader.HasLines)
{
qualSequences.Add(ParseOne(bioReader, isReadOnly));
}
return(qualSequences);
}
}
/// <summary>
/// Parses a list of sequences using a BioTextReader.
/// </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="bioReader">bio text reader</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 IList <ISequence> Parse(BioTextReader bioReader, bool isReadOnly)
{
_lineCount = 0;
_sequenceCount = 0;
_lineLength = 0;
_sequenceBeginsAt = 1;
if (bioReader == null)
{
throw new ArgumentNullException("bioReader");
}
// no empty files allowed
if (!bioReader.HasLines)
{
string message = Resource.Parser_NoTextErrorMessage;
Trace.Report(message);
throw new InvalidOperationException(message);
}
// Check if DV is enabled and sidecar creation is possible
if (!string.IsNullOrEmpty(bioReader.FileName) && IsDataVirtualizationEnabled && SidecarFileProvider.IsIndexFileExists(bioReader.FileName))
{
while (bioReader.HasLines)
{
// Parse and forget as the list is now maintained by DV using sequence pointers
ParseOne(bioReader, isReadOnly);
}
// Create sidecar
SidecarFileProvider provider = SidecarFileProvider.CreateIndexFile(bioReader.FileName, _sequencePointers);
VirtualSequenceList virtualSequences =
new VirtualSequenceList(provider, this, _sequencePointers.Count)
{
CreateSequenceAsReadOnly = isReadOnly
};
_sequencePointers.Clear();
return(virtualSequences);
}
else
{
List <ISequence> sequences = new List <ISequence>();
while (bioReader.HasLines)
{
sequences.Add(ParseOne(bioReader, isReadOnly));
}
return(sequences);
}
}
