/// <summary>
/// Parses a list of biological sequence data from a file.
/// </summary>
/// <param name="filename">The name of a biological sequence file.</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 public IList <IQualitativeSequence> Parse(string filename, bool isReadOnly)
{
_fileName = filename;
//check DV is requried
if (filename != null)
{
_fileLoadHelper = new FileLoadHelper(filename);
_blockSize = _fileLoadHelper.BlockSize;
_maxNumberOfBlocks = _fileLoadHelper.MaxNumberOfBlocks;
if (_isDataVirtualizationForced)
{
_blockSize = FileLoadHelper.DefaultBlockSize;
}
}
else
{
_blockSize = FileLoadHelper.DefaultFullLoadBlockSize;
_maxNumberOfBlocks = 0;
}
SidecarFileProvider indexedProvider = null;
// Check for sidecar
if (IsDataVirtualizationEnabled)
{
try
{
indexedProvider = SidecarFileProvider.GetProvider(filename);
}
catch (OperationCanceledException)
{
indexedProvider = null;
}
}
if (indexedProvider != null)
{
// Create virtual list and return
return(new VirtualQualitativeSequenceList(indexedProvider, this, indexedProvider.Count)
{
CreateSequenceAsReadOnly = isReadOnly
});
}
else
{
using (BioTextReader bioReader = new BioTextReader(filename))
{
return(Parse(bioReader, isReadOnly));
}
}
}
