internal FastASequence(FastAFile owner, bool loadAllIntoMemory, string header, long startPos, int length,
int firstNonGap, int count, IBioValidator validator)
{
Debug.Assert(header.Length > 0);
string[] bits = header.Split(new[] { "::" }, StringSplitOptions.None);
if (bits.Length == 3)
{
ScientificName = /*bits[0] +":" +*/ bits[1];
CommonName = bits[2];
}
else
{
ScientificName = header;
}
Validator = validator;
FirstDataColumn = firstNonGap;
if (string.IsNullOrEmpty(CommonName))
{
CommonName = "<Not Available>";
}
if (string.IsNullOrEmpty(ScientificName))
{
ScientificName = CommonName;
}
_dp = new FastAFileSequenceDataProvider(owner, startPos, length, count, validator);
if (loadAllIntoMemory)
{
_alignedList = new List <IBioSymbol>(_dp.LoadRange(0, length));
_dp.Dispose();
_dp = null;
}
else
{
_alignedList = new VirtualizingList <IBioSymbol>(_dp, Math.Min(1024, length), 60);
}
}
public FastAFileSequenceDataProvider(FastAFile owner, long startPos, int length, int count, IBioValidator bv)
{
_fs = owner.MmFile.CreateViewStream(startPos, length, MemoryMappedFileAccess.Read);
_count = count;
_validator = bv;
}
