/// <summary>
/// Initializes a new instance of the VirtualQualitativeSequenceList class with a specified provider,
/// a specified parser, and a specifed sequence count.
/// </summary>
/// <param name="provider">SequencePointer provider from sidecar file.</param>
/// <param name="parser">Parser used to parse sequence data on request.</param>
/// <param name="count">Number of items in the actual file.</param>
public VirtualQualitativeSequenceList(SidecarFileProvider provider, IVirtualSequenceParser parser, int count)
{
_sequenceParser = parser;
_sidecarProvider = provider;
_count = count;
_sequenceDictionary = new Dictionary <int, WeakReference>(_count);
}
/// <summary>
/// Initializes a new instance of MBF.IO.FileVirtualSequenceProvider
/// class to hold a sequence parser, a sidecar file provider and
/// the index of the sequence.
/// </summary>
/// <param name="parser">A virtual parser object.</param>
/// <param name="pointer">The sequence pointer.</param>
/// <param name="sidecarFileProvider">A sidecar file provider.</param>
/// <param name="index">The zero-based index of the sequence within the file.</param>
public FileVirtualSequenceProvider(IVirtualSequenceParser parser, SequencePointer pointer, SidecarFileProvider sidecarFileProvider, int index)
: this(parser, pointer)
{
if (sidecarFileProvider == null)
{
throw new ArgumentNullException("sidecarFileProvider");
}
_sidecarProvider = sidecarFileProvider;
_sequenceIndex = index;
}
/// <summary>
/// Initializes a new instance of the MBF.IO.FileVirtualQualitativeSequenceProvider
/// class to hold a sequence pointer with a parser.
/// </summary>
/// <param name="parser">A virtual parser object.</param>
/// <param name="pointer">The sequence pointer.</param>
public FileVirtualQualitativeSequenceProvider(IVirtualSequenceParser parser, SequencePointer pointer)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
if (pointer == null)
{
throw new ArgumentNullException("pointer");
}
_parser = parser;
_count = (int)(pointer.IndexOffsets[1] - pointer.IndexOffsets[0]);
SequencePointerInstance = pointer;
//set the default DV properties.
_virtualData = new VirtualData <Sequence>
{
BlockSize = FileLoadHelper.DefaultBlockSize,
MaxNumberOfBlocks = FileLoadHelper.DefaultMaxNumberOfBlocks
};
}
/// <summary>
/// Initializes a new instance of the MBF.IO.FileVirtualSequenceProvider
/// class to hold a sequence pointer with a parser.
/// </summary>
/// <param name="parser">A virtual parser object.</param>
/// <param name="pointer">The sequence pointer.</param>
public FileVirtualSequenceProvider(IVirtualSequenceParser parser, SequencePointer pointer)
{
if (parser == null)
{
throw new ArgumentNullException("parser");
}
if (pointer == null)
{
throw new ArgumentNullException("pointer");
}
_parser = parser;
_count = (int)(pointer.IndexOffsets[1] - pointer.IndexOffsets[0]);
SequencePointerInstance = pointer;
_alphabet = Alphabets.All.FirstOrDefault(A => A.Name.Equals(pointer.AlphabetName));
//set the default DV properties.
_virtualData = new VirtualData <byte[]>
{
BlockSize = FileLoadHelper.DefaultBlockSize,
MaxNumberOfBlocks = FileLoadHelper.DefaultMaxNumberOfBlocks
};
}
