/// <summary>
/// Parses a range of sequence items starting from the specified index in the sequence.
/// </summary>
/// <param name="startIndex">The zero-based index at which to begin parsing.</param>
/// <param name="count">The number of symbols to parse.</param>
/// <param name="seqPointer">The sequence pointer of that sequence.</param>
/// <returns>The parsed sequence.</returns>
public ISequence ParseRange(int startIndex, int count, SequencePointer seqPointer)
{
if (string.IsNullOrEmpty(_fileName))
{
throw new NotSupportedException(Resource.DataVirtualizationNeedsInputFile);
}
if (startIndex < 0)
{
throw new ArgumentOutOfRangeException("startIndex");
}
if (count <= 0)
{
throw new ArgumentOutOfRangeException("count");
}
IAlphabet alphabet = Alphabets.All.Single(A => A.Name.Equals(seqPointer.AlphabetName));
Sequence sequence = new Sequence(alphabet)
{
IsReadOnly = false
};
int start = (int)seqPointer.StartingIndex + startIndex;
if (start >= seqPointer.EndingIndex)
{
return(null);
}
int includesNewline = seqPointer.StartingLine * Environment.NewLine.Length;
int len = (int)(seqPointer.EndingIndex - seqPointer.StartingIndex);
using (BioTextReader bioReader = new BioTextReader(_fileName))
{
string str = bioReader.ReadBlock(startIndex, seqPointer.StartingIndex + includesNewline, count, len);
sequence.InsertRange(0, str);
}
// default for partial load
sequence.IsReadOnly = true;
return(sequence);
}
/// <summary>
/// Parses a range of sequence items starting from the specified index in the sequence.
/// </summary>
/// <param name="startIndex">The zero-based index at which to begin parsing.</param>
/// <param name="count">The number of symbols to parse.</param>
/// <param name="seqPointer">The sequence pointer of that sequence.</param>
/// <returns>The parsed sequence.</returns>
public ISequence ParseRange(int startIndex, int count, SequencePointer seqPointer)
{
if (0 > startIndex)
{
throw new ArgumentOutOfRangeException("startIndex");
}
if (0 >= count)
{
throw new ArgumentOutOfRangeException("count");
}
IAlphabet alphabet = Alphabets.All.Single(A => A.Name.Equals(seqPointer.AlphabetName));
Sequence sequence = new Sequence(alphabet);
sequence.IsReadOnly = false;
int start = (int)seqPointer.StartingIndex + startIndex;
if (start >= seqPointer.EndingIndex)
{
return(null);
}
int includesNewline = seqPointer.StartingLine * Environment.NewLine.Length;
int len = (int)(seqPointer.EndingIndex - seqPointer.StartingIndex);
using (BioTextReader bioReader = new BioTextReader(_fileName))
{
string sequenceString = bioReader.ReadBlock(startIndex, seqPointer.StartingIndex + includesNewline, count, len);
sequence.InsertRange(0, sequenceString);
}
// default for partial load
sequence.IsReadOnly = true;
return(sequence);
}