/// <summary>
/// Returns a sparse sequence composed of one of the two alleles for the current
/// chromosome pointed to by the SnpReader. If ParseAlleleOne is set to true (default),
/// this parses AlleleOne, else AlleleTwo.
///
/// The Sequence Items correspond to AlleleOne or Two in the reader and their position
/// in the sparse sequence corresponds to their Position in the SnpItem.
///
/// This starts parsing from the current line and continues until EOF or the chromosome
/// number changes.
///
/// </summary>
/// <param name="reader"></param>
/// <param name="isReadOnly">
/// Flag to indicate whether the resulting sequence should be in readonly mode or not.
/// If this flag is set to true then the resulting sequence's isReadOnly property
/// will be set to true, otherwise it will be set to false.
/// </param>
/// <returns>Returns a SparseSequence containing Snp items from the first contiguous
/// chromosome number read from the reader, retaining the same position in the sparse sequence
/// as the chromosome position.</returns>
public ISequence ParseOne(TextReader reader, bool isReadOnly)
{
ISnpReader snpReader = GetSnpReader(reader);
snpReader.MoveNext();
return(ParseOne(snpReader, isReadOnly));
}
/// <summary>
/// Returns a sparse sequence composed of one of the two alleles for the current
/// chromosome pointed to by the SnpReader. If ParseAlleleOne is set to true (default),
/// this parses AlleleOne, else AlleleTwo.
///
/// The Sequence Items correspond to AlleleOne or Two in the reader and their position
/// in the sparse sequence corresponds to their Position in the SnpItem.
///
/// This starts parsing from the current line and continues until EOF or the chromosome
/// number changes.
///
/// </summary>
/// <param name="reader"></param>
/// <param name="isReadOnly">
/// Flag to indicate whether the resulting sequence should be in readonly mode or not.
/// If this flag is set to true then the resulting sequence's isReadOnly property
/// will be set to true, otherwise it will be set to false.
/// </param>
/// <returns>Returns a SparseSequence containing Snp items from the first contiguous
/// chromosome number read from the reader, retaining the same position in the sparse sequence
/// as the chromosome position.</returns>
public ISequence ParseOne(TextReader reader, bool isReadOnly)
{
// Check input arguments
if (reader == null)
{
throw new ArgumentNullException("reader", "Text reader to read SNP sequence from cannot be null");
}
ISnpReader snpReader = GetSnpReader(reader);
snpReader.MoveNext();
return(ParseOne(snpReader, isReadOnly));
}
/// <summary>
/// Parses a list of sparse sequences from the reader, one per contiguous
/// chromosome present in the reader. There is one SequenceItem per SnpItem with
/// either of the two alleles in the SnpItem (determined by the ParseAlleleOne property)
/// and at the same position in the sequence as the SnpItem.Position.
/// </summary>
/// <param name="reader">Text reader to read the Snpitems from using a SnpReader created for it</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>Returns a list of sparse sequences containing Snp items that were read
/// from the reader, one sequence per contiguous chromosome number and
/// retaining the same position in the sequence as the chromosome position.</returns>
public IList <ISequence> Parse(TextReader reader, bool isReadOnly)
{
ISnpReader snpReader = GetSnpReader(reader);
snpReader.MoveNext();
List <ISequence> sequenceList = new List <ISequence>();
while (snpReader.Current != null)
{
sequenceList.Add(ParseOne(snpReader, isReadOnly));
}
return(sequenceList);
}
/// <summary>
/// The common ParseOne method called for parsing SNPs
/// NOTE: The snpReader.MoveNext must have already been called and
/// the ISnpReader.Current have the first SnpItem to parse into the sequence
/// </summary>
/// <param name="snpReader">The ISnpReader to read a Snp chromosome sequence from</param>
/// <param name="isReadOnly">
/// Flag to indicate whether the resulting sequence should be in readonly mode or not.
/// If this flag is set to true then the resulting sequence's isReadOnly property
/// will be set to true, otherwise it will be set to false.
/// </param>
/// <returns>Returns a SparseSequence containing Snp items from the first contiguous
/// chromosome number read from the snp reader.</returns>
protected ISequence ParseOne(ISnpReader snpReader, bool isReadOnly)
{
// Check input arguments
if (snpReader == null)
{
throw new ArgumentNullException("snpReader", "SNP Reader to read SNP sequences from cannot be null");
}
if (snpReader.Current == null)
{
return new SparseSequence(Alphabet)
{
ID = "Empty"
}
}
;
int sequenceChromosome = snpReader.Current.Chromosome;
SparseSequence sequence = new SparseSequence(Alphabet);
sequence.ID = ("Chr" + sequenceChromosome);
do
{
SnpItem snp = snpReader.Current;
// increase the size of the sparse sequence
if (sequence.Count <= snp.Position)
{
sequence.Count = snp.Position + 1;
}
sequence[snp.Position] = ParseAlleleOne
? Alphabet.LookupBySymbol(snp.AlleleOne)
: Alphabet.LookupBySymbol(snp.AlleleTwo);
} while (snpReader.MoveNext() && snpReader.Current.Chromosome == sequenceChromosome);
sequence.IsReadOnly = isReadOnly;
return(sequence);
}
#endregion Protected Methods of SnpParser
}
/// <summary>
/// Parses a list of sparse sequences from the reader, one per contiguous
/// chromosome present in the reader. There is one SequenceItem per SnpItem with
/// either of the two alleles in the SnpItem (determined by the ParseAlleleOne property)
/// and at the same position in the sequence as the SnpItem.Position.
/// </summary>
/// <param name="reader">Text reader to read the Snpitems from using a SnpReader created for it</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>Returns a list of sparse sequences containing Snp items that were read
/// from the reader, one sequence per contiguous chromosome number and
/// retaining the same position in the sequence as the chromosome position.</returns>
public IList <ISequence> Parse(TextReader reader, bool isReadOnly)
{
// Check input arguments
if (reader == null)
{
throw new ArgumentNullException("reader", "Text reader to read SNP sequences from cannot be null");
}
ISnpReader snpReader = GetSnpReader(reader);
snpReader.MoveNext();
List <ISequence> sequenceList = new List <ISequence>();
while (snpReader.Current != null)
{
sequenceList.Add(ParseOne(snpReader, isReadOnly));
}
return(sequenceList);
}
/// <summary>
/// The common ParseOne method called for parsing SNPs
/// NOTE: The snpReader.MoveNext must have already been called and
/// the ISnpReader.Current have the first SnpItem to parse into the sequence
/// </summary>
/// <param name="snpReader">The ISnpReader to read a Snp chromosome sequence from</param>
/// <returns>Returns a SparseSequence containing Snp items from the first contiguous
/// chromosome number read from the snp reader.</returns>
protected ISequence ParseOne(ISnpReader snpReader)
{
// Check input arguments
if (snpReader == null)
{
throw new ArgumentNullException("snpReader", Properties.Resource.snpTextReaderNull);
}
if (snpReader.Current == null)
{
return new SparseSequence(Alphabet)
{
ID = "Empty"
}
}
;
int sequenceChromosome = snpReader.Current.Chromosome;
SparseSequence sequence = new SparseSequence(Alphabet);
sequence.ID = ("Chr" + sequenceChromosome);
do
{
SnpItem snp = snpReader.Current;
// increase the size of the sparse sequence
if (sequence.Count <= snp.Position)
{
sequence.Count = snp.Position + 1;
}
sequence[snp.Position] = ParseAlleleOne
? (byte)snp.AlleleOne
: (byte)snp.AlleleTwo;
} while (snpReader.MoveNext() && snpReader.Current.Chromosome == sequenceChromosome);
return(sequence);
}
#endregion Protected Methods of SnpParser
}
/// <summary>
/// The common ParseOne method called for parsing SNPs
/// NOTE: The snpReader.MoveNext must have already been called and
/// the ISnpReader.Current have the first SnpItem to parse into the sequence
/// </summary>
/// <param name="snpReader">The ISnpReader to read a Snp chromosome sequence from</param>
/// <returns>Returns a SparseSequence containing Snp items from the first contiguous
/// chromosome number read from the snp reader.</returns>
protected ISequence ParseOne(ISnpReader snpReader)
{
// Check input arguments
if (snpReader == null)
{
throw new ArgumentNullException("snpReader",Properties.Resource.snpTextReaderNull);
}
if (snpReader.Current == null)
return new SparseSequence(Alphabet)
{
ID = "Empty"
};
int sequenceChromosome = snpReader.Current.Chromosome;
SparseSequence sequence = new SparseSequence(Alphabet) { ID = "Chr" + sequenceChromosome };
do
{
SnpItem snp = snpReader.Current;
// increase the size of the sparse sequence
if (sequence.Count <= snp.Position)
sequence.Count = snp.Position + 1;
sequence[snp.Position] = ParseAlleleOne
? (byte)snp.AlleleOne
: (byte)snp.AlleleTwo;
} while (snpReader.MoveNext() && snpReader.Current.Chromosome == sequenceChromosome);
return sequence;
}
