/// <summary>
/// Go to the next line in the text reader, unless it is the first line in which case,
/// it has already been called in the constructor and we do not move
/// the TextReader.
/// </summary>
/// <returns>True if we have a valid SnpItem in the next line moved to</returns>
public bool MoveNext()
{
if (!isFirstLine)
{
GoToNextLine();
}
else
{
// skip...we've already read the first line
isFirstLine = false;
}
// parse the next SNP...if next line not present, set currentSnpitem to null and return false
if (!HasLines)
{
currentSnpItem = null;
return(false);
}
try
{
// we have a current Snp
currentSnpItem = MakeSnpForCurrentLine();
}
catch (Exception ex)
{
throw new FormatException(Properties.Resource.Parser_InvalidFileFormat, ex);
}
return(true);
}
/// <summary>
/// Go to the next line in the text reader, unless it is the first line in which case,
/// it has already been called by MBFTextReader in the constructor and we do not move
/// the TextReader.
/// </summary>
/// <returns>True if we have a valid SnpItem in the next line moved to</returns>
public bool MoveNext()
{
if (!isFirstLine)
{
GoToNextLine();
}
else
{
// skip...we've already read the first line
isFirstLine = false;
}
// parse the next SNP...if next line not present, set currentSnpitem to null and return false
if (!HasLines)
{
currentSnpItem = null;
return(false);
}
try
{
// we have a current Snp
currentSnpItem = MakeSnpForCurrentLine();
}
catch (Exception ex)
{
throw new Exception("Error parsing line: " + Line, ex);
}
return(true);
}
public void SnpItemBvtValidateGetHashCode()
{
SnpItem snpItem1 = new SnpItem();
snpItem1.AlleleOne = 'A';
snpItem1.AlleleTwo = 'G';
Assert.AreEqual(0, snpItem1.GetHashCode());
ApplicationLog.WriteLine("Snp Bvt : Successfully validated GetHashCode().");
}
public void SnpItemValidateEqualsObject()
{
SnpItem snpItem1 = new SnpItem();
snpItem1.AlleleOne = 'A';
snpItem1.AlleleTwo = 'G';
SnpItem snpItem2 = new SnpItem();
snpItem2.AlleleOne = 'A';
snpItem2.AlleleTwo = 'G';
Assert.IsTrue(snpItem2.Equals((object)snpItem1));
}
/// <summary>
/// Makes a SNP item for the current line in the XSV reader.
/// Since the XSV reader reads ahead, this is actually the next
/// SNP item for the enumerator.
/// </summary>
/// <returns>Creates a SnpItem for the current line in the XsvReader</returns>
private SnpItem MakeSnpForCurrentLine()
{
SnpItem snpItem = new SnpItem();
snpItem.Chromosome = (byte)ushort.Parse(GetFieldValue(FieldNames.Chromosome));
snpItem.Position = int.Parse(GetFieldValue(FieldNames.Position));
string allele = GetFieldValue(FieldNames.AlleleOne);
snpItem.AlleleOne = (!string.IsNullOrEmpty(allele)) ? allele[0] : char.MinValue;
allele = GetFieldValue(FieldNames.AlleleTwo);
snpItem.AlleleTwo = (!string.IsNullOrEmpty(allele)) ? allele[0] : char.MinValue;
return(snpItem);
}
public void SnpItemValidateEqualsObject()
{
SnpItem snpItem1 = new SnpItem();
snpItem1.AlleleOne = 'A';
snpItem1.AlleleTwo = 'G';
SnpItem snpItem2 = new SnpItem();
snpItem2.AlleleOne = 'A';
snpItem2.AlleleTwo = 'G';
Assert.IsTrue(snpItem2.Equals((object)snpItem1));
}
public void SnpItemBvtValidateEqualsObject()
{
SnpItem snpItem1 = new SnpItem();
snpItem1.AlleleOne = 'A';
snpItem1.AlleleTwo = 'G';
SnpItem snpItem2 = new SnpItem();
snpItem2.AlleleOne = 'A';
snpItem2.AlleleTwo = 'G';
Assert.IsTrue(snpItem2.Equals((object)snpItem1));
ApplicationLog.WriteLine("Snp Bvt : Successfully validated Equals(object).");
}
/// <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>
/// 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
}
public void SnpItemBvtValidateGetHashCode()
{
SnpItem snpItem1 = new SnpItem();
snpItem1.AlleleOne = 'A';
snpItem1.AlleleTwo = 'G';
Assert.AreEqual(0, snpItem1.GetHashCode());
ApplicationLog.WriteLine("Snp Bvt : Successfully validated GetHashCode().");
}
public void SnpItemBvtValidateEqualsObject()
{
SnpItem snpItem1 = new SnpItem();
snpItem1.AlleleOne = 'A';
snpItem1.AlleleTwo = 'G';
SnpItem snpItem2 = new SnpItem();
snpItem2.AlleleOne = 'A';
snpItem2.AlleleTwo = 'G';
Assert.IsTrue(snpItem2.Equals((object)snpItem1));
ApplicationLog.WriteLine("Snp Bvt : Successfully validated Equals(object).");
}
