public static SNPInfo Read(BinaryReader reader)
{
var result = new SNPInfo();
result.id = reader.ReadString();
result.descriptionWikiText = reader.ReadString();
result.gene = reader.ReadString();
result.chromosome = reader.ReadString();
result.position = reader.ReadInt32();
result.orientation = (Orientation)reader.ReadByte();
result.updateTime = DateTime.FromBinary(reader.ReadInt64());
result.genotypes = new SNPGenotypeInfo[reader.ReadInt32()];
for (int genotypeIndex = 0; genotypeIndex < result.genotypes.Length; genotypeIndex++)
{
var genotypeInfo = new SNPGenotypeInfo();
genotypeInfo.genotype = DiploidGenotype.Read(reader);
genotypeInfo.trait = reader.ReadString();
genotypeInfo.populationFrequencies = new Dictionary <string, float>();
int numPopulations = reader.ReadInt32();
for (int populationIndex = 0; populationIndex < numPopulations; populationIndex++)
{
var populationTag = reader.ReadString();
var populationFrequency = reader.ReadSingle();
genotypeInfo.populationFrequencies.Add(populationTag, populationFrequency);
}
result.genotypes[genotypeIndex] = genotypeInfo;
}
return(result);
}
public static DiploidGenotype Read(BinaryReader reader)
{
var result = new DiploidGenotype();
result.a = (Genotype)reader.ReadByte();
result.b = (Genotype)reader.ReadByte();
return(result);
}
public static SNPGenotype Read(BinaryReader reader)
{
var result = new SNPGenotype();
result.orientation = (Orientation)reader.ReadByte();
result.genotype = DiploidGenotype.Read(reader);
return(result);
}
public static SNPGenotype ReadLegacy(BinaryReader reader)
{
var result = new SNPGenotype();
var legacyGenotype = DiploidGenotype.Read(reader);
var legacyOrientation = reader.ReadByte();
result.orientation = Orientation.Plus;
result.genotype = DiploidGenotype.Read(reader);
return(result);
}
/** Determines the orientation of the genotypes of a SNP. */
public Orientation GetOrientation(SNPInfo snpInfo)
{
// Check whether any of the SNP's genotypes and their complements don't match the valid alleles for this orientation.
var matches = new bool[2] {
true, true
};
foreach (var genotypeInfo in snpInfo.genotypes)
{
// Determine whether this genotype or its complement matches the valid alleles for this orientation.
var orientedGenotypes = new DiploidGenotype[]
{
genotypeInfo.genotype,
genotypeInfo.genotype.GetComplement()
};
for (int tryIndex = 0; tryIndex < orientedGenotypes.Length; tryIndex++)
{
if (!DoesGenotypeMatch(orientedGenotypes[tryIndex].a) ||
!DoesGenotypeMatch(orientedGenotypes[tryIndex].b))
{
matches[tryIndex] = false;
}
}
}
if (matches[0] && !matches[1])
{
// If the SNP's genotypes all match this orientation's valid alleles, they have the same orientation.
return(orientation);
}
else if (matches[1] && !matches[0])
{
// If the SNP's genotypes' complements all match this orientation's valid alleles, the SNP's genotypes have the opposite orientation.
return(GetOppositeOrientation());
}
else
{
// If none of the SNP's genotypes or their complements mismatch this orientation's alleles, we can't determine the orientation of the SNP's genotypes.
return(Orientation.Unknown);
}
}
public SimpleDiploidTraitPage(
SNPInfo snpInfo,
DiploidGenotype personalGenotype
)
{
InitializeComponent();
// Setup the SNP information controls.
nameLabel.Content = snpInfo.id;
descriptionLabel.Text = Utilities.ConvertWikiTextToPlainText(snpInfo.descriptionWikiText);
snpediaLink.NavigateUri = new Uri(string.Format("http://www.snpedia.com/index.php?title={0}", snpInfo.id));
// Setup the list of genotypes for this SNP.
bHasMatchingGenotype = false;
foreach (var genotypeInfo in snpInfo.genotypes)
{
bool bGenotypeMatchesPersonalGenome = personalGenotype.Equals(genotypeInfo.genotype);
if (bGenotypeMatchesPersonalGenome)
{
bHasMatchingGenotype = true;
}
genotypeList.Items.Add(new SNPGenotypeUIAdapter(
genotypeInfo,
bGenotypeMatchesPersonalGenome
));
}
// If the genome doesn't match any of the genotypes, create a placeholder genotype for it.
if (!bHasMatchingGenotype)
{
var genotypeInfo = new SNPGenotypeInfo();
genotypeInfo.genotype = personalGenotype;
genotypeInfo.trait = "";
genotypeInfo.populationFrequencies = new Dictionary <string, float>();
genotypeList.Items.Add(new SNPGenotypeUIAdapter(
genotypeInfo,
true
));
}
}
public static DiploidGenotype StringToDiploidGenotype(string genotypeString)
{
var result = new DiploidGenotype();
result.a = Genotype.Unknown;
result.b = Genotype.Unknown;
var regexMatch = diploidGenotypeRegex.Match(genotypeString);
if (regexMatch.Success)
{
if (regexMatch.Groups.Count >= 2 && regexMatch.Groups[1].Value.Length > 0)
{
result.a = CharacterToGenotype(regexMatch.Groups[1].Value[0]);
}
if (regexMatch.Groups.Count >= 3 && regexMatch.Groups[2].Value.Length > 0)
{
result.b = CharacterToGenotype(regexMatch.Groups[2].Value[0]);
}
}
return(result);
}
public bool Equals(DiploidGenotype otherPair)
{
return((a == otherPair.a && b == otherPair.b) ||
(a == otherPair.b && b == otherPair.a));
}
