public IndividualGenomeDatabase Read()
{
// Initialize the database.
var database = new IndividualGenomeDatabase();
// Read the table of SNP genotypes.
tableReader.Read(
delegate(string[] columns)
{
if (columns.Length == 4)
{
// Parse a column of this format: rs# chromosome position genotype
var snpId = columns[0];
var snpValue = new SNPGenotype();
snpValue.genotype = DNA.StringToDiploidGenotype(columns[3]);
snpValue.orientation = Orientation.Plus;
// Add the SNP genotype to the database.
database.AddSNPValue(snpId, snpValue);
}
});
return(database);
}
public IndividualGenomeDatabase Read()
{
// Initialize the database.
var database = new IndividualGenomeDatabase();
// Read the table of SNP genotypes.
tableReader.Read(
delegate(string[] columns)
{
if (columns.Length == 6)
{
// Parse a column of this format: rs4477212,A/G,1,72017,+,AA
var snpId = columns[0];
var snpValue = new SNPGenotype();
snpValue.genotype = DNA.StringToDiploidGenotype(columns[5]);
snpValue.orientation = DNA.StringToOrientation(columns[4]);
// Add the SNP genotype to the database.
database.AddSNPValue(snpId, snpValue);
}
});
return(database);
}
public static GenomeLoadResult Load(Stream stream, string password, ref IndividualGenomeDatabase outResult)
{
var reader = new BinaryReader(stream);
// Read the file magic and version.
char[] fileMagic = reader.ReadChars(referenceFileMagic.Length);
// If the file doesn't have the expected magic header, abort and return an error.
bool bFileHasMagic = Utilities.ArrayCompare(fileMagic, referenceFileMagic);
bool bFileHasLegacyMagic = Utilities.ArrayCompare(fileMagic, referenceFileMagicLegacy);
if (!bFileHasMagic && !bFileHasLegacyMagic)
{
return(GenomeLoadResult.UnrecognizedFile);
}
// The encryption system doesn't handle short passwords gracefully, so extend them to 16 characters with spaces.
password = password.PadRight(16, ' ');
// Read the saved password hash from the file, and compare it to the hash of the password we're trying to load with.
// This can't be done by saving some magic header inside the encrypted part of the file, as the CryptoStream will crash when decrypting with the wrong password.
byte[] passwordASCII = ASCIIEncoding.ASCII.GetBytes(password);
byte[] passwordHash = (new SHA512Managed()).ComputeHash(passwordASCII);
byte[] savedPasswordHash = reader.ReadBytes(passwordHash.Length);
if (!Utilities.ArrayCompare(passwordHash, savedPasswordHash))
{
return(GenomeLoadResult.IncorrectPassword);
}
// Read the initialization vector.
byte[] initializationVector = reader.ReadBytes(16);
// Create a decrypting stream to read the encrypted data from the file.
reader = new BinaryReader(
new CryptoStream(
stream,
Rijndael.Create().CreateDecryptor(
ASCIIEncoding.ASCII.GetBytes(password),
initializationVector),
CryptoStreamMode.Read));
// Create the genome database that's about to be loaded.
outResult = new IndividualGenomeDatabase();
outResult.password = password;
// Read SNPs until the end of the file.
while (stream.Position < stream.Length)
{
// Read a SNP ID and value pair, and add them to the database.
var Key = reader.ReadString();
SNPGenotype Genotype;
if (bFileHasLegacyMagic)
{
Genotype = SNPGenotype.ReadLegacy(reader);
}
else
{
Genotype = SNPGenotype.Read(reader);
}
outResult.AddSNPValue(Key, Genotype);
}
return(GenomeLoadResult.Success);
}
private void menuClick_FileOpen(object sender, RoutedEventArgs args)
{
bool bSuccessfullyLoaded = false;
var dialog = new WinForms.OpenFileDialog();
dialog.Filter = "Personal Genome Explorer files|*.PersonalGenomeData|All files (*.*)|*.*";
if (dialog.ShowDialog() == WinForms.DialogResult.OK)
{
// If we had a file stream open for saving the current document, close it now to ensure that it doesn't prevent us from opening the user's new file.
if (App.documentSaveStream != null)
{
App.documentSaveStream.Close();
App.documentSaveStream = null;
}
// Open the chosen file.
using (var fileStream = dialog.OpenFile())
{
int TryIndex = 0;
while (true)
{
// Seek to the beginning of the file.
fileStream.Seek(0, SeekOrigin.Begin);
// Try a blank password before prompting the user.
string password = "";
if (TryIndex > 0)
{
// Prompt the user for the genome file's password.
var passwordWindow = new PasswordWindow();
passwordWindow.Owner = this;
passwordWindow.ShowDialog();
password = passwordWindow.password;
if (!passwordWindow.bOkPressed)
{
// The user cancelled the password dialog, abort the open.
break;
}
}
// Try to load the genome from the chosen file.
GenomeLoadResult result = IndividualGenomeDatabase.Load(fileStream, password, ref App.document);
// If there was an error, display the appropriate dialog.
if (result == GenomeLoadResult.IncorrectPassword)
{
if (TryIndex > 0)
{
// If the user entered the wrong password, give them another chance to enter it.
WinForms.MessageBox.Show("The file cannot be decrypted with that password.", "Incorrect Password");
}
}
else if (result == GenomeLoadResult.UnrecognizedFile)
{
WinForms.MessageBox.Show("The file doesn't appear to be a valid PersonalGenomeData file.", "Unrecognized file");
break;
}
else
{
bSuccessfullyLoaded = true;
break;
}
++TryIndex;
}
;
}
}
if (bSuccessfullyLoaded)
{
// Reanalyze after loading the data.
InitAnalysis();
}
}
