public BafFileReader(string bafFilePath)
{
if (string.IsNullOrWhiteSpace(bafFilePath))
{
throw new ArgumentNullException("bafFilePath");
}
if (!File.Exists(bafFilePath))
{
throw new FileNotFoundException("Baf file not exists.");
}
this.bafFilePath = bafFilePath;
try
{
sqlFilePath = Baf2SqlWrapper.GetSQLiteCacheFilename(bafFilePath);
// First argument = 1, ignore contents of Calibrator.ami (if it exists)
baf2SqlHandle = Baf2SqlWrapper.baf2sql_array_open_storage(1, bafFilePath);
if (baf2SqlHandle == 0)
{
Baf2SqlWrapper.ThrowLastBaf2SqlError();
}
linq2BafSql = new Linq2BafSql(sqlFilePath);
model = MzLiteJson.HandleExternalModelFile(this, GetModelFilePath());
supportedVariables = SupportedVariablesCollection.ReadSupportedVariables(linq2BafSql);
}
catch (Exception ex)
{
throw new MzLiteIOException(ex.Message, ex);
}
}
public void Dispose()
{
if (disposed)
{
return;
}
if (baf2SqlHandle != 0)
{
Baf2SqlWrapper.baf2sql_array_close_storage(baf2SqlHandle);
}
if (linq2BafSql != null)
{
linq2BafSql.Dispose();
}
disposed = true;
}
public Peak1DArray ReadSpectrumPeaks(UInt64 spectrumId, bool getCentroids)
{
BafSqlSpectrum bafSpec = linq2BafSql.GetBafSqlSpectrum(this.linq2BafSql.Core, spectrumId);
if (bafSpec == null)
{
throw new MzLiteIOException("No spectrum found for id: " + spectrumId);
}
Peak1DArray pa = new Peak1DArray(
BinaryDataCompressionType.NoCompression,
BinaryDataType.Float32,
BinaryDataType.Float32);
double[] masses;
UInt32[] intensities;
// if profile data available we prefer to get profile data otherwise centroided data (line spectra)
if (getCentroids && bafSpec.LineMzId.HasValue && bafSpec.LineIntensityId.HasValue)
{
masses = Baf2SqlWrapper.GetBafDoubleArray(baf2SqlHandle, bafSpec.LineMzId.Value);
intensities = Baf2SqlWrapper.GetBafUInt32Array(baf2SqlHandle, bafSpec.LineIntensityId.Value);
}
else if (getCentroids == false && bafSpec.ProfileMzId.HasValue && bafSpec.ProfileIntensityId.HasValue)
{
masses = Baf2SqlWrapper.GetBafDoubleArray(baf2SqlHandle, bafSpec.ProfileMzId.Value);
intensities = Baf2SqlWrapper.GetBafUInt32Array(baf2SqlHandle, bafSpec.ProfileIntensityId.Value);
}
else
{
masses = new double[0];
intensities = new UInt32[0];
}
pa.Peaks = new BafPeaksArray(masses, intensities);
return(pa);
}