/// <summary>
/// Populates a <see cref="T:System.Runtime.Serialization.SerializationInfo"/> with the data needed to serialize the target object.
/// </summary>
/// <param name="info">The <see cref="T:System.Runtime.Serialization.SerializationInfo"/> to populate with data. </param><param name="context">The destination (see <see cref="T:System.Runtime.Serialization.StreamingContext"/>) for this serialization. </param><exception cref="T:System.Security.SecurityException">The caller does not have the required permission. </exception>
public void GetObjectData(SerializationInfo info, StreamingContext context)
{
if (info == null)
{
throw new ArgumentNullException("info");
}
info.AddValue(Constants.ConfidenceDataKey, ToByteArray(ConfidenceData));
info.AddValue(Constants.PeakLocationDataKey, ToByteArray(PeakLocations));
info.AddValue(Constants.AdenineColorDataKey, Ab1ColorData.ToByteArray(AdenineColorData));
info.AddValue(Constants.CytosineColorDataKey, Ab1ColorData.ToByteArray(CytosineColorData));
info.AddValue(Constants.ThymineColorDataKey, Ab1ColorData.ToByteArray(ThymineColorData));
info.AddValue(Constants.GuanineColorDataKey, Ab1ColorData.ToByteArray(GuanineColorData));
}
/// <summary>
/// Converts the color data to a byte array. Does not include redundant information only the color data.
/// </summary>
/// <param name="data">Color Data</param>
/// <returns>Readings</returns>
public static byte[] ToByteArray(Ab1ColorData data)
{
if (data == null) throw new ArgumentNullException("data");
int dataPointCount = data.DataByResidue.Sum(residue => residue.Data.Length);
var values = new byte[dataPointCount * 2];
int index = 0;
foreach (Ab1ResidueColorData residue in data.DataByResidue)
{
short[] residueData = residue.Data;
for (int i = 0; i < residueData.Length; i++)
{
short value = residueData[i];
values[index++] = (byte)value;
values[index++] = (byte)(value >> 8);
}
}
return values;
}
/// <summary>
/// Serialization constructor.
/// </summary>
/// <param name="info"></param>
/// <param name="context"></param>
private Ab1Metadata(SerializationInfo info, StreamingContext context)
{
if (info == null) throw new ArgumentNullException("info");
ConfidenceData = Ab1ColorData.FromByteArray((byte[])info.GetValue(Constants.ConfidenceDataKey, typeof(byte[])));
PeakLocations =
Ab1ColorData.FromByteArray((byte[])info.GetValue(Constants.PeakLocationDataKey, typeof(byte[])));
AdenineColorData = new Ab1ColorData(PeakLocations,
Ab1ColorData.FromByteArray(
(byte[])info.GetValue(Constants.AdenineColorDataKey, typeof(byte[]))));
CytosineColorData = new Ab1ColorData(PeakLocations,
Ab1ColorData.FromByteArray(
(byte[])info.GetValue(Constants.CytosineColorDataKey, typeof(byte[]))));
ThymineColorData = new Ab1ColorData(PeakLocations,
Ab1ColorData.FromByteArray(
(byte[])info.GetValue(Constants.ThymineColorDataKey, typeof(byte[]))));
GuanineColorData = new Ab1ColorData(PeakLocations,
Ab1ColorData.FromByteArray(
(byte[])info.GetValue(Constants.GuanineColorDataKey, typeof(byte[]))));
}
/// <summary>
/// Serialization constructor.
/// </summary>
/// <param name="info"></param>
/// <param name="context"></param>
private Ab1Metadata(SerializationInfo info, StreamingContext context)
{
if (info == null)
{
throw new ArgumentNullException("info");
}
ConfidenceData = Ab1ColorData.FromByteArray((byte[])info.GetValue(Constants.ConfidenceDataKey, typeof(byte[])));
PeakLocations =
Ab1ColorData.FromByteArray((byte[])info.GetValue(Constants.PeakLocationDataKey, typeof(byte[])));
AdenineColorData = new Ab1ColorData(PeakLocations,
Ab1ColorData.FromByteArray(
(byte[])info.GetValue(Constants.AdenineColorDataKey, typeof(byte[]))));
CytosineColorData = new Ab1ColorData(PeakLocations,
Ab1ColorData.FromByteArray(
(byte[])info.GetValue(Constants.CytosineColorDataKey, typeof(byte[]))));
ThymineColorData = new Ab1ColorData(PeakLocations,
Ab1ColorData.FromByteArray(
(byte[])info.GetValue(Constants.ThymineColorDataKey, typeof(byte[]))));
GuanineColorData = new Ab1ColorData(PeakLocations,
Ab1ColorData.FromByteArray(
(byte[])info.GetValue(Constants.GuanineColorDataKey, typeof(byte[]))));
}
/// <summary>
/// Sets color data based on the specific sequence.
/// </summary>
/// <param name="item"></param>
/// <param name="data"></param>
public void SetColorData(byte item, Ab1ColorData data)
{
if (item == DnaAlphabet.Instance.A)
{
AdenineColorData = data;
}
else if (item == DnaAlphabet.Instance.T)
{
ThymineColorData = data;
}
else if (item == DnaAlphabet.Instance.G)
{
GuanineColorData = data;
}
else if (item == DnaAlphabet.Instance.C)
{
CytosineColorData = data;
}
else
{
throw new ArgumentException(item.ToString(CultureInfo.InvariantCulture), "item");
}
}
/// <summary>
/// Converts the color data to a byte array. Does not include redundant information only the color data.
/// </summary>
/// <param name="data"></param>
/// <returns></returns>
public static byte[] ToByteArray(Ab1ColorData data)
{
if (data == null)
{
throw new ArgumentNullException("data");
}
int dataPointCount = data.DataByResidue.Sum(residue => residue.Data.Length);
var values = new byte[dataPointCount * 2];
int index = 0;
foreach (Ab1ResidueColorData residue in data.DataByResidue)
{
short[] residueData = residue.Data;
for (int i = 0; i < residueData.Length; i++)
{
short value = residueData[i];
values[index++] = (byte)value;
values[index++] = (byte)(value >> 8);
}
}
return(values);
}
/// <summary>
/// Sets color data based on the specific sequence.
/// </summary>
/// <param name="item"></param>
/// <param name="data"></param>
public void SetColorData(byte item, Ab1ColorData data)
{
if (item == DnaAlphabet.Instance.A)
{
AdenineColorData = data;
}
else if (item == DnaAlphabet.Instance.T)
{
ThymineColorData = data;
}
else if (item == DnaAlphabet.Instance.G)
{
GuanineColorData = data;
}
else if (item == DnaAlphabet.Instance.C)
{
CytosineColorData = data;
}
else
{
throw new ArgumentException(item.ToString(CultureInfo.InvariantCulture), "item");
}
}