/// <summary>
/// Creates a new BasicSequenceInfo that is a copy of the current BasicSequenceInfo.
/// </summary>
/// <returns>A new BasicSequenceInfo that is a copy of this BasicSequenceInfo.</returns>
public BasicSequenceInfo Clone()
{
BasicSequenceInfo cloneObject = new BasicSequenceInfo();
cloneObject.id = id;
cloneObject.displayID = displayID;
cloneObject._moleculeType = _moleculeType;
cloneObject.alphabet = alphabet;
foreach (KeyValuePair <string, object> metadataKeyValue in metadata)
{
object value = metadataKeyValue.Value;
// If the object in the medata is ICloneable then get the clone copy.
ICloneable cloneValue = value as ICloneable;
if (cloneValue != null)
{
value = cloneValue.Clone();
}
cloneObject.metadata.Add(metadataKeyValue.Key, value);
}
return(cloneObject);
}
/// <summary>
/// Creates a VirtualSequence instance.
/// </summary>
/// <param name="alphabet">
/// The alphabet the sequence uses (eg. Alphabets.DNA or Alphabets.RNA or Alphabets.Protein)
/// </param>
public VirtualSequence(IAlphabet alphabet)
{
if (alphabet == null)
{
throw new ArgumentNullException(Properties.Resource.ParameterNameAlphabet);
}
_seqInfo = new BasicSequenceInfo();
Alphabet = alphabet;
}
/// <summary>
/// Constructor for deserialization.
/// </summary>
/// <param name="info">Serialization Info.</param>
/// <param name="context">Streaming context.</param>
protected VirtualSequence(SerializationInfo info, StreamingContext context)
{
if (info == null)
{
throw new ArgumentNullException("info");
}
_seqInfo = (BasicSequenceInfo)info.GetValue("VirtualSequence:seqInfo", typeof(BasicSequenceInfo));
Documentation = info.GetValue("VirtualSequence:Documentation", typeof(object));
MoleculeType = (MoleculeType)info.GetValue("VirtualSequence:MoleculeType", typeof(MoleculeType));
}
/// <summary>
/// Gets the index of last non gap character within the specified end position.
/// </summary>
/// <param name="endPos">Index value below which to search for non-Gap character.</param>
/// <returns>If found returns an zero based index of the last non gap character, otherwise returns -1.</returns>
public int LastIndexOfNonGap(int endPos)
{
return(BasicSequenceInfo.LastIndexOfNonGap(this, endPos));
}
/// <summary>
/// Returns the position of the first item from startPos that does not
/// have a Gap character.
/// </summary>
/// <param name="startPos">Index value above which to search for non-Gap character.</param>
/// <returns>If found returns an zero based index of the first non gap character, otherwise returns -1.</returns>
public int IndexOfNonGap(int startPos)
{
return(BasicSequenceInfo.IndexOfNonGap(this, startPos));
}
