| public ClearAndSetNewLength ( int length ) : void | ||
| length | int | /// New chain length. /// |
| return | void | |
/// <summary>
/// Reorganizes source chain.
/// </summary>
/// <param name="source">
/// Source chain.
/// </param>
/// <returns>
/// <see cref="AbstractChain"/>.
/// </returns>
/// <exception cref="InvalidOperationException">
/// Thrown if level is less than 0.
/// </exception>
public override AbstractChain Reorganize(AbstractChain source)
{
if (level < 0)
{
throw new InvalidOperationException("Markov chain level can't be less than 0");
}
if (level == 0)
{
return source;
}
var result = new BaseChain();
result.ClearAndSetNewLength(source.GetLength() + level);
for (int i = 0; i < source.GetLength(); i++)
{
result[i] = source[i];
}
var iterator = new IteratorStart(source, level, 1);
iterator.Reset();
iterator.Next();
AbstractChain addition = iterator.Current();
for (int i = 0; i < addition.GetLength(); i++)
{
result[source.GetLength() + i] = addition[i];
}
return result;
}
/// <summary>
/// Reorganizes <see cref="AbstractChain"/> into <see cref="AbstractChain"/>.
/// </summary>
/// <param name="source">
/// Source chain.
/// </param>
/// <returns>
/// The <see cref="AbstractChain"/>.
/// </returns>
public override AbstractChain Reorganize(AbstractChain source)
{
var result = source.Clone() as AbstractChain;
if (result != null)
{
return result;
}
result = new BaseChain();
result.ClearAndSetNewLength(source.GetLength());
var iteratorRead = new IteratorSimpleStart(source, 1);
var iteratorWrite = new IteratorWritableStart(result);
iteratorRead.Reset();
iteratorWrite.Reset();
iteratorRead.Next();
iteratorWrite.Next();
for (int i = 0; i < source.GetLength(); i++)
{
iteratorWrite.WriteValue(iteratorRead.Current());
iteratorRead.Next();
iteratorWrite.Next();
}
return result;
}
/// <summary>
/// Reorganizes <see cref="AbstractChain"/> into <see cref="AbstractChain"/>.
/// </summary>
/// <param name="source">
/// Source chain.
/// </param>
/// <returns>
/// The <see cref="AbstractChain"/>.
/// </returns>
public override AbstractChain Reorganize(AbstractChain source)
{
var resent = new BaseChain();
resent.ClearAndSetNewLength(source.GetLength());
for (int i = 0; i < source.GetLength(); i++)
{
var phantom = source[i] as ValuePhantom;
resent.Set(phantom != null ? phantom[0] : source[i], i);
}
return resent;
}
/// <summary>
/// Generates sequence.
/// </summary>
/// <param name="length">
/// Length of generated sequence.
/// </param>
/// <param name="chainRank">
/// Rank of used markov chain.
/// </param>
/// <returns>
/// Generated sequence as <see cref="BaseChain"/>.
/// </returns>
public override BaseChain Generate(int length, int chainRank)
{
var temp = new BaseChain();
temp.ClearAndSetNewLength(length);
var read = Rank > 1 ? new IteratorStart(temp, Rank - 1, 1) : null;
var write = new IteratorWritableStart(temp);
if (read != null)
{
read.Reset();
read.Next();
}
write.Reset();
Generator.Reset();
int m = 0;
for (int j = 0; j < length; j++)
{
if (m == HeterogeneityRank + 1)
{
m = 0;
}
m += 1;
write.Next();
if (j >= Rank)
{
if (read != null)
{
read.Next();
}
}
if (read != null)
{
BaseChain chain = (BaseChain)read.Current();
var indexedChain = new int[chain.GetLength()];
for (int k = 0; k < chain.GetLength(); k++)
{
indexedChain[k] = Alphabet.IndexOf(chain[k]);
}
write.WriteValue(GetObject(ProbabilityMatrixes[m - 1].GetProbabilityVector(Alphabet, indexedChain)));
}
}
return temp;
}
/// <summary>
/// Returns current value of iterator.
/// </summary>
/// <returns>
/// Current subsequence.
/// </returns>
/// <exception cref="InvalidOperationException">
/// Thrown if current position is invalid.
/// </exception>
public virtual AbstractChain Current()
{
if (Position < 0 || Position > MaxPosition)
{
throw new InvalidOperationException("Iterator position is out of range.");
}
var result = new BaseChain();
result.ClearAndSetNewLength(Length);
for (int i = 0; i < Length; i++)
{
result[i] = Source[Position + i];
}
return result;
}