/// <summary>
/// Gets the value of the given INucleotide in the parent IGeneticCode.
/// The INucleotide's value is determined by its index position in the IGeneticCode's
/// list of INucleotides.
///
/// The 0th INucleotide has a value of 0.
/// The nth INucleotide has a value of n.
/// </summary>
/// <param name="nucleotide"></param>
/// <returns></returns>
protected int GetValueOfNucleotide(INucleotide nucleotide)
{
for (var i = 0; i < this.Parent.Nucleotides.Count; i++)
if (this.Parent.Nucleotides.Values[i].Equals(nucleotide))
return i;
throw new ValueNotYetSupported(nucleotide, typeof(INucleotide));
}
/// <summary>
/// Creates an IGEPCodon for the given IFunctionPair and INucleotide Sequence.
///
/// Adds the IGEPCodon to the IGEPGeneticCode.
/// </summary>
/// <param name="functionPair"></param>
/// <param name="nucleotideSequence"></param>
private void AddCodonFunctionPair(IFunctionPair functionPair, INucleotide[] nucleotideSequence, Action onCodonAdded = null)
{
var codon = new GEPCodon(geneticCode: this,
codonIdentifier: new CodonIdentifier(nucleotideSequence.Select(n => n.Identifier.ToString()).ConcatContents()),
codonType: CodonType.Standard,
nucleotides: nucleotideSequence,
functions: functionPair);
this.AddCodon(codon);
if (onCodonAdded != null)
onCodonAdded();
}
/// <summary>
/// Adds the specified INucleotide to the IGeneticCode.
/// </summary>
/// <param name="nucleotide"></param>
public void AddNucleotide(INucleotide nucleotide)
{
this.Nucleotides.Add(key: nucleotide.Identifier, value: nucleotide);
}
/// <summary>
/// Gets the previous INucleotide before the given INucleotide.
///
/// Returns null if the given INucleotide is the first INucleotide.
/// </summary>
/// <param name="currentNucleotide"></param>
/// <returns></returns>
public INucleotide GetPreviousNucleotide(INucleotide currentNucleotide)
{
for (var i = this.Nucleotides.Count - 1; i > 0; i--)
{
if (this.Nucleotides.Values[i].Equals(currentNucleotide))
return this.Nucleotides.Values[i - 1];
}
return null;
}
/// <summary>
/// Gets the next INucleotide after the given INucleotide.
///
/// Returns null if the given INucleotide is the last INucleotide.
/// </summary>
/// <param name="currentNucleotide"></param>
/// <returns></returns>
public INucleotide GetNextNucleotide(INucleotide currentNucleotide)
{
for (var i = 0; i < this.Nucleotides.Count; i++)
{
if (this.Nucleotides.Values[i].Equals(currentNucleotide))
return this.Nucleotides.Values[i + 1];
}
return null;
}
public int IndexOf(INucleotide item)
{
return this.Nucleotides.IndexOf(item: item);
}
public void Insert(int index, INucleotide item)
{
this.Nucleotides.Insert(index: index, item: item);
}
public void CopyTo(INucleotide[] array, int arrayIndex)
{
this.Nucleotides.CopyTo(array: array, arrayIndex: arrayIndex);
}
public bool Remove(INucleotide item)
{
return this.Nucleotides.Remove(item: item);
}
public bool Contains(INucleotide item)
{
return this.Nucleotides.Contains(item: item);
}
public void Add(INucleotide item)
{
this.Nucleotides.Add(item: item);
}
public bool Equals(INucleotide other)
{
return this.Identifier.Equals(other.Identifier);
}
public int CompareTo(INucleotide other)
{
return this.Identifier.CompareTo(other.Identifier);
}
public NucleotideEditorModel(INucleotide nucleotide, string geneticCodeName, int? geneticCodePrimaryKey)
: base(nucleotide: nucleotide, geneticCodeName: geneticCodeName, geneticCodePrimaryKey: geneticCodePrimaryKey)
{
}
