/// <summary>
/// Constructs a Block of aligned sequences
/// (<see cref="QUT.Bio.BioPatML.Patterns.PWM"> PWM </see>).
/// </summary>
/// <param name="name">Name for element block</param>
/// <param name="sequenceList"> List of aligned sequences. </param>
/// <param name="background"> Histogram with base counts of the background
/// sequences.</param>
/// <param name="threshold"> Similarity threshold. </param>
public Block
(String name, SequenceList sequenceList,
HistogramSymbol background, double threshold)
: base(name, sequenceList[0].Alphabet, threshold)
{
Estimate(sequenceList, background);
}
/** Tests the adding of a histogram to the histogram */
public void TestAddHistogram()
{
HistogramSymbol histo2 = new HistogramSymbol();
histo.Add(new Sequence(AlphabetType.DNA, "gactt"));
histo2.Add(new Sequence(AlphabetType.DNA, "act"));
histo.Add(histo2);
Assert.AreEqual(2, histo.HistoValue(alpha['a']));
Assert.AreEqual(2, histo.HistoValue(alpha['c']));
Assert.AreEqual(3, histo.HistoValue(alpha['t']));
Assert.AreEqual(1, histo.HistoValue(alpha['g']));
}
/// <summary>
/// Estimates the weights of the PWM that's behind a Block pattern.
/// </summary>
/// <exception cref="System.ArgumentException">
/// Thrown when sequences length are not equal</exception>
/// <param name="sequenceList"> List of aligned sequences. </param>
/// <param name="background"> Histogram with base counts of the background
/// sequences. Can be null. In that case all frequencies are set equally.</param>
private void Estimate
(SequenceList sequenceList, HistogramSymbol background)
{
int length = sequenceList.MinLength();
if (sequenceList.MaxLength() != length)
throw new ArgumentException
("Sequences must be of equal length!");
if (background == null)
{
background = new HistogramSymbol();
foreach (Symbol sym in PWMalphabet)
background.Add(sym);
}
base.Init(length);
base.Estimate(sequenceList, 1, background);
}
/// <summary>
/// Adds all symbols and their frequencies of the given histogram to this histogram.
/// </summary>
/// <param name="histogram"> A symbol histogram. </param>
public void Add(HistogramSymbol histogram)
{
for (int i = 0; i < histogram.Count; i++)
{
Symbol symbol = histogram[i];
Add(symbol, histogram.HistoValue(i));
}
}
public void Setup()
{
histo = new HistogramSymbol();
alpha = AlphabetFactory.Instance(AlphabetType.DNA);
}