/// <summary>
/// Compares two symbol and returns the "similarity" (weight) between the symbols
/// </summary>
/// <param name="symbol1">First symbol.</param>
/// <param name="symbol2">Second symbol.</param>
/// <returns>Returns the "similarity" (weight) between the symbols.</returns>
protected double Compare
(Symbol symbol1, Symbol symbol2)
{
if (repeat.weights == null)
return symbol1.Equals(symbol2) ? 1.0 : 0.0;
return repeat.Weight(symbol1, symbol2);
}
public void SetUp()
{
alphabet = new TestAlphabetClass();
alphabet2 = new TestAlphabetClass();
sym1 = new Symbol('a', "Ade", "Adenine");
sym2 = new Symbol('u', "Ura", "Uracil");
sym3 = new SymbolMeta('-', "GAP", "Gap");
}
/** Tests the construction of symbols */
public void TestConstructor()
{
char[] adenine = { 'A', 'd', 'e', 'n', 'i', 'n', 'e' };
Symbol sym1 = new Symbol('a', "Ade", "Adenine");
Symbol sym2 = new Symbol('a', "Ade", new String(adenine));
Assert.AreEqual('a', sym1.Letter);
Assert.AreEqual("Adenine", sym1.Name);
Assert.AreEqual(sym1, sym1.Complement);
Assert.IsTrue(sym1.Name == sym2.Name);
}
/** Tests the comparions of symbols */
public void TestEquals()
{
char[] adenine = { 'A', 'd', 'e', 'n', 'i', 'n', 'e' };
Symbol sym1 = new Symbol('a', "Ade", new string(adenine));
Symbol sym2 = new Symbol('a', "Ade", "Adenine");
Symbol sym3 = new Symbol('u', "Ura", "Uracil");
Assert.AreEqual(true, sym1.Equals(sym2));
Assert.AreEqual(true, sym2.Equals(sym1));
Assert.AreEqual(false, sym1.Equals(sym3));
Assert.AreEqual(false, sym3.Equals(sym1));
}
/** Tests the replacement of symbols within the symbol set */
public void TestReplace()
{
SymbolMeta sym = new SymbolMeta('X', "XXX", "Unknown");
Symbol sym1 = new Symbol('a', "Ade", "Adenine");
Symbol sym2 = new Symbol('u', "Ura", "Uracil");
Symbol sym3 = new Symbol('t', "Thy", "Thymine");
sym.Add(sym1);
sym.Add(sym2);
Assert.AreEqual(2, sym.SymbolNumber);
sym.Replace(sym2, sym3);
Assert.AreEqual(2, sym.SymbolNumber);
Assert.AreEqual(sym3, sym[1]);
}
/** Tests the removal of symbols from the symbol set */
public void TestRemove()
{
SymbolMeta sym = new SymbolMeta('X', "XXX", "Unknown");
Symbol sym1 = new Symbol('a', "Ade", "Adenine");
Symbol sym2 = new Symbol('u', "Ura", "Uracil");
sym.Remove(sym1);
sym.Add(sym1);
sym.Add(sym2);
Assert.AreEqual(2, sym.SymbolNumber);
sym.Remove(sym1);
Assert.AreEqual(1, sym.SymbolNumber);
Assert.AreEqual(sym2, sym[0]);
}
/** Tests the comparision with a meta symbol */
public void TestEquals()
{
SymbolMeta sym = new SymbolMeta('X', "XXX", "Unknown");
Symbol sym2 = new Symbol('a', "Ade", "Adenine");
Symbol sym3 = new Symbol('u', "Ura", "Uracil");
Assert.AreEqual(true, sym.Equals(sym2));
Assert.AreEqual(true, sym2.Equals(sym));
sym.Add(sym2);
Assert.AreEqual(true, sym.Equals(sym2));
Assert.AreEqual(true, sym2.Equals(sym));
Assert.AreEqual(false, sym.Equals(sym3));
Assert.AreEqual(false, sym3.Equals(sym));
sym.Add(sym3);
Assert.AreEqual(true, sym.Equals(sym));
Assert.AreEqual(true, sym.Equals(sym2));
Assert.AreEqual(true, sym.Equals(sym3));
}
/// <summary>
/// Constructs a <see cref="QUT.Bio.BioPatML.Symbols.SymbolArray"> Symbol Array </see>
/// base on the given symbol array.
/// <para></para>
/// Note - the symbol array is not copied. Any changes in the
/// symbol array will effect the content of SymbolArray as well.
/// <para></para>
/// Furthermore there is no check if the symbols within the array are valid.
/// </summary>
/// <param name="alphabet"> The alphabet the symbols in the array belong to. </param>
/// <param name="symbols"> Array of symbols. </param>
public SymbolArray
(Alphabet alphabet, Symbol[] symbols)
{
Symbols = symbols;
SymAlphabet = alphabet;
}
public void TearDown()
{
this.alphabet = null;
this.alphabet2 = null;
this.sym1 = null;
this.sym2 = null;
this.sym3 = null;
}
/// <summary>
/// Determines if a the given amino acid is aliphatic or not.
///
/// Classification according to http://en.wikipedia.org/wiki/Amino_acid wiki amino acid
/// </summary>
/// <param name="symbol"> Symbol to classify. </param>
/// <returns>
/// Returns true: if the amino acid is aliphatic, false: otherwise.
/// </returns>
public bool IsAliphatic ( Symbol symbol ) {
if ( symbol is SymbolAA )
return ( (SymbolAA) symbol ).IsAliphatic;
return false;
}
/// <summary>
/// Gets a pairing weight
/// </summary>
/// <param name="symbol1">First symbol.</param>
/// <param name="symbol2">Second symbol</param>
/// <returns>Returns the weight for the given pairing of symbols.</returns>
public double Weight(Symbol symbol1, Symbol symbol2)
{
return Weight(symbol1.Letter, symbol2.Letter);
}
/// <summary>
/// Determines if a the given amino acid is negatively charged or not.
///
/// Classification according to http://en.wikipedia.org/wiki/Amino_acid"> wiki amino acid
/// </summary>
/// <param name="symbol">Symbol to classify.</param>
/// <returns>
/// Returns true: if the amino acid is negatively charged, false: otherwise.
/// </returns>
public bool IsNegative ( Symbol symbol ) {
if ( symbol is SymbolAA )
return ( (SymbolAA) symbol ).IsNegative;
return false;
}
/// <summary>
/// Determines if a the given amino acid is small or not.
///
/// Classification according to http://en.wikipedia.org/wiki/Amino_acid wiki amino acid
/// </summary>
/// <param name="symbol">Symbol to classify.</param>
/// <returns>
/// Returns true: if the amino acid is small, false: otherwise.
/// </returns>
public bool IsSmall ( Symbol symbol ) {
if ( symbol is SymbolAA )
return ( (SymbolAA) symbol ).IsSmall;
return false;
}
/// <summary>
/// Gets for the bin index the given symbol belongs to.
/// </summary>
/// <param name="symbol"> The symbol. </param>
/// <returns> Bin index, or -1 if the symbol isn't contained </returns>
public int CalSymIndex(Symbol symbol)
{
Counter counter = null;
if(DictionaryCounter.ContainsKey(symbol.Name))
counter = DictionaryCounter[symbol.Name];
if (counter == null)
return (-1);
return (counter.binIndex);
}
/// <summary>
/// Creates a counter instance.
/// </summary>
/// <param name="counts"> Counter for the symbol. </param>
/// <param name="symbol"> The symbol itself. </param>
/// <param name="binIndex"> Index of the histogram where the symbol belongs to. </param>
public Counter
(int counts, Symbol symbol, int binIndex)
{
this.counts = counts;
this.symbol = symbol;
this.binIndex = binIndex;
}
/// <summary>
/// Getter for the histogram value (=counts) for the specified object.
/// </summary>
/// <param name="symbol"> Symbol </param>
/// <returns> Histogram value (=counts) for the given object. Zero if the
/// symbol is not in the histogram. </returns>
public int HistoValue(Symbol symbol)
{
Counter counter = null;
if(DictionaryCounter.ContainsKey(symbol.Name))
counter = DictionaryCounter[symbol.Name];
if (counter == null) //unknown symbol
return (0);
return (counter.counts);
}
/// <summary>
/// Returns the relative frequency of the given symbol within the histogram.
/// </summary>
/// <param name="symbol"> A symbol. </param>
/// <returns> Returns the relative frequency or zero if the symbol is unknown. </returns>
public double Frequency(Symbol symbol)
{
return (sum > 0 ? (double)HistoValue(symbol) / sum : 0);
}
/// <summary>
/// Adds an symbol to the histogram with a given number of counts.
/// </summary>
/// <param name="symbol"> A symbol. </param>
/// <param name="counts"> Counts for the given symbol. </param>
public void Add(Symbol symbol, int counts)
{
Counter counter = null; //did the C# style
if (DictionaryCounter.ContainsKey(symbol.Name))
counter = DictionaryCounter[symbol.Name];
if (counter == null)
{
counter = new Counter(counts, symbol, list.Count);
DictionaryCounter.Add(symbol.Name, counter);
list.Add(counter);
sum++;
}
else
{
counter.counts += counts;
sum += counts;
}
}
/// <summary>
/// Adds a symbol to the histogram.
/// </summary>
/// <param name="symbol"> The symbol to add. </param>
public void Add(Symbol symbol)
{
Add(symbol, 1);
}
/// <summary>
/// Setter for a pairing weight.
/// </summary>
/// <param name="symbol1">First symbol.</param>
/// <param name="symbol2">Second symbol.</param>
/// <param name="weight">Weight for the given pairing of symbols. Has to be in interval [0,1]</param>
internal void Weight(Symbol symbol1, Symbol symbol2, double weight)
{
Weight(symbol1.Letter, symbol2.Letter, weight);
}
/// <summary> Determines if a the given amino acid is hydrophobic or not.
///
/// Classification according to http://en.wikipedia.org/wiki/Amino_acid"> wiki amino acid
///
/// </summary>
/// <param name="symbol"> Symbol to classify. </param>
/// <returns> Returns true: if the amino acid is hydrophobic, false: otherwise. </returns>
public bool IsHydrophobic ( Symbol symbol ) {
if ( symbol is SymbolAA )
return ( (SymbolAA) symbol ).IsHydrophobic;
return false;
}
/// <summary>
/// Gets the symbol weight
/// </summary>
/// <param name="symbol">Symbol</param>
/// <returns>Returns the weight for the Symbol or the default weight if no weight
/// for the symbol is defined.</returns>
public double Weight(Symbol symbol)
{
//Fix on 17 March
if(SymDictionary.ContainsKey(symbol))
return SymDictionary[symbol];
return defaultWeight;
}
/// <summary>
/// Determines if a the given amino acid is polar or not.
///
/// Classification according to http://en.wikipedia.org/wiki/Amino_acid wiki amino acid
/// </summary>
/// <param name="symbol"> Symbol to classify. </param>
/// <returns> Returns true: if the amino acid is polar, false: otherwise. </returns>
public bool IsPolar ( Symbol symbol ) {
if ( symbol is SymbolAA )
return ( (SymbolAA) symbol ).IsPolar;
return false;
}
/// <summary>
/// Replaces the first occurrences of a symbol(symbol1) with a specified replacement symbol (symbol2).
/// </summary>
/// <param name="symbol1"> First symbol (to be replaced). </param>
/// <param name="symbol2"> Second symbol (replacement). </param>
public void Replace(Symbol symbol1, Symbol symbol2)
{
int index = symbolset.IndexOf(symbol1);
if (index >= 0)
{
symbolset.RemoveAt(index);
symbolset.Insert(index, symbol2);
}
}
/// <summary>
/// Determines if a the given amino acid is charged or not.
///
/// Classification according to http://en.wikipedia.org/wiki/Amino_acid"> wiki amino acid
/// </summary>
/// <param name="symbol">Symbol to classify.</param>
/// <returns>
/// Returns true: if the amino acid is charged, false: otherwise.
/// </returns>
public bool IsCharged ( Symbol symbol ) {
if ( symbol is SymbolAA )
return ( (SymbolAA) symbol ).IsCharged;
return false;
}
/// <summary>
/// Returns true if the symbol set is empty or if the given symbol is in the
/// symbol set.
/// </summary>
/// <param name="symbol"> Given object </param>
/// <returns> See summary </returns>
public override Boolean Equals(Symbol symbol)
{
if (symbolset == null || symbol.Name == this.Name)
return true;
for (int i = 0; i < SymbolNumber; i++)
if (this[i].Name == symbol.Name)
return true;
return false;
}
/// <summary>
/// Determines if a the given amino acid is tiny or not.
/// Classification according to http://en.wikipedia.org/wiki/Amino_acid wiki Amino acid
/// </summary>
/// <param name="symbol">Symbol to classify.</param>
/// <returns>Returns true: if the amino acid is tiny, false: otherwise.</returns>
public bool IsTiny ( Symbol symbol ) {
if ( symbol is SymbolAA )
return ( (SymbolAA) symbol ).IsTiny;
return false;
}
/// <summary>
/// Adds a symbol to the set of symbols described by this meta symbol.
/// </summary>
/// <param name="symbol"> The symbol to add. </param>
public void Add(Symbol symbol)
{
if (symbolset == null)
this.symbolset = new List<Symbol>();
symbolset.Add(symbol);
}
/// <summary>
/// Removes the given symbol from the symbol set.
/// </summary>
/// <param name="symbol"></param>
public void Remove(Symbol symbol)
{
if (symbolset != null)
if(symbolset.Contains(symbol))
symbolset.Remove(symbol);
}
/// <summary>
/// Creates a map with all DNA symbols. This constructor is private
/// to ensure that there will be always only one DNA alphabet. Use
/// the Instance() method or the <see cref="QUT.Bio.BioPatML.Alphabets.AlphabetFactory"> AlphabetFactory </see> to create to create
/// the alphabet.
/// <para></para>
/// Unknown symbols will be mapped to 'n'.
///
/// </summary>
private DnaAlphabet ()
: base( "DNA" ) {
#region Prefixed set of DNA symbols
Add( new SymbolMeta( 'n', "Any", "Any Nucleotide" ) );
Add( new SymbolMeta( 'x', "Any", "Any Nucleotide" ) );
Add( new SymbolMeta( '.', "NON", "No Nucleotide" ) );
Add( new SymbolMeta( '-', "Gap", "Gap" ) );
Add( new Symbol( 'g', "Gua", "Guanine" ) );
Add( new Symbol( 'a', "Ade", "Adenine" ) );
Add( new Symbol( 't', "Thy", "Thymine" ) );
Add( new Symbol( 'c', "Cyt", "Cytosine" ) );
#endregion
#region Meta symbols of DNA
Add( new SymbolMeta( 'm', "A/C", "Ade or Cyt" ) );
Add( new SymbolMeta( 'r', "A/G", "Ade or Gua" ) );
Add( new SymbolMeta( 'w', "A/T", "Ade or Thy" ) );
Add( new SymbolMeta( 's', "C/G", "Cyt or Gua" ) );
Add( new SymbolMeta( 'y', "C/T", "Cyt or Thy" ) );
Add( new SymbolMeta( 'k', "G/T", "Gua or Thy" ) );
Add( new SymbolMeta( 'v', "ACG", "Ade or Cyt or Gua" ) );
Add( new SymbolMeta( 'h', "ACT", "Ade or Cyt or Thy" ) );
Add( new SymbolMeta( 'd', "AGT", "Ade or Gua or Thy" ) );
Add( new SymbolMeta( 'b', "CGT", "Cyt or Gua or Thy" ) );
#endregion
#region Complements
this['g'].Complement = ( this['c'] );
this['a'].Complement = ( this['t'] );
this['t'].Complement = ( this['a'] );
this['c'].Complement = ( this['g'] );
this['m'].Complement = ( this['k'] );
this['r'].Complement = ( this['y'] );
this['w'].Complement = ( this['w'] );
this['s'].Complement = ( this['s'] );
this['y'].Complement = ( this['r'] );
this['k'].Complement = ( this['m'] );
this['v'].Complement = ( this['b'] );
this['h'].Complement = ( this['d'] );
this['d'].Complement = ( this['h'] );
this['b'].Complement = ( this['v'] );
#endregion
#region equivalents
// equals symbols
( (SymbolMeta) this['.'] ).Add( this['.'] );
( (SymbolMeta) this['-'] ).Add( this['-'] );
( (SymbolMeta) this['m'] ).Add( this['a'] );
( (SymbolMeta) this['m'] ).Add( this['c'] );
( (SymbolMeta) this['r'] ).Add( this['a'] );
( (SymbolMeta) this['r'] ).Add( this['g'] );
( (SymbolMeta) this['w'] ).Add( this['a'] );
( (SymbolMeta) this['w'] ).Add( this['t'] );
( (SymbolMeta) this['s'] ).Add( this['c'] );
( (SymbolMeta) this['s'] ).Add( this['g'] );
( (SymbolMeta) this['y'] ).Add( this['c'] );
( (SymbolMeta) this['y'] ).Add( this['t'] );
( (SymbolMeta) this['k'] ).Add( this['g'] );
( (SymbolMeta) this['k'] ).Add( this['t'] );
( (SymbolMeta) this['v'] ).Add( this['a'] );
( (SymbolMeta) this['v'] ).Add( this['c'] );
( (SymbolMeta) this['v'] ).Add( this['g'] );
( (SymbolMeta) this['h'] ).Add( this['a'] );
( (SymbolMeta) this['h'] ).Add( this['c'] );
( (SymbolMeta) this['h'] ).Add( this['t'] );
( (SymbolMeta) this['d'] ).Add( this['a'] );
( (SymbolMeta) this['d'] ).Add( this['g'] );
( (SymbolMeta) this['d'] ).Add( this['t'] );
( (SymbolMeta) this['b'] ).Add( this['c'] );
( (SymbolMeta) this['b'] ).Add( this['g'] );
( (SymbolMeta) this['b'] ).Add( this['t'] );
( (SymbolMeta) this['n'] ).Add( this['a'] );
( (SymbolMeta) this['n'] ).Add( this['t'] );
( (SymbolMeta) this['n'] ).Add( this['c'] );
( (SymbolMeta) this['n'] ).Add( this['g'] );
( (SymbolMeta) this['x'] ).Add( this['a'] );
( (SymbolMeta) this['x'] ).Add( this['t'] );
( (SymbolMeta) this['x'] ).Add( this['c'] );
( (SymbolMeta) this['x'] ).Add( this['g'] );
#endregion
defaultSymbol = this['n'];
}