/// <summary>
/// Determines the proper pixel color for a given BioSymbol.
/// </summary>
/// <param name="bioSymbol"></param>
/// <returns></returns>
private int GetPixelColor(IBioSymbol bioSymbol)
{
// None translates to whitespace.
if (bioSymbol.Type == Data.BioSymbolType.None)
{
return(_whiteBlock);
}
if (_parent != null && _parent.NucleotideColorSelector != null)
{
return(ColorToInt(_parent.NucleotideColorSelector.GetSymbolColor(bioSymbol)));
}
// Fallback for testing.
switch (bioSymbol.Value)
{
case 'A':
return(ColorToInt(Colors.Red));
case 'G':
return(ColorToInt(Colors.Green));
case 'U':
return(ColorToInt(Colors.Blue));
case 'I':
return(ColorToInt(Colors.RosyBrown));
default:
return(_whiteBlock);
}
}
public override Brush GetSymbolBrush(IBioSymbol symbol)
{
TextAttributes ta = new TextAttributes();
_options.GetAttributes(symbol, ref ta);
return(ta.Foreground);
}
public CircleBasePairViewModel(CircleSequenceViewModel sequence, IBasePairEntity basePair)
{
_basePairEntity = basePair;
_fivePrimeNt = sequence.Sequence.RawData[_basePairEntity.FivePrimeIndex];
_threePrimeNt = sequence.Sequence.RawData[_basePairEntity.ThreePrimeIndex];
Connector = sequence.ComputeBinaryConnector(FivePrimeIndex, ThreePrimeIndex, MAX_RADIUS_FACTOR);
}
public CircleElementViewModel(IBioSymbol symbol, int index, int nextIndex, Point start, Point end, double circleRadius, double rayAngle)
{
Symbol = symbol;
Index = index;
NextIndex = nextIndex;
Position = start;
NextPosition = end;
_rayAngle = rayAngle;
}
public bool AddSymbol(IBioSymbol s)
{
Debug.Assert(Validator != null);
if (Validator.IsValid(s))
{
_rawData.Add(s);
return(true);
}
return(false);
}
/// <summary>
/// Returns the proper color for a given symbol
/// </summary>
/// <param name="bioSymbol">BioSymbol</param>
/// <returns>Brush</returns>
public Brush GetNucleotideColor(IBioSymbol bioSymbol)
{
Brush brush;
return(_nucleotideColors.TryGetValue(bioSymbol.Value, out brush)
? brush
: (_nucleotideColors.TryGetValue(Char.ToUpper(bioSymbol.Value), out brush)
? brush
: Brushes.Black));
}
public override Color GetSymbolColor(IBioSymbol symbol)
{
TextAttributes ta = new TextAttributes();
_options.GetAttributes(symbol, ref ta);
if (ta.Foreground is SolidColorBrush)
{
SolidColorBrush scb = (SolidColorBrush)ta.Foreground;
return(scb.Color);
}
return(Colors.Black);
}
public SSSymbolViewModel(IBioSymbol symbol, int index,
FontFamily fontFace, FontStyle fontStyle, FontWeight fontWeight, Brush color, double fontSize, double centerX, double centerY)
{
Symbol = symbol;
Index = index;
Color = color;
FontSize = fontSize;
Typeface = new Typeface(fontFace, fontStyle, fontWeight, FontStretches.Normal);
var renderedElement = new FormattedText(symbol.ToString().Substring(0, 1),
CultureInfo.GetCultureInfo("en-us"), FlowDirection.LeftToRight, Typeface, FontSize, Brushes.Black);
Width = renderedElement.WidthIncludingTrailingWhitespace;
Height = renderedElement.Height;
X = centerX - (0.5 * Width);
Y = centerY - (0.5 * renderedElement.Baseline);
}
private static IBioSymbol CharacterToBioSymbol(IBioValidator bioValidator, char ch)
{
IBioSymbol symbol = null;
switch (ch)
{
case '~':
case '|':
symbol = BioSymbol.None;
break;
case '-':
symbol = BioSymbol.Gap;
break;
default:
if (bioValidator.IsValid(ch))
{
symbol = new BioSymbol(BioSymbolType.Nucleotide, ch);
}
break;
}
return(symbol);
}
public override TextAttributes GetSequenceAttributes(IList <IBioSymbol> symbols, int start, out bool canMergeDuplicates)
{
TextAttributes defaultAttributes = new TextAttributes();
IBioSymbol symbol = symbols[start];
canMergeDuplicates = true;
if (_mainVm.SelectedReferenceSequences.Count > 0 &&
symbol.Type != BioSymbolType.None && symbol.Type != BioSymbolType.Missing)
{
if (_mainVm.SelectedReferenceSequences.Where(rs => rs.AlignedData == symbols).FirstOrDefault() == null)
{
canMergeDuplicates = false;
var rs = _mainVm.SelectedReferenceSequences.FirstOrDefault(seq => seq.AlignedData[start].Value == symbol.Value);
if (rs != null)
{
defaultAttributes.Background = rs.ReferenceSequenceColor;
}
}
}
_options.GetAttributes(symbol, ref defaultAttributes);
return(defaultAttributes);
}
/// <summary>
/// Indicates whether the current object is equal to another object of the same type.
/// </summary>
/// <returns>
/// true if the current object is equal to the <paramref name="other"/> parameter; otherwise, false.
/// </returns>
/// <param name="other">An object to compare with this object.
/// </param>
public bool Equals(IBioSymbol other)
{
return((other == null)
? false
: other.Value == _value);
}
/// <summary>
/// Sets the nucelotide attributes from the selected options
/// </summary>
/// <param name="bioSymbol"></param>
/// <param name="ta"></param>
public void GetAttributes(IBioSymbol bioSymbol, ref TextAttributes ta)
{
ta.Foreground = GetNucleotideColor(bioSymbol);
}
public abstract Color GetSymbolColor(IBioSymbol symbol);
public abstract Brush GetSymbolBrush(IBioSymbol symbol);
public bool IsValid(IBioSymbol bioSymbol)
{
return(IsValid(bioSymbol.Value) && _validTypes.Contains(bioSymbol.Type));
}
public NestedElementViewModel(NestedViewModel parent, IBioSymbol symbol, int index) : base(parent)
{
Symbol = symbol;
Index = index;
ComputePosition();
}
