/// <summary>
/// Show a string with overall effect
/// </summary>
/// <param name="shortFormat"></param>
/// <param name="showAaChange"></param>
/// <param name="showBioType"></param>
/// <param name="useSeqOntology"></param>
/// <param name="useFirstEffect"></param>
/// <returns></returns>
public string Effect(bool shortFormat, bool showAaChange, bool showBioType, bool useSeqOntology, bool useFirstEffect)
{
string effectString = "";
string codonEffect = CodonEffect(showAaChange, showBioType, useFirstEffect); // Codon effect
if (codonEffect != "")
{
effectString = codonEffect;
}
else if (EffectTypeMethods.IsIntergenic(EffectTypes) || EffectTypeMethods.IsIntron(EffectTypes) || EffectTypeMethods.IsSpliceSite(EffectTypes))
{
effectString = EffectTypeMethods.GetEffectTypeString(useFirstEffect, EffectTypes);
}
else if (Message != "")
{
effectString = EffectTypeMethods.GetEffectTypeString(useFirstEffect, EffectTypes) + ": " + Message;
}
else if (Marker == null)
{
// There are cases when no marker is associated (e.g. "Out of chromosome", "No such chromosome", etc.)
effectString = EffectTypeMethods.GetEffectTypeString(useFirstEffect, EffectTypes);
}
else
{
effectString = EffectTypeMethods.GetEffectTypeString(useFirstEffect, EffectTypes); // + ": " + marker.getId();
}
if (shortFormat)
{
effectString = effectString.Split(':')[0];
}
return(effectString);
}
public string GetGeneRegion()
{
EffectType eff = EffectTypeMethods.GetGeneRegion(GetEffectType());
if (eff == EffectType.TRANSCRIPT && EffectTypeMethods.IsExon(Marker, EffectTypes))
{
eff = EffectType.EXON;
}
return(eff.ToString());
}
public override string ToString()
{
StringBuilder sb = new StringBuilder();
sb.Append("Transcript : " + Transcript.ID + "\n");
sb.Append("Variant : " + Variant + "\n");
sb.Append("Codons : " + CodonsReference + "/" + CodonsAlternate + "\tnum: " + CodonStartNumber + "\tidx: " + CodonStartIndex + "\n");
sb.Append("Effects :\n");
foreach (VariantEffect veff in VariantEffects.Effects)
{
sb.Append(
"\t" + EffectTypeMethods.GetEffectTypeString(false, veff.EffectTypes) +
"\t" + veff.CodonsRef + "/" + veff.CodonsAlt +
"\t" + veff.ReferenceAA + "/" + veff.AlternateAA + "\n");
}
return(sb.ToString());
}
/// <summary>
/// Create a string for codon effect
/// @param showAaChange : If true, include codon change, biotype, etc.
/// </summary>
/// <param name="showAaChange"></param>
/// <param name="showBioType"></param>
/// <param name="useSeqOntology"></param>
/// <param name="useFirstEffect"></param>
/// <returns></returns>
private string CodonEffect(bool showAaChange, bool showBioType, bool useFirstEffect)
{
if ((Marker == null) || (CodonNum < 0))
{
return("");
}
if (!showAaChange)
{
return(EffectTypeMethods.GetEffectTypeString(useFirstEffect, EffectTypes));
}
StringBuilder sb = new StringBuilder();
sb.Append(EffectTypeMethods.GetEffectTypeString(useFirstEffect, EffectTypes));
sb.Append("(");
sb.Append(GetAaChange());
sb.Append(")");
return(sb.ToString());
}