public void Set(Interval marker, EffectType effectType, EffectImpact effectImpact, string message)
{
SetMarker(marker); // Use setter because it takes care of warnings
SetEffectType(effectType);
SetEffectImpact(effectImpact);
Message = message;
}
/// <summary>
/// One or more exons fully included (no partial overlap)
/// </summary>
private void exons()
{
Interval cdsMarker = null;
if (Transcript.IsProteinCoding())
{
cdsMarker = Transcript.CdsMarker();
}
foreach (Exon ex in Transcript.Exons)
{
if (Variant.Intersects(ex))
{
EffectImpact impact = EffectImpact.LOW;
// Is the variant affecting a coding part of the exon?
// If so, then this is a HIGH impact effect.
if (cdsMarker != null && Variant.Intersect(ex).Intersects(cdsMarker))
{
impact = EffectImpact.HIGH;
}
// Is the whole exon inverted or just part of it?
EffectType effType = Variant.Includes(ex) ? EffectType.EXON_INVERSION : EffectType.EXON_INVERSION_PARTIAL;
EffectNoCodon(ex, effType, impact);
}
}
}
protected override void Exons()
{
if (BeyondTranscript())
{
// Is the effect of a duplication beyond transcript's end?
// Then it probably does not have much impact
EffectImpact impact = coding ? EffectImpact.LOW : EffectImpact.MODIFIER;
if (exonFull > 0)
{
EffectNoCodon(Transcript, EffectType.EXON_DUPLICATION, impact);
}
if (exonPartial > 0)
{
EffectNoCodon(Transcript, EffectType.EXON_DUPLICATION_PARTIAL, impact);
}
return;
}
if (coding)
{
ExonsCoding();
}
else
{
ExonsNoncoding();
}
}
/// <summary>
/// Add an effect
/// </summary>
/// <param name="marker"></param>
/// <param name="effectType"></param>
/// <param name="effectImpact"></param>
/// <param name="codonsOld"></param>
/// <param name="codonsNew"></param>
/// <param name="codonNum"></param>
/// <param name="codonIndex"></param>
/// <param name="allowReplace"></param>
/// <returns></returns>
private VariantEffect Effect(Interval marker, EffectType effectType, EffectImpact effectImpact, string codonsOld, string codonsNew, int codonNum, int codonIndex, bool allowReplace)
{
// Create and add variant affect
long cDnaPos = Transcript.BaseNumber2MRnaPos(Variant.OneBasedStart);
VariantEffect varEff = new VariantEffect(Variant, marker, effectType, effectImpact, codonsOld, codonsNew, codonNum, codonIndex, cDnaPos);
VariantEffects.AddEffect(varEff);
// Are there any additional effects? Sometimes a new effect arises from setting codons (e.g. FRAME_SHIFT disrupts a STOP codon)
EffectType addEffType = AdditionalEffect(codonsOld, codonsNew, codonNum, codonIndex);
if (addEffType != EffectType.NONE && addEffType != effectType)
{
if (allowReplace && addEffType.CompareTo(effectType) < 0)
{
// Replace main effect (using default impact)
varEff.SetEffect(addEffType);
}
else
{
// Add effect to list (using default impact)
varEff.AddEffect(addEffType);
}
}
return(varEff);
}
/// <summary>
/// Add an effect
/// </summary>
/// <param name="variant"></param>
/// <param name="marker"></param>
/// <param name="effectType"></param>
/// <param name="effectImpact"></param>
/// <param name="message"></param>
private void AddEffect(Variant variant, Interval marker, EffectType effectType, EffectImpact effectImpact, String message)
{
VariantEffect effNew = new VariantEffect(variant);
effNew.Set(marker, effectType, effectImpact, message);
AddEffect(effNew);
}
public void SetEffectImpact(EffectImpact effectImpact)
{
EffectImpacts.Clear();
EffectImpacts.Add(effectImpact);
}
public VariantEffect(Variant variant, Interval marker, EffectType effectType, EffectImpact effectImpact, string codonsOld, string codonsNew, int codonNum, int codonIndex, long cDnaPos)
{
Variant = variant;
EffectTypes = new List <EffectType>();
EffectImpacts = new List <EffectImpact>();
Set(marker, effectType, effectImpact, "");
SetCodons(codonsOld, codonsNew, codonNum, codonIndex);
CDnaPos = cDnaPos;
}
protected VariantEffect EffectNoCodon(Interval marker, EffectType effectType, EffectImpact effectImpact)
{
return(Effect(marker, effectType, effectImpact, "", "", -1, -1, false));
}
