/// <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 override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
// Has the whole UTR been deleted?
if (variant.Includes(this) && variant.VarType == Variant.VariantType.DEL)
{
variantEffects.AddEffect(variant, this, EffectType.UTR_5_DELETED, ""); // A UTR was removed entirely
return(true);
}
// Add distance
Transcript tr = (Transcript)FindParent(typeof(Transcript));
long distance = utrDistance(variant, tr);
VariantEffect variantEffect = new VariantEffect(variant);
variantEffect.Set(this, IntervalType, EffectTypeMethods.EffectDictionary[IntervalType], distance >= 0 ? distance + " bases from TSS" : "");
variantEffect.Distance = distance;
variantEffects.AddEffect(variantEffect);
// Start gained?
string gained = startGained(variant);
if (gained != "")
{
variantEffects.AddEffect(variant, this, EffectType.START_GAINED, gained);
}
return(true);
}
public override bool CreateVariantEffect(Variant variant, VariantEffects variantEffects)
{
if (!Intersects(variant))
{
return(false);
}
if (variant.Includes(this) && variant.VarType == Variant.VariantType.DEL)
{
variantEffects.AddEffectType(variant, this, EffectType.UTR_3_DELETED); // A UTR was removed entirely
return(true);
}
Transcript tr = (Transcript)FindParent(typeof(Transcript));
long distance = utrDistance(variant, tr);
VariantEffect variantEffect = new VariantEffect(variant);
variantEffect.Set(this, EffectType.UTR_3_PRIME, EffectTypeMethods.EffectDictionary[EffectType.UTR_3_PRIME], distance >= 0 ? distance + " bases from CDS" : "");
variantEffect.Distance = distance;
variantEffects.AddEffect(variantEffect);
return(true);
}
