/// <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); }