/// <summary>
/// Can we add an effectType to the previous variatnEffect?
/// </summary>
/// <param name="variant"></param>
/// <param name="marker"></param>
/// <returns>true if transcript IDs and variant's genotypes match (i.e. we can add effectType)</returns>
private bool CanAddType(Variant variant, Interval marker)
{
VariantEffect veff = Get();
if (veff == null || veff.Variant == null)
{
return(false);
}
// Do genotypes match?
var gt = veff.Variant.Genotype;
var vgt = variant.Genotype;
if (((vgt != null) ^ (gt != null)) || // One null and one non-null?
((vgt != null) && (gt != null) && !variant.Genotype.Equals(variant.Genotype)) // Both non-null, but different?
)
{
return(false);
}
// Do transcripts match?
Transcript trMarker = (Transcript)marker.FindParent(typeof(Transcript));
Transcript tr = veff.GetTranscript();
if (tr == null || trMarker == null)
{
return(false);
}
return(tr.ID == trMarker.ID);
}
/// <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);
}
/// <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);
}
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 void SetMarker(Interval marker)
{
VariantEffect veff = Get();
if (veff != null)
{
veff.SetMarker(marker);
}
}
public bool HasMarker()
{
VariantEffect veff = Get();
if (veff == null)
{
return(false);
}
return(veff.Marker != null);
}
/// <summary>
/// Add an error or warning
/// </summary>
/// <param name="variant"></param>
/// <param name="errwarn"></param>
public void AddErrorWarning(Variant variant, ErrorWarningType errwarn)
{
VariantEffect veff = Get();
if (veff != null)
{
veff.AddErrorWarningInfo(errwarn);
}
else
{
veff = new VariantEffect(variant);
veff.AddErrorWarningInfo(errwarn);
AddEffect(veff);
}
}
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);
}
/// <summary>
/// Add an effect
/// </summary>
/// <param name="variantEffect"></param>
public void AddEffect(VariantEffect variantEffect)
{
Effects.Add(variantEffect);
}
