/// <summary>
/// Compare to another variantEffect
/// </summary>
/// <param name="variantEffect"></param>
/// <returns></returns>
public int CompareTo(VariantEffect varEffOther)
{
// Sort by impact
int comp = GetEffectImpact().CompareTo(varEffOther.GetEffectImpact());
if (comp != 0)
{
return(comp);
}
// Sort by effect
comp = GetEffectType().CompareTo(varEffOther.GetEffectType());
if (comp != 0)
{
return(comp);
}
//---
// Transcript based comparisons
//---
Transcript trThis = GetTranscript();
Transcript trOther = varEffOther.GetTranscript();
// This transcript data
//int tslThis = TranscriptSupportLevel.TSL_NULL_VALUE;
//int canonThis = 0;
long startThis = 0;
long endThis = 0;
string idThis = null;
string chrThis = null;
if (trThis != null)
{
//tslThis = TranscriptSupportLevel.tsl(trThis.getTranscriptSupportLevel());
//canonThis = trThis.isCanonical() ? 1 : 0;
idThis = trThis.ID;
chrThis = trThis.ChromosomeID;
startThis = trThis.OneBasedStart;
endThis = trThis.OneBasedEnd;
}
// Other transcript data
//int tslOther = TranscriptSupportLevel.TSL_NULL_VALUE;
//int canonOther = 0;
long startOther = 0;
long endOther = 0;
string idOther = null;
string chrOther = null;
if (trOther != null)
{
//tslOther = TranscriptSupportLevel.tsl(trOther.getTranscriptSupportLevel());
//canonOther = trOther.isCanonical() ? 1 : 0;
idOther = trOther.ID;
chrOther = trOther.ChromosomeID;
startOther = trOther.OneBasedStart;
endOther = trOther.OneBasedEnd;
}
// Compare by TSL: Smaller first
//comp = tslThis - tslOther;
//if (comp != 0) return comp;
// Compare by canonical transcript: Larger first
//comp = canonOther - canonThis;
//if (comp != 0) return comp;
// Compare genomic coordinate
comp = CompareNull(chrThis, chrOther);
if (comp != 0)
{
return(comp);
}
comp = startThis.CompareTo(startOther);
if (comp != 0)
{
return(comp);
}
comp = endThis.CompareTo(endOther);
if (comp != 0)
{
return(comp);
}
// Compare IDs
comp = CompareNull(idThis, idOther);
if (comp != 0)
{
return(comp);
}
//---
// Marker based comparisons
//---
Interval mThis = Marker;
Interval mOther = varEffOther.Marker;
startThis = 0;
endThis = 0;
idThis = null;
chrThis = null;
if (Marker != null)
{
//idThis = mThis.getId();
chrThis = mThis.ChromosomeID;
startThis = mThis.OneBasedStart;
endThis = mThis.OneBasedEnd;
}
startOther = 0;
endOther = 0;
idOther = null;
chrOther = null;
if (mOther != null)
{
//idOther = mOther.getId();
chrOther = mOther.ChromosomeID;
startOther = mOther.OneBasedStart;
endOther = mOther.OneBasedEnd;
}
// Compare genomic coordinate
comp = CompareNull(chrThis, chrOther);
if (comp != 0)
{
return(comp);
}
comp = startThis.CompareTo(startOther);
if (comp != 0)
{
return(comp);
}
comp = endThis.CompareTo(endOther);
if (comp != 0)
{
return(comp);
}
// Compare IDs
comp = CompareNull(idThis, idOther);
if (comp != 0)
{
return(comp);
}
//---
// Variant based comparison
//---
return(Variant.CompareTo(varEffOther.Variant));
}
