/// <summary>
/// Apply a Variant to a marker. Variant is a duplication
/// </summary>
/// <param name="variant"></param>
/// <returns></returns>
protected Interval ApplyDup(Variant variant)
{
Interval m = new Interval(this);
if (variant.OneBasedEnd < m.OneBasedStart)
{
// Duplication before marker start? => Adjust both coordinates
long lenChange = variant.LengthChange();
m.OneBasedStart += lenChange;
m.OneBasedEnd += lenChange;
}
else if (variant.Includes(m))
{
// Duplication includes whole marker? => Adjust both coordinates
long lenChange = variant.LengthChange();
m.OneBasedStart += lenChange;
m.OneBasedEnd += lenChange;
}
else if (m.Includes(variant))
{
// Duplication included in marker? => Adjust end coordinate
m.OneBasedEnd += variant.LengthChange();
}
else if (variant.Intersects(m))
{
// Duplication includes part of marker? => Adjust end
m.OneBasedEnd += variant.IntersectSize(m);
}
else
{
// Duplication after end, no effect on marker coordinates
}
return(m);
}
/// <summary>
/// Apply a Variant to a marker. Variant is a deletion
/// </summary>
/// <param name="variant"></param>
/// <returns></returns>
protected Interval ApplyDel(Variant variant)
{
Interval m = new Interval(this);
if (variant.OneBasedEnd < m.OneBasedStart)
{
// Deletion before start: Adjust coordinates
long lenChange = variant.LengthChange();
m.OneBasedStart += lenChange;
m.OneBasedEnd += lenChange;
}
else if (variant.Includes(m))
{
// Deletion completely includes this marker => The whole marker deleted
return(null);
}
else if (m.Includes(variant))
{
// This marker completely includes the deletion, but deletion does not include
// marker. Marker is shortened (i.e. only 'end' coordinate needs to be updated)
m.OneBasedEnd += variant.LengthChange();
}
else
{
// Variant is partially included in this marker.
// This is treated as three different type of deletions:
// 1- One after the marker
// 2- One inside the marker
// 3- One before the marker
// Note that type 1 and 3 cannot exists at the same time, otherwise the
// deletion would fully include the marker (previous case)
// Part 1: Deletion after the marker
if (m.OneBasedEnd < variant.OneBasedEnd)
{
// Actually this does not affect the coordinates, so we don't care about this part
}
// Part 2: Deletion matching the marker (intersection)
long istart = Math.Max(variant.OneBasedStart, m.OneBasedStart);
long iend = Math.Min(variant.OneBasedEnd, m.OneBasedEnd);
if (iend < istart)
{
throw new ArgumentOutOfRangeException("This should never happen!");
} // Sanity check
m.OneBasedEnd -= (iend - istart + 1); // Update end coordinate
// Part 3: Deletion before the marker
if (variant.OneBasedStart < m.OneBasedEnd)
{
// Update coordinates shifting the marker to the left
long delta = m.OneBasedStart - variant.OneBasedStart;
m.OneBasedStart -= delta;
m.OneBasedEnd -= delta;
}
}
return(m);
}
/// <summary>
/// Apply a Variant to a marker. Variant is an insertion
/// </summary>
/// <param name="variant"></param>
/// <returns></returns>
protected Interval ApplyIns(Variant variant)
{
Interval m = new Interval(this);
if (variant.OneBasedStart < m.OneBasedStart)
{
// Insertion point before marker start? => Adjust both coordinates
long lenChange = variant.LengthChange();
m.OneBasedStart += lenChange;
m.OneBasedEnd += lenChange;
}
else if (variant.OneBasedStart <= m.OneBasedEnd)
{
// Insertion point after start, but before end? => Adjust end coordinate
m.OneBasedEnd += variant.LengthChange();
}
else
{
// Insertion point after end, no effect on marker coordinates
}
return(m);
}