public bool Subset(NullableInterval <T> other)
{
return
((!this.min.HasValue || (other.min.HasValue && this.min.Value.CompareTo(other.min.Value) <= 0))
&&
(!this.max.HasValue || (other.max.HasValue && other.max.Value.CompareTo(this.max.Value) <= 0)));
}
public NullableInterval <T> Union(NullableInterval <T> other)
{
T?minVal = !min.HasValue || !other.min.HasValue ? (T?)null : min.Value.CompareTo(other.min.Value) > 0 ? other.min.Value : min.Value;
T?maxVal = !max.HasValue || !other.max.HasValue ? (T?)null : max.Value.CompareTo(other.max.Value) < 0 ? other.max.Value : max.Value;
return(new NullableInterval <T>(minVal, maxVal));
}
public bool Overlaps(NullableInterval <T> other)
{
return(!(
(max.HasValue && other.min.HasValue && max.Value.CompareTo(other.min.Value) <= 0) ||
(other.max.HasValue && min.HasValue && other.max.Value.CompareTo(min.Value) <= 0)
));
}
private static void AssignExtended(string transcriptReferenceAllele, string transcriptAlternateAllele,
NullableInterval cdsInterval, NullableInterval proteinInterval, ISequence codingSequence, out string refCodons, out string altCodons)
{
refCodons = null;
altCodons = null;
if (cdsInterval.Start == null || cdsInterval.End == null || proteinInterval.Start == null ||
proteinInterval.End == null)
{
return;
}
int aminoAcidStart = proteinInterval.Start.Value * 3 - 2;
int aminoAcidEnd = proteinInterval.End.Value * 3;
int prefixLen = cdsInterval.Start.Value - aminoAcidStart;
int suffixLen = aminoAcidEnd - cdsInterval.End.Value;
int start1 = aminoAcidStart - 1;
int start2 = aminoAcidEnd - suffixLen;
int maxSuffixLen = codingSequence.Length - start2;
var atTailEnd = false;
if (suffixLen > maxSuffixLen)
{
suffixLen = maxSuffixLen;
atTailEnd = true;
}
if (suffixLen > maxSuffixLen)
{
suffixLen = maxSuffixLen;
}
string prefix = start1 + prefixLen < codingSequence.Length
? codingSequence.Substring(start1, prefixLen).ToLower()
: "AAA";
string suffix = suffixLen > 0
? codingSequence.Substring(start2, suffixLen).ToLower()
: "";
var needExtend = !atTailEnd && !Codons.IsTriplet(prefixLen + suffixLen + transcriptAlternateAllele.Length);
var extendedLen = (maxSuffixLen - suffixLen) > 45 ? 45 : (maxSuffixLen - suffixLen) / 3 * 3;
if (needExtend)
{
suffix = codingSequence.Substring(start2, suffixLen + extendedLen);
}
refCodons = Codons.GetCodon(transcriptReferenceAllele, prefix, suffix);
altCodons = Codons.GetCodon(transcriptAlternateAllele, prefix, suffix);
}
public NullableInterval <T>?Intersection(NullableInterval <T> other)
{
T?minVal = min.HasValue && other.min.HasValue ? (min.Value.CompareTo(other.min.Value) > 0 ? min.Value : other.min.Value) : min ?? other.min;
T?maxVal = max.HasValue && other.max.HasValue ? (max.Value.CompareTo(other.max.Value) < 0 ? max.Value : other.max.Value) : max ?? other.max;
if (minVal.HasValue && maxVal.HasValue && minVal.Value.CompareTo(maxVal.Value) >= 0)
{
return(null);
}
return(new NullableInterval <T>(minVal, maxVal));
}
public int CompareTo(NullableInterval <T> other)
{
if (min == null && other.min == null)
{
return(0);
}
var temp = min.HasValue.CompareTo(other.min.HasValue);
if (temp != 0)
{
return(temp);
}
#pragma warning disable CS8629 // Nullable value type may be null. CSBUG
return(min.Value.CompareTo(other.min.Value));
#pragma warning restore CS8629 // Nullable value type may be null.
}
private static string GetNullablePositionRange(NullableInterval interval)
{
if (interval.Start == null && interval.End == null)
{
return(null);
}
if (interval.Start == null)
{
return("?-" + interval.End.Value);
}
if (interval.End == null)
{
return(interval.Start.Value + "-?");
}
var start = interval.Start.Value;
var end = interval.End.Value;
if (start > end)
{
Swap.Int(ref start, ref end);
}
return(start == end?start.ToString(CultureInfo.InvariantCulture) : start + "-" + end);
}
public bool Equals(NullableInterval <T> other)
{
return(other.min.Equals(min) && other.max.Equals(max));
}
