public static IEnumerable <Coverage> SplitTrackMatchedRegions(this IEnumerable <MatchedWith> entries,
double queryLength, double trackLength, double fingerprintLength, double permittedGap)
{
var list = new List <Coverage>();
var ordered = entries.OrderBy(_ => _.TrackMatchAt).ToList();
if (!ordered.Any())
{
return(list);
}
var stack = new Stack <MatchedWith>();
stack.Push(ordered.First());
foreach (var matchedWith in ordered.Skip(1))
{
var prev = stack.Peek();
var trackGap = SubFingerprintsToSeconds.GapLengthToSeconds(matchedWith.TrackMatchAt, prev.TrackMatchAt, fingerprintLength);
var queryGap = SubFingerprintsToSeconds.GapLengthToSeconds(matchedWith.QueryMatchAt, prev.QueryMatchAt, fingerprintLength);
if (trackGap > permittedGap || queryGap > permittedGap)
{
list.AddRange(GetMatchedWithsFromStack(stack, queryLength, trackLength, fingerprintLength, permittedGap));
stack = new Stack <MatchedWith>();
}
stack.Push(matchedWith);
}
list.AddRange(GetMatchedWithsFromStack(stack, queryLength, trackLength, fingerprintLength, permittedGap));
return(list);
}
private static double CalculateExactQueryLength(IEnumerable <HashedFingerprint> hashedFingerprints, FingerprintConfiguration fingerprintConfiguration)
{
double startsAt = double.MaxValue, endsAt = double.MinValue;
foreach (var hashedFingerprint in hashedFingerprints)
{
startsAt = System.Math.Min(startsAt, hashedFingerprint.StartsAt);
endsAt = System.Math.Max(endsAt, hashedFingerprint.StartsAt);
}
return(SubFingerprintsToSeconds.AdjustLengthToSeconds(endsAt, startsAt, fingerprintConfiguration.FingerprintLengthInSeconds));
}
public static double QueryLength(this IEnumerable <HashedFingerprint> hashedFingerprints, FingerprintConfiguration configuration)
{
double startsAt = double.MaxValue, endsAt = double.MinValue;
foreach (var hashedFingerprint in hashedFingerprints)
{
startsAt = System.Math.Min(startsAt, hashedFingerprint.StartsAt);
endsAt = System.Math.Max(endsAt, hashedFingerprint.StartsAt);
}
return(SubFingerprintsToSeconds.MatchLengthToSeconds(endsAt, startsAt, configuration.FingerprintLengthInSeconds));
}
private static IEnumerable <Gap> FindGaps(this IEnumerable <Tuple <uint, float> > entries, double permittedGap, double fingerprintLength)
{
Tuple <uint, float>[] matches = entries.ToArray();
for (int i = 1; i < matches.Length; ++i)
{
float startsAt = matches[i - 1].Item2;
float endsAt = matches[i].Item2;
float gap = (float)SubFingerprintsToSeconds.GapLengthToSeconds(endsAt, startsAt, fingerprintLength);
bool sequenceNumberIncremented = matches[i].Item1 - matches[i - 1].Item1 > 1;
float start = endsAt - gap;
if (!(endsAt <= start) && gap > permittedGap && sequenceNumberIncremented)
{
yield return(new Gap(start, endsAt, false));
}
}
}