public static IIntervalForest <ISupplementaryInterval> CreateIntervalArray(
IEnumerable <ISupplementaryInterval> intervals, IChromosomeRenamer renamer)
{
if (intervals == null)
{
return(new NullIntervalSearch <ISupplementaryInterval>());
}
var numRefSeqs = renamer.NumRefSeqs;
var intervalLists = new List <IntervalArray <ISupplementaryInterval> .Interval> [numRefSeqs];
for (var i = 0; i < numRefSeqs; i++)
{
intervalLists[i] = new List <IntervalArray <ISupplementaryInterval> .Interval>();
}
foreach (var interval in intervals)
{
ushort index = renamer.GetReferenceIndex(interval.ReferenceName);
if (index == ChromosomeRenamer.UnknownReferenceIndex)
{
continue;
}
intervalLists[index].Add(new IntervalArray <ISupplementaryInterval> .Interval(interval.Start, interval.End, interval));
}
// create the interval arrays
var refIntervalArrays = new IntervalArray <ISupplementaryInterval> [numRefSeqs];
for (var i = 0; i < numRefSeqs; i++)
{
var sortedIntervals = intervalLists[i].OrderBy(x => x.Begin).ThenBy(x => x.End).ToArray();
refIntervalArrays[i] = new IntervalArray <ISupplementaryInterval>(sortedIntervals);
}
return(new IntervalForest <ISupplementaryInterval>(refIntervalArrays));
}
public static IIntervalForest <T> CreateIntervalForest <T>(T[] refIntervals, int numRefSeqs)
where T : ReferenceAnnotationInterval
{
if (refIntervals == null)
{
return(new NullIntervalSearch <T>());
}
//Array.Sort(refIntervals);
var intervalLists = new List <IntervalArray <T> .Interval> [numRefSeqs];
for (var i = 0; i < numRefSeqs; i++)
{
intervalLists[i] = new List <IntervalArray <T> .Interval>();
}
foreach (var transcript in refIntervals)
{
//debugging to see if both ensembl and refseq transcripts come up
//var Transcript = transcript as Transcript;
//if (Transcript?.TranscriptSource == TranscriptDataSource.RefSeq)
// Console.WriteLine("found refseq transcript");
intervalLists[transcript.ReferenceIndex].Add(
new IntervalArray <T> .Interval(transcript.Start, transcript.End, transcript));
}
// create the interval arrays
var refIntervalArrays = new IntervalArray <T> [numRefSeqs];
for (var i = 0; i < numRefSeqs; i++)
{
refIntervalArrays[i] = new IntervalArray <T>(intervalLists[i].ToArray());
}
return(new IntervalForest <T>(refIntervalArrays));
}
