/// <summary>
/// loads the transcript cache
/// </summary>
private static void LoadTranscriptCache(Stream stream, int numRefSeqs,
out IIntervalForest <Transcript> transcriptIntervalForest)
{
GlobalCache cache;
using (var reader = new GlobalCacheReader(stream)) cache = reader.Read();
transcriptIntervalForest = IntervalArrayFactory.CreateIntervalForest(cache.Transcripts, numRefSeqs);
}
public void Load(string ucscReferenceName, IChromosomeRenamer renamer)
{
if (_ciDirs.Count == 0 || ucscReferenceName == _currentUcscReferenceName)
{
return;
}
var intervals = GetIntervals(ucscReferenceName);
_intervalForest = IntervalArrayFactory.CreateIntervalArray(intervals, renamer);
_hasIntervals = !(_intervalForest is NullIntervalSearch <ICustomInterval>);
_currentUcscReferenceName = ucscReferenceName;
}
public MockCustomIntervalProvider(Stream stream, ChromosomeRenamer renamer)
{
var intervals = new List <ICustomInterval>();
using (var reader = new CustomIntervalReader(stream))
{
while (true)
{
var interval = reader.GetNextCustomInterval();
if (interval == null)
{
break;
}
intervals.Add(interval);
}
}
_hasIntervals = intervals.Count > 0;
_intervalForest = IntervalArrayFactory.CreateIntervalArray(intervals, renamer);
}
public IIntervalForest <ISupplementaryInterval> GetIntervalForest(IChromosomeRenamer renamer)
{
return(IntervalArrayFactory.CreateIntervalArray(GetSupplementaryIntervals(renamer), renamer));
}
public void CreateIntervalForest_NullIntervals()
{
var intervalForest = IntervalArrayFactory.CreateIntervalForest<IRegulatoryRegion>(null, 17);
Assert.True(intervalForest is NullIntervalSearch<IRegulatoryRegion>);
}
public void CreateIntervalForest_WithIntervals()
{
var intervalForest = IntervalArrayFactory.CreateIntervalForest(_regulatoryRegions, 17);
var observedResult = intervalForest.OverlapsAny(_chr11.Index, 160, 170);
Assert.True(observedResult);
}
/// <summary>
/// constructor
/// </summary>
public MockCustomIntervalProvider(List <ICustomInterval> intervals, ChromosomeRenamer renamer)
{
_hasIntervals = intervals.Count > 0;
_intervalForest = IntervalArrayFactory.CreateIntervalArray(intervals, renamer);
}
public static IIntervalForest <Transcript> GetIntervalForest(Transcript[] transcripts, int numRefSeqs)
{
return(transcripts == null
? null
: IntervalArrayFactory.CreateIntervalForest(transcripts, numRefSeqs));
}
