public BufferedPositions Purge()
{
var copyOfBuffer = BufferedPositions;
BufferedPositions = BufferedPositions.CreatEmptyBufferedPositions();
return(copyOfBuffer);
}
} // used to find overlap genes for now
public PositionBuffer(ICodonInfoProvider codonInfoProvider, IIntervalForest <IGene> geneIntervalForest)
{
CodonInfoProvider = codonInfoProvider;
GeneIntervalForest = geneIntervalForest;
CurrentChromosome = new EmptyChromosome(string.Empty);
BufferedPositions = BufferedPositions.CreatEmptyBufferedPositions();
}
private void ResetBuffer(ISimplePosition simplePosition, bool recomposable)
{
var functionBlockRanges = recomposable ? new List <int> {
CodonInfoProvider.GetLongestFunctionBlockDistance(simplePosition)
} : new List <int>();
BufferedPositions = new BufferedPositions(new List <ISimplePosition> {
simplePosition
}, new List <bool> {
recomposable
}, functionBlockRanges);
CurrentChromosome = simplePosition.Chromosome;
}
public BufferedPositions AddPosition(ISimplePosition simplePosition)
{
bool recomposable = IsRecomposable(simplePosition);
bool isPositionWithinRange = !simplePosition.Chromosome.IsEmpty() && PositionWithinRange(simplePosition);
if (isPositionWithinRange)
{
BufferedPositions.SimplePositions.Add(simplePosition);
BufferedPositions.Recomposable.Add(recomposable);
if (recomposable)
{
UpdateFunctionBlockRanges(simplePosition);
}
return(BufferedPositions.CreatEmptyBufferedPositions());
}
var copyOfBuffer = BufferedPositions;
ResetBuffer(simplePosition, recomposable);
return(copyOfBuffer);
}
internal IEnumerable <ISimplePosition> GenerateOutput(BufferedPositions bufferedPositions)
{
if (bufferedPositions.SimplePositions.Count == 0)
{
return(new List <ISimplePosition>()); // nothing to output
}
var recomposablePositions = bufferedPositions.GetRecomposablePositions();
if (recomposablePositions.Count <= 1)
{
return(bufferedPositions.SimplePositions); // nothing to recompose
}
var functionBlockRanges = bufferedPositions.FunctionBlockRanges;
var recomposedPositions = _variantGenerator.Recompose(recomposablePositions, functionBlockRanges).ToList();
if (recomposedPositions.Count == 0)
{
return(bufferedPositions.SimplePositions); // nothing has been recomposed
}
return(bufferedPositions.SimplePositions.Concat(recomposedPositions).OrderBy(x => x.Start));
}
