/// <summary>
/// Initializes a new instance of the ParallelDeNovoAssembler class.
/// Sets thresholds to default values.
/// Also initializes instances implementing different steps
/// </summary>
public ParallelDeNovoAssembler()
{
// Initialize to default here.
// Values set to -1 here will be reset based on input sequences.
_kmerLength = -1;
_dangleThreshold = -1;
_redundantPathLengthThreshold = -1;
_sequenceReads = new List <ISequence>();
// Contig and scaffold Builder are required modules. Set this to default.
_contigBuilder = new SimplePathContigBuilder();
// Default values for parameters used in building scaffolds.
ScaffoldRedundancy = 2;
Depth = 10;
AllowKmerLengthEstimation = true;
}
/// <summary>
/// Dispose field instances.
/// </summary>
/// <param name="disposeManaged">If disposeManaged equals true, clean all resources.</param>
protected virtual void Dispose(bool disposeManaged)
{
if (disposeManaged)
{
if (this.scaffoldBuilder != null)
{
this.scaffoldBuilder.Dispose();
}
this.graph = null;
this.sequenceReads = null;
this.danglingLinksPurger = null;
this.redundantPathsPurger = null;
this.contigBuilder = null;
this.scaffoldBuilder = null;
}
}
/// <summary>
/// Dispose field instances
/// </summary>
/// <param name="disposeManaged">If disposeManaged equals true, clean all resources</param>
protected virtual void Dispose(bool disposeManaged)
{
if (disposeManaged)
{
if (_graph != null)
{
_graph.Dispose();
}
if (_scaffoldBuilder != null)
{
_scaffoldBuilder.Dispose();
}
_graph = null;
_sequenceReads = null;
_danglingLinksPurger = null;
_redundantPathsPurger = null;
_contigBuilder = null;
_scaffoldBuilder = null;
}
}
