/**
* 20 2 3 15 true 8
*
* */
public void Run(int cycleLenghtThreshold, int smoothingThreshold, int propagationRadius, int simplificationSteps, bool smooth, int dustThreshold, string outdir)
{
IList <int> sequence = _dataReader.ReadSequences(cycleLenghtThreshold); //读序列存在sequence中
_sequenceSmother.RemoveDust(ref sequence, dustThreshold); //将基因个数大于repeatThreshold的去除
_aBruijnGraph.ThreadSequence(sequence);
HashSet <int> splitNodeGlobal = new HashSet <int>();
for (int i = 0; i < simplificationSteps; i++)
{
bool shouldSmooth = false;
if (smooth)
{
shouldSmooth = i == simplificationSteps - 2;
}
if (simplificationSteps == 1)
{
shouldSmooth = true;//for test pass
}
HashSet <int> splitNodes;
HashSet <KeyValuePair <int, int> > edgesSet = _aBruijnGraph.Simplify(cycleLenghtThreshold, smoothingThreshold, shouldSmooth, out splitNodes);
if (edgesSet != null && edgesSet.Count != 0)
{
_colorTracker.AppendColorEdges(edgesSet); //把edgesSet里面的点存起来
}
if (splitNodes.Count != 0)
{
splitNodeGlobal.UnionWith(splitNodes); //取并集
}
}
IList <int> multiplicities;
IList <IList <int> > simplePaths = _aBruijnGraph.GetSimplePath(out multiplicities);
IDictionary <IList <int>, int> multiplicityBySimplePathList = new Dictionary <IList <int>, int>();
//sort the simplePath by its multiplicity
for (int i = 0; i < simplePaths.Count; i++)
{
multiplicityBySimplePathList.Add(simplePaths[i], multiplicities[i]); //key路径，value所对应的个数
}
((List <IList <int> >)simplePaths).Sort((a, b) => multiplicityBySimplePathList[a].CompareTo(multiplicityBySimplePathList[b]));
((List <int>)multiplicities).Sort();
//write the splitNodeGlobal
IList <int> modifiedSequence = _aBruijnGraph.GetModifiedSequence(); //获得修改后的sequence
IDictionary <int, int> colorByNodeID = _colorTracker.BackTracking(simplePaths); //_aBruijnGraph.PropagateSkeletonColor(simplePaths,propagationRadius);
IList <int> smoothColor = _sequenceSmother.Smooth(sequence, colorByNodeID);
IList <int> listColors = _sequenceSmother.ReStoreDust(ref sequence, smoothColor);
IList <IList <int> > blocksSign = _sequenceSmother.GetBlocksSign(modifiedSequence, simplePaths, 2);
IList <Node <int> > modifiedNodeSequence = _aBruijnGraph.GetModifiedNodeSequence();
IDictionary <Node <int>, Node <int> > workToSource = _aBruijnGraph.GetWorkToSource();
IDictionary <int, IList <IList <Node <int> > > > SynNodeListBySynId = _sequenceSmother.getSynNodeListBySynId(modifiedNodeSequence, simplePaths);
_dataWriter.WriteSplit(splitNodeGlobal, outdir);
_dataWriter.WriteSyntenyConsensus(multiplicities, simplePaths, SynNodeListBySynId, workToSource, outdir);
_dataWriter.WriteSequenceWithColor(sequence, listColors);
_dataWriter.WriteModifiedSequence(modifiedSequence);
_dataWriter.WriteBlocksSign(blocksSign, outdir);
}