/// <summary>
/// Simplify the graph by removing the cycles and smoothing techniques. On the way of removing the cycle, if any nodes
/// disappear from the graph, the edge color mapping should be return back
/// </summary>
/// <param name="cycleLenghtThreshold">The maximum cycle length that can be re-route</param>
/// <param name="smoothingThreshold">the maximum length of the simple path that can be splitted</param>
/// <param name="shouldSmooth">If we should smooth the graph</param>
/// <param name="splitNodes">Split nodes Set</param>
/// <returns>Color edge Set</returns>
public HashSet <KeyValuePair <int, int> > Simplify(int cycleLenghtThreshold, int smoothingThreshold, bool shouldSmooth, out HashSet <int> splitNodes)
{
splitNodes = new HashSet <int>();
HashSet <KeyValuePair <int, int> > colorEdges = new HashSet <KeyValuePair <int, int> >();
IDictionary <Pair <int>, int> multiplicityByEdge = GenerateMultiplicityByEdge(_workingSequence.GetMembersValue()); //用字典记录有多少边,key是边，value是个数
Console.Out.WriteLine("Number of edges: " + multiplicityByEdge.Count);
IList <Pair <int> > weakEdges = _graphTool.GetWeakEdges(multiplicityByEdge); //找到循环
while (weakEdges.Count != 0)
{
Pair <int> currentWeakEdge = weakEdges[0];
weakEdges.RemoveAt(0);
HashSet <KeyValuePair <int, int> > suspectedWeakEdges = _graphTool.ReSolveCycle(currentWeakEdge, cycleLenghtThreshold, ref _graph); //去除循环，返回颜色边界
if (suspectedWeakEdges != null)
{
foreach (KeyValuePair <int, int> edge in suspectedWeakEdges) //标记所有颜色边界
{
if (!colorEdges.Contains(edge))
{
colorEdges.Add(edge);
}
}
}
/*
* foreach (pair<int> edge in suspectedweakedges)
* weakedges.insert(0, edge);
*/
}
Console.Out.WriteLine("Nodes:" + _graph.Keys.Count);
//平滑需要
if (shouldSmooth)
{
//PRocess tandem Repeat A-A
_graphTool.ProcessTandem(ref _workingSequence, ref _graph);
//smoothing step
IDictionary <Pair <int>, int> newMultiplicityByEdge =
GenerateMultiplicityByEdge(_workingSequence.GetMembersValue()); //返回一个字典，key是一个边的pair，value是边的个数
IDictionary <int, IList <int> > graphLinkStructure =
GenerateGraphLinkStructure(_workingSequence.GetMembersValue()); //返回一个字典，key是基因，value是这个基因所有邻居的列表
IDictionary <int, int> multiplicityByNodeID = GetMultiplicityByNodeID(); //返回一个字典，key是基因，value是基因的个数
IList <IList <int> > simplePaths = _graphTool.GetSimplePath(graphLinkStructure, newMultiplicityByEdge, multiplicityByNodeID); //获得多条简单路径
foreach (IList <int> path in simplePaths)
{
if (path.Count < smoothingThreshold && _graph[path[0]].Count > 1) //只有小于2个点的基因才可以平滑
{
IList <int> smooth = _graphTool.Smooth(path, ref _graph); //path可分才返回path，不然返回null
foreach (int i in smooth)
{
if (!splitNodes.Contains(i))
{
splitNodes.Add(i);
}
}
}
}
//ProcessPalindrome(_workingSequence);
_graphTool.ProcessPalindrome(ref _workingSequence, ref _graph);
}
return(colorEdges);
}
/// <summary>
/// Return the list nodes in the modified sequence
/// </summary>
/// <returns></returns>
public IList <int> GetModifiedSequence()
{
return(_workingSequence.GetMembersValue());
}
