/// <summary>
/// Thread a sequence of integer through an ABruijn Graph
/// </summary>
/// <param name="sequence">sequence wanted to thread</param>
public void ThreadSequence(IList <int> sequence)
{
_sequence = sequence;
_workingSequence.AddList(sequence); //把List转换成单链表
_sourceSequence.AddList(sequence); //把List转换成单链表
IList <Node <int> > _workingMembers = _workingSequence.GetMembers();
IList <Node <int> > _sourceMembers = _sourceSequence.GetMembers();
IList <IList <Node <int> > > sourceSequencesChrs = new List <IList <Node <int> > >(); //获得原序列对应的坐标
IList <Node <int> > chr = new List <Node <int> >();
for (int i = 1; i < _sourceMembers.Count - 1; i++)
{
if (_sourceMembers[i].Value >= 0)
{
chr.Add(_sourceMembers[i]);
}
else
{
sourceSequencesChrs.Add(chr);
chr = new List <Node <int> >();
while (i < _sourceMembers.Count && _sourceMembers[i].Value < 0)
{
i++;
}
i--;
}
}
sourceSequencesChrs.Add(chr); //拆分成Chrs
for (int i = 0; i < sourceSequencesChrs.Count; i++)
{
for (int j = 0; j < sourceSequencesChrs[i].Count; j++)
{
_nodeToIndex.Add(sourceSequencesChrs[i][j], new Pair <int>(i, j));
}
}
for (int i = 0; i < _workingMembers.Count; i++) //生成map
{
_workToSource.Add(_workingMembers[i], _sourceMembers[i]);
}
_graph = GenerateGraph(_workingSequence);
_graphTool.setWorkToSource(_workToSource);
}
/// <summary>
/// Generate a mapping from NodeValue to all nodes that has that value.
/// </summary>
/// <param name="sequence">An Eulerian sequences of programmed Nodes</param>
/// <returns></returns>
private static IDictionary <int, IList <Node <int> > > GenerateGraph(SimpleLinkList <int> sequence)
{
IDictionary <int, IList <Node <int> > > nodeListByValue = new Dictionary <int, IList <Node <int> > >();
foreach (Node <int> node in sequence.GetMembers()) //反射获取sequence的成员是个list的keyValue对,遍历这个list
{
if (nodeListByValue.ContainsKey(node.Value)) //键是node的值，也就是sequence的值，就是基因
{
nodeListByValue[node.Value].Add(node); //字典把相同基因，加入list变成一条链
}
else
{
nodeListByValue.Add(node.Value, new List <Node <int> > {
node
});
}
}
Console.Out.WriteLine("Nodes: " + nodeListByValue.Count); //统计一共多少基因
return(nodeListByValue);
}
