/// <summary>
/// Propagate the color of the skeleton color throught the ABruijn Graph
/// </summary>
/// <param name="blockColors"> A list of Blocks. The color ID of each block is also its its position in the list </param>
/// <param name="propagationRadius"> The maximum radius that the color can propagate </param>
/// <returns>a mapping between nodeids and their colors</returns>
public IDictionary <int, int> PropagateSkeletonColor(IList <IList <int> > blockColors, int propagationRadius)
{
SimpleLinkList <int> origialSequence = new SimpleLinkList <int>();
origialSequence.AddList(_sequence);
IDictionary <int, IList <Node <int> > > graph = GenerateGraph(origialSequence);
IDictionary <int, int> colorByNodeID = new Dictionary <int, int>();
//initially, all nodes are uncolored ( -1)
foreach (int i in _sequence)
{
colorByNodeID[i] = -1;
}
//add colors
for (int i = 0; i < blockColors.Count; i++)
{
foreach (int nodeID in blockColors[i])
{
colorByNodeID[nodeID] = i;
}
}
HashSet <int> unColorNodes = new HashSet <int>();
foreach (KeyValuePair <int, int> pair in colorByNodeID)
{
if (pair.Value == -1)
{
unColorNodes.Add(pair.Key);
}
}
for (int i = 0; i < propagationRadius; i++)
{
for (int j = 0; j < blockColors.Count; j++)
{
HashSet <int> modifiedUnColoredNodes = new HashSet <int>(unColorNodes);
foreach (int node in modifiedUnColoredNodes)
{
int newColor = FindDominantColor(node, colorByNodeID, graph);
if (newColor != -1)
{
colorByNodeID[node] = newColor;
unColorNodes.Remove(node);
}
}
}
}
return(colorByNodeID);
}
/// <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>
/// 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
_graph = GenerateGraph(_workingSequence);
}
