protected void UpdateNeighborsByNode(INode root, IDataPoints data, DynamicProgrammingParameter parameter)
{
Queue <INode> queue = new Queue <INode>();
Queue <int> steps = new Queue <int>();
queue.Enqueue(root);
steps.Enqueue(parameter.GetMaxDistance());
while (queue.Count > 0)
{
INode node = queue.Dequeue();
int avail = steps.Dequeue();
if (avail == 0)
{
continue;
}
foreach (INode n in node.CreateNodes())
{
if (!MatchAndUpdate(n, data, parameter))
{
queue.Enqueue(n);
steps.Enqueue(avail - 1);
}
}
}
}
protected void UpdateNeighbors(IPoint current, IDataPoints data, DynamicProgrammingParameter parameter)
{
List <INode> bestNodes = current.GetMaxNode();
foreach (INode root in bestNodes)
{
UpdateNeighborsByNode(root, data, parameter);
}
}
protected bool MatchAndUpdate(INode node, IDataPoints points, DynamicProgrammingParameter parameter)
{
bool updated = false;
foreach (IPoint pt in points.Match(node, parameter))
{
pt.Update(node);
updated = true;
}
return(updated);
}
public void Search(List <INode> rootList, IDataPoints data, DynamicProgrammingParameter parameter)
{
// initialization
foreach (INode root in rootList)
{
MatchAndUpdate(root, data, parameter);
}
// dynamic programming on points
foreach (IPoint point in data.GetPoints())
{
if (point.HasNodes())
{
point.MaxNodes(); // max for dp
UpdateNeighbors(point, data, parameter); // transfer point[n] <- point[i]
}
}
}
public List <IPoint> Match(INode node, DynamicProgrammingParameter parameter)
{
List <IPoint> pointList = new List <IPoint>();
NGlycoPeptideNode n = node as NGlycoPeptideNode;
double mass = n.GetMass();
int index = FindBucket(mass);
if (pointTable.ContainsKey(index))
{
foreach (PeakPoint pt in pointTable[index])
{
if (n.isAssociated(pt, parameter))
{
pointList.Add(pt);
}
}
}
if (pointTable.ContainsKey(index - 1))
{
foreach (PeakPoint pt in pointTable[index - 1])
{
if (n.isAssociated(pt, parameter))
{
pointList.Add(pt);
}
}
}
if (pointTable.ContainsKey(index + 1))
{
foreach (PeakPoint pt in pointTable[index + 1])
{
if (n.isAssociated(pt, parameter))
{
pointList.Add(pt);
}
}
}
return(pointList);
}
public bool isAssociated(IPoint point, DynamicProgrammingParameter parameter)
{
return(Math.Abs(mass - (point as PeakPoint).GetMass()) < parameter.GetTolerance());
//double ppm = calculator.CalcPPM(mass, (point as PeakPoint).GetMass());
//return ppm < parameter.GetTolerance();
}