} //Total score is the score of matched ions that are used for localization. For O-glycan, it is the score of all matched c/zDot ions.
public LocalizationGraph(int[] modPos, ModBox modBox, ModBox[] childModBoxes, int id)
{
ModPos = modPos;
ModBox = modBox;
ModBoxId = id;
ChildModBoxes = childModBoxes;
//array is localization graph matrix. array is composed of 2d array of node. From left to right, node is build under a glycosite. From up to down, node is build for each child box.
array = new AdjNode[modPos.Length][];
for (int i = 0; i < modPos.Length; i++)
{
array[i] = new AdjNode[ChildModBoxes.Length];
}
}
//The modification problem is turned into a Directed Acyclic Graph. The Graph was build with matrix, and dynamic programming is used.
//The function goes through the AdjNode[][] array from left to right, assign weight to each AdjNode, keep track of the heaviest previous AdjNode.
public static void LocalizeOGlycan(LocalizationGraph localizationGraph, Ms2ScanWithSpecificMass theScan, Tolerance productTolerance, List <Product> products)
{
var boxSatisfyBox = BoxSatisfyBox(localizationGraph.ChildModBoxes);
for (int i = 0; i < localizationGraph.ModPos.Length; i++)
{
//maxLength: the most mods we can have up to current mod pos; minlengtt: the least mods we can have up to current mod pos.
int maxLength = i + 1;
int minlength = localizationGraph.ModBox.ModIds.Length - (localizationGraph.ModPos.Length - 1 - i);
for (int j = 0; j < localizationGraph.ChildModBoxes.Length; j++)
{
if (localizationGraph.ChildModBoxes[j].NumberOfMods <= maxLength && localizationGraph.ChildModBoxes[j].NumberOfMods >= minlength)
{
AdjNode adjNode = new AdjNode(i, j, localizationGraph.ModPos[i], localizationGraph.ChildModBoxes[j]);
double cost = 0;
if (i != localizationGraph.ModPos.Length - 1)
{
var fragments = GlycoPeptides.GetLocalFragment(products, localizationGraph.ModPos, i, localizationGraph.ModBox, localizationGraph.ChildModBoxes[j]);
cost = CalculateCost(theScan, productTolerance, fragments);
}
adjNode.CurrentCost = cost;
//The first line of the graph didnot have Sources.
if (i == 0)
{
//Get cost
adjNode.maxCost = cost;
}
else
{
double maxCost = 0;
for (int prej = 0; prej <= j; prej++)
{
//Check if a previous AdjNode exist and the current AdjNode could link to previous AdjNode.
if (boxSatisfyBox[j][prej] && localizationGraph.array[i - 1][prej] != null)
{
adjNode.AllSources.Add(prej);
var tempCost = cost + localizationGraph.array[i - 1][prej].maxCost;
if (tempCost > maxCost)
{
adjNode.CummulativeSources.Clear();
adjNode.CummulativeSources.Add(prej);
maxCost = tempCost;
}
else if (tempCost == maxCost)
{
adjNode.CummulativeSources.Add(prej);
}
}
}
adjNode.maxCost = maxCost;
}
localizationGraph.array[i][j] = adjNode;
}
}
}
var unlocalFragments = GlycoPeptides.GetUnlocalFragment(products, localizationGraph.ModPos, localizationGraph.ModBox);
var noLocalScore = CalculateCost(theScan, productTolerance, unlocalFragments);
localizationGraph.NoLocalCost = noLocalScore;
localizationGraph.TotalScore = localizationGraph.array[localizationGraph.ModPos.Length - 1][localizationGraph.ChildModBoxes.Length - 1].maxCost + noLocalScore;
}