/// <summary>
/// Removes the overlap from the boxcar ranges
/// so that each boxcar shares a startpoint with the endpoint of the previous car
/// and an endpoint with the startpoint of the next car.
///
/// Does this process by taking the mean between the boxcar ranges and setting the cars' start and endpoints to the means of their neighbors.
/// Overlap removal is important because when these boxcar ranges are matched with the scan data, they will remove the edge effects from the scan.
/// Edge effects: sometimes the scan picks up on peaks that it shouldn't near the beginning and end of that boxcar.
///
/// EXAMPLE:
///
/// boxcars[0] boxcars[1] boxcars[2] ... (if you took more kinds of boxcar scans they would be additional columns)
/// (400, 426) (424, 451) (449, 476)
/// (474, 501) (499, 526) (524, 551) (these rows are the BoxcarRanges)
/// . . .
/// . . .
/// . . .
/// (1124, 1151) (1149, 1176) (1174,1201)
///
/// How the loop works:
/// there are x columns and y rows.
/// Each column is a SetOfBoxcarRanges (which is stored in an arraylist)
/// Each row contains some BoxcarRanges, and if you read across the rows or down the columns they increase.
/// The nested for loops look at the rows first, and then the columns.
/// This way, each BoxcarRange that is looped through is greater than the last BoxcarRange and you can calculate the means.
///
/// So, once the function loops through, the entries are changed to:
///
/// boxcars[0] boxcars[1] boxcars[2] ...
/// (400, 425) (425, 450) (450, 475)
/// (475, 500) (500, 525) (525, 550)
/// . . .
/// . . .
/// . . .
/// (1125, 1150) (1150, 1175) (1175,1201) - the last entry (and the first entry) doesn't change because there's no next entry to compute the mean
///
/// In reality, the intervals are not all the same, so it's slightly more complicated than the example
///
/// </summary>
/// <param name="boxcars"></param>
/// <returns></returns>
public static SetOfBoxcarRanges[] RemoveOverlap(SetOfBoxcarRanges[] boxcars)
{
int numBoxcarScans = boxcars.Count();
SetOfBoxcarRanges[] newBoxcars = new SetOfBoxcarRanges[numBoxcarScans];
if (numBoxcarScans > 1)
{
BoxcarRange rangeA = boxcars[0].ElementAt(0);
BoxcarRange rangeB = boxcars[1].ElementAt(0);
// loop through all complete rows and columns of the "matrix":
for (int y = 0; y < boxcars[0].Count(); y++) // loops through all rows including a possibly incomplete last row w/ nulls/empty cells in it
{
for (int x = 0; x < numBoxcarScans; x++)
{
if (x < (numBoxcarScans - 1) && (y <= boxcars[x + 1].Count())) // if you aren't on the last column and there is an entry in the yth row of the next column, the rangeB is in the next column
{
rangeB = boxcars[x + 1].ElementAt(y);
}
else if (x == (numBoxcarScans - 1) && (y != (boxcars[0].Count() - 1))) // if you're on the last column and there is another row (even a partial row), rangeB is the first column in the next row
{
rangeB = boxcars[0].ElementAt(y + 1);
}
else // if you've reached the last entry
{
return(boxcars);
}
// find the mean of the endpoint of rangeA and the startpoint of rangeB
double endA = rangeA.End;
double startB = rangeB.Start;
double mean = CalculateMean(endA, startB);
// change the endpoint of rangeA and the startpoint of rangeB to be that number
rangeA.End = mean;
rangeB.Start = mean;
// insert rangeA and rangeB
boxcars[x].ReplaceAtIndex(rangeA, y);
if (x < (numBoxcarScans - 1) && (y <= boxcars[x + 1].Count())) // if you aren't on the last column, insert rangeB into the next column
{
boxcars[x + 1].ReplaceAtIndex(rangeB, y);
}
else if (x == (numBoxcarScans - 1) && (y != boxcars[0].Count())) // if you're on the last column, insert rangeB into the first column in the next row
{
boxcars[0].ReplaceAtIndex(rangeB, y + 1);
}
rangeA = rangeB;
}
}
return(boxcars);
}
else
{
return(boxcars);
}
}
/// <summary>
/// Helper method for FindBoxcarScan
/// Finds the first and last index in the given scan where the m/z value in the scan is between the startpoint and endpoint of the given boxcar.
/// The m/z value at the first index will be > the startpoint of the boxcar.
/// The m/z value at the last index will be >= the endpoint of the boxcar.
/// </summary>
/// <param name="scan"></param>
/// <param name="boxcar"></param>
/// <returns></returns> BestScan object with a first index, last index, and total intensity of the scan.
public static BestScan FindScanRange(MsDataScan scan, BoxcarRange range)
{
double[] xArray = scan.MassSpectrum.XArray;
double[] yArray = scan.MassSpectrum.YArray;
int len = xArray.Count();
// find the first index where the m/z values of the scan are in the range of the boxcar
int firstIndex = 0;
double firstValue = xArray[firstIndex];
bool nextIndexExists = true;
while ((firstValue < range.Start) && nextIndexExists)
{
firstIndex++;
firstValue = xArray[firstIndex];
if (!(firstIndex + 1 < len))
{
nextIndexExists = false;
}
}
// find the last index where the m/z values of the scan are in the range of the boxcar
int lastIndex = firstIndex;
double totalIntensity = yArray[lastIndex];
if (nextIndexExists)
{
int nextIndex = lastIndex + 1;
double nextValue = xArray[nextIndex];
while (nextValue <= range.End && nextIndexExists)
{
lastIndex++;
nextIndex++;
totalIntensity += yArray[lastIndex];
if (nextIndex < len)
{
nextValue = xArray[nextIndex];
}
else
{
nextIndexExists = false;
}
}
}
return(new BestScan(firstIndex, lastIndex, totalIntensity, scan));
}
/// <summary>
/// Helper method for CombineScans
/// Identifies which scan in the set has the most points in the boxcar range
/// </summary>
/// <param name="set"></param>
/// <param name="boxcar"></param> BestScan object with first index, last index, total intensity, and scan
public static BestScan FindBoxcarScan(SetOfScans set, BoxcarRange range, int count)
{
double bestIntensity = 0;
MsDataScan bestScan = set.BoxcarScans[0];
int bestFirstIndex = 0;
int bestLastIndex = 0;
int bestLen = 0;
List <MsDataScan> boxcarScans = set.BoxcarScans;
// Check each scan to find the one that corresponds best to the boxcar scan range
foreach (var scan in boxcarScans)
{
BestScan bestrange = FindScanRange(scan, range);
// the scan is better than the previous scan if:
// it has more m/z values in the range, and if
// the total intensity is higher
int firstIndex = bestrange.FirstIndex;
int lastIndex = bestrange.LastIndex;
int currentLen = lastIndex - firstIndex;
if (currentLen > bestLen)
{
if (bestrange.TotalIntensity < bestIntensity)
{
Console.WriteLine("ACK! scan#: " + count + " has a lot of very low intensity scans and may have been incorrectly counted in a boxcar range!");
}
// if the scan has more m/z points in the boxcar range than the previously best scan, update variables.
bestLen = currentLen;
bestLastIndex = lastIndex;
bestFirstIndex = firstIndex;
bestScan = scan;
}
}
return(new BestScan(bestFirstIndex, bestLastIndex, bestIntensity, bestScan));
}
/// <summary>
/// Inserts the given BoxcarRange object at the specified index.
/// Replaces the previous object at that index.
/// </summary>
/// <param name="boxcarRange"></param>
/// <param name="index"></param>
public void ReplaceAtIndex(BoxcarRange boxcarRange, int index)
{
Set[index] = boxcarRange;
}
/// <summary>
/// Add a BoxcarRange object at the end of the SetOfBoxcarRanges.
/// </summary>
/// <param name="boxcarRange"></param>
public void AddBoxcarRange(BoxcarRange boxcarRange)
{
Set.Add(boxcarRange);
}