Binary search related bug in MzSpectrum.Extract

[avcarr2]

mzLib/mzLib/MassSpectrometry/MzSpectra/MzSpectrum.cs

Lines 718 to 730 in b0f82ea

	public IEnumerable<MzPeak> Extract(double minX, double maxX)
	{
	int ind = Array.BinarySearch(XArray, minX);
	if (ind < 0)
	{
	ind = ~ind;
	}
	while (ind < Size && XArray[ind] <= maxX)
	{
	yield return GetPeak(ind);
	ind++;
	}
	}

The linked method has an error commonly associated with performig binary searches on double arrays. The method as written uses a binary search to find the minimum mz value in the MzSpectrum.XArray and does not test to see if the correct, closest value is the index to the right or the left.

To fix this issue, replace lines currently binary search associated code should be replaced with the following:
`
int ind = Array.BinarySearch(XArray, minX);
if (ind < 0)
{
ind = ~ind;
}

        if (ind >= XArray.Length)
        {
            ind = XArray.Length - 1;
        }

        if (ind != 0 && XArray[ind] - minX >
            minX - XArray[ind - 1])
        {
            ind--;
        }`

[avcarr2]

https://github.com/smith-chem-wisc/mzLib/blob/b0f82ea7bf47321ad2b81833961bff6d5706fe13/mzLib/MassSpectrometry/Deconvolution/Algorithms/ClassicDeconvolutionAlgorithm.cs#L290C8-L311

Another probably incorrect implementation of handling binary search on double arrays.

[avcarr2]

Here, starting index again doesn't correctly determine which index it is closer to. This one is more serious because it has 17 references.

mzLib/mzLib/MassSpectrometry/MzSpectra/MzSpectrum.cs

Lines 673 to 695 in b0f82ea

	public int NumPeaksWithinRange(double minX, double maxX)
	{
	int startingIndex = Array.BinarySearch(XArray, minX);
	if (startingIndex < 0)
	{
	startingIndex = ~startingIndex;
	}
	if (startingIndex >= Size)
	{
	return 0;
	}
	int endIndex = Array.BinarySearch(XArray, maxX);
	if (endIndex < 0)
	{
	endIndex = ~endIndex;
	}
	if (endIndex == 0)
	{
	return 0;
	}
	return endIndex - startingIndex;
	}