public IActionResult Get(int id)
{
SortingScheme sortingScheme = _context.SortingScheme.FirstOrDefault(x => x.SchemeID == id);
if (sortingScheme == null)
{
return(NotFound());
}
return(new ObjectResult(sortingScheme));
}
public IActionResult Post([FromBody] SortingScheme sortingScheme)
{
if (sortingScheme == null)
{
return(BadRequest());
}
_context.SortingScheme.Add(sortingScheme);
_context.SaveChanges();
return(Ok(sortingScheme));
}
private static double getValue(Peptide p, SortingScheme s)
{
switch (s)
{
case SortingScheme.MASS:
return(ARBITRARILY_LARGE_MASS - p.getMass());
case SortingScheme.RT_START:
return(p.getRetentionTime().getRetentionTimePeak());
case SortingScheme.RT_END:
return(p.getRetentionTime().getRetentionTimePeak());
default:
return(Double.NaN);
}
}
/*
* A recursive implementation of binary search Returns the index of a peptide
* within the mass tolerance of the query mass
*/
private static int findPosition(List <Peptide> list, Peptide p, SortingScheme s, int high, int low)
{
// Not found
if (high < low)
{
return(-1);
}
// Search peptide at the middle of the list
int mid = (high + low) / 2;
Peptide midPep = list[mid];
double midValue = getValue(midPep, s);
double targetValue = getValue(p, s);
if (midPep == p)
{
return(mid);
}
else
{
if (midValue > targetValue)
{
// Search the bottom half of the list
return(findPosition(list, p, s, mid - 1, low));
}
else if (midValue < targetValue)
{
// Search the top half of the list
return(findPosition(list, p, s, high, mid + 1));
}
else
{
return(-1);
}
}
}
/*
* input: List<Peptide> list which is a list of peptides you want to
* search, Peptide p the peptide you are looking for, SortingScheme s how the
* original list is sorted by to find where Peptide p belongs output: the index
* of peptide p or -1 if not found
*/
public static int findPosition(List <Peptide> list, Peptide p, SortingScheme s)
{
return(findPosition(list, p, s, list.Count - 1, 0));
}
/*
* A recursive implementation of binary search Returns the index of a peptide
* within the mass tolerance of the query mass
*/
private static int findPositionToAdd(List <Peptide> list, Peptide p, SortingScheme s, int high, int low)
{
// System.out.println(p);
// System.out.println(s);
// System.out.println("hi: " + high + "\tlo: " + low);
// System.out.println(list.Count);
//
// if (list.Count > 1 && s.Equals(SortingScheme.MASS)) {
// System.out.println("asdf");
// System.out.println(getValue(p, s));
// }
// // Not found
double targetValue = getValue(p, s);
if (high <= low)
{
if (list.Count == 0)
{
return(0);
}
if (targetValue > getValue(list[low], s))
{
return(low + 1);
}
else
{
return(low);
}
}
// Search peptide at the middle of the list
int mid = (high + low) / 2;
Peptide midPep = list[mid];
double midValue = getValue(midPep, s);
// System.out.println("mid: " + midValue + "\ttarget: " + targetValue);
////commented this out because this should already be checked in a previous step
//if (midPep == p)
//{
// // prevents adding the same peptide to the list
// return -1;
//}
//else
//{
//}
if (midValue > targetValue)
{
// Search the bottom half of the list
return(findPositionToAdd(list, p, s, mid - 1, low));
}
else if (midValue < targetValue)
{
// Search the top half of the list
return(findPositionToAdd(list, p, s, high, mid + 1));
}
else
{
return(mid);
// if RT, needs a tie breaker...
// TODO this is a problem if RToffset is too high or too low, so we need to
// check the peak value instead
}
}
