public static IEnumerable <TItem> EnumRange <TItem>(IMzLiteArray <TItem> items, IndexRange range)
{
for (int i = range.Low; i <= range.Heigh; i++)
{
yield return(items[i]);
}
}
/// <summary>
/// Extract a rt profile for specified target mass and rt range.
/// Mz range peak aggregation is closest lock mz.
/// </summary>
/// <returns>
/// Profile array with index corresponding to continous mass spectra over rt range and mz range given.
/// </returns>
public static Peak2D[] RtProfile(
this IMzLiteDataReader dataReader,
IMzLiteArray <RtIndexEntry> rtIndex,
RangeQuery rtRange,
RangeQuery mzRange)
{
if (dataReader == null)
{
throw new ArgumentNullException("dataReader");
}
if (rtIndex == null)
{
throw new ArgumentNullException("rtIndex");
}
var entries = rtIndex.Search(rtRange).ToArray();
var profile = new Peak2D[entries.Length];
for (int rtIdx = 0; rtIdx < entries.Length; rtIdx++)
{
var entry = entries[rtIdx];
var peaks = dataReader.ReadSpectrumPeaks(entry).Peaks;
var p = peaks.MzSearch(mzRange)
.DefaultIfEmpty(new Peak1D(0, mzRange.LockValue))
.ClosestMz(mzRange.LockValue)
.AsPeak2D(entry.Rt);
profile[rtIdx] = p;
}
return(profile);
}
public static T[] ToCLRArray <T>(this IMzLiteArray <T> array)
{
T[] copy = new T[array.Length];
for (int i = 0; i < array.Length; i++)
{
copy[i] = array[i];
}
return(copy);
}
/// <summary>
/// Get all peaks by rt range.
/// </summary>
public static IEnumerable <TPeak> RtSearch <TPeak>(
this IMzLiteArray <TPeak> peaks,
RangeQuery rtRange) where TPeak : Peak2D
{
if (peaks == null)
{
throw new ArgumentNullException("peaks");
}
return(BinarySearch.Search(peaks, rtRange, RtSearchCompare));
}
/// <summary>
/// Get all rt index entries by rt range.
/// </summary>
public static IEnumerable <RtIndexEntry> Search(
this IMzLiteArray <RtIndexEntry> rti,
RangeQuery rtRange)
{
if (rti == null)
{
throw new ArgumentNullException("rti");
}
return(BinarySearch.Search(rti, rtRange, RtSearchCompare));
}
public static IEnumerable <TItem> Search <TItem, TQuery>(
IMzLiteArray <TItem> items,
TQuery query,
Func <TItem, TQuery, int> searchCompare)
{
IndexRange result;
if (Search(items, query, searchCompare, out result))
{
return(IndexRange.EnumRange(items, result));
}
else
{
return(Enumerable.Empty <TItem>());
}
}
public static bool Search <TItem, TQuery>(
IMzLiteArray <TItem> items,
TQuery query,
Func <TItem, TQuery, int> searchCompare,
out IndexRange result)
{
int lo = 0;
int hi = items.Length - 1;
while (lo <= hi)
{
int mid = lo + ((hi - lo) >> 1);
int c = searchCompare(items[mid], query);
if (c == 0)
{
int resultLow = mid;
int resultHeigh = mid;
// search tees low
for (int i = mid - 1; i >= 0; i--)
{
if (searchCompare(items[i], query) == 0)
{
resultLow = i;
}
else
{
break;
}
}
// search tees heigh
for (int i = mid + 1; i < items.Length; i++)
{
if (searchCompare(items[i], query) == 0)
{
resultHeigh = i;
}
else
{
break;
}
}
result = new IndexRange(resultLow, resultHeigh);
return(true);
}
if (c < 0)
{
lo = mid + 1;
}
else
{
hi = mid - 1;
}
}
result = null;
return(false);
}
