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Class Summary |
| AccurateMassAdjuster |
For adjusting the masses of features found in a resampled space, to take
advantage of the higher mass accuracy to be found in the unresampled space |
| BackgroundRemover |
Removes background noise from spectra |
| BasePeakCombiner |
superclass for peak combiners |
| DefaultFeatureScorer |
Default feature scorer. |
| DefaultPeakCombiner |
Default class for creating Features from Peaks
07/29/20008 dhmay enhanced to handle negatively-charged ions |
| FeatureFinder |
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| FeatureFindingBroker |
This class exists to bridge the gap between old-school and new-school feature finders. |
| SmallMoleculePeakCombiner |
class for creating Features from Peaks, specific to small-molecule analysis, e.g., metabolites. |
| SmootherCreator |
// Utility methods for creating different kinds of smoothers
// So what's up with all these smoothers???
//
// Really this is a problem, the sample rate varies drastically
// across experimental setups. |
| SpectrumResampler |
Resample spectra onto a grid with the specified frequency. |
| WaveletPeakExtractor |
smooth, ExtractMaxima2D.analyze()
Sort by decreasing intensity
Throw out peaks with < 5 scans
Break up what look like double-humped elution profiles by breaking peaks
at valleys in the profile
For each peak:
-Compute the extents
-Walking down scans, make sure that the peak's intensity
is greater than the intensities of the two m/z's around it
-Make sure that intensity is above threshold
-If you start going back up in intensity, stop
-Same for end scan
-If too short (<5 scans), toss it out
-"Integrate" to determine total intensity: for each scan, add a
block of intensity corresponding to the intensity on that scan
multiplied by half the amount of time between the adjoining scans
-Create a feature to represent the individual peak
Exclude all features initially
Filter features: for each feature:
find all neighbors within 5 scans and 1.1 m/z units
if the m/z's are too close (within 1.5 / _resamplingFrequency, for some reason), no dice
make sure they're lined up, scan-wise
If not enough scans combined in the two features, no dice
If intensities not high enough, no dice
If we got here, unexclude both |