ThermoFisher.CommonCore.PeakDetect

The peak detection algorithm originally in the PPD data system

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Integrator.

This class supports Avalon peak detection and integration. All of the settings for this integrator are expressed as events. The property is used to attach the initial and timed events to the algorithm. Initial events could just be viewed as properties of the peak detector, especially when you wish a fixed set of parameters to detect all peaks. A set of initial events can be calculated from real data, by calling . So, you can perform peak detection in a default way on any data by: Call AutoDetectInitialValues, then set the result as the Events property for the peak detector


            Avalon av = new Avalon();
            av.AutoDetectInitialValues(myChromatogram);
            LinkedList<Peak> detectedPeaks = av.DetectPeaks(myChromatogram);

Use the class to add timed events, or modify the initial values

The avalon integrator.

The list of initial and timed peak detector events.

Gets the list of events from the integrator

Setup the initial detection and Integration values. Values are estimated from supplied data.

Chromatogram to analyze A set of initial events, or null on error

Do the detection and Integration - MAIN Entry Point

The chromatogram to detect A list of Detected peaks. If the signal is invalid, this is null

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current AvalonIntegrator.

The peak type shoulder.

The peak type parent.

The peak type child.

The peak type cluster.

The peak type negative.

The peak type normal.

The tension not set.

The tension infinite.

The min data points.

The avalon peak info.

Gets or sets the type of baseline at startIndex.

Gets or sets the type of baseline at endIndex.

Gets or sets the baseline corrected area of the peak.

Gets or sets the baseline corrected height..

Gets or sets the Index of the first point of the peak (absolute).

Gets or sets the Index of the top of the peak (absolute).

Gets or sets the Index of the last point of the peak (abs).

Gets or sets a value indicating whether this is a negative peak.

Gets or sets the y 0. same as "_ystart" in TpIntPeak: start of peak height

Gets or sets the y 1. same as "_yend" in TpIntPeak: end of peak height

Gets or sets the Peak Retention time.

Gets or sets the x 0.

Gets or sets the x 1.

The int results.

Calculate bunch factor.

The bunch factor.

Baseline average delta y.

The p signal. The baseline average delta y.

The integrator info.

Integrator: find event.

The kind. The code. The event number. The event which was found

Set standard events.

The average delta y. The bunch.

Initialize to "no events".

The index pair.

The derivatives.

Find next inflection.

The find next inflection.

Test if the previous is peak not negative.

The previous peak. true if the previous peak is not negative.

Test if starting another peak.

The specific. The signal. True if starting another peak.

Peak detection is complete for the current peak, now append it to | the peak list...

The specific. The signal.

Return the number of peaks in the TpIntPeak peak list (linked list).

The peak list. The counted tp int peaks.

Copy the finalized "TpIntPeak"s into a "IntResults" data structure.

The specific. The signal.

Find end of cluster.

The cluster list. The final peak in the cluster.

Given the starting peak in a cluster, this function finds the peak at the end of the cluster and creates a baseline for the cluster (first peak start, x0,y0) - (last peak stop, x1,y1). Then the baseline is drawn for each peak in the cluster and a baseline type is assigned.

The first peak in the cluster list. The signal. The next peak after the cluster is returned.

Assign peak baseline.

The peak. The signal.

This function checks for penetration over the entire range of a peak.

The peak. The signal. The status.

This function checks for penetration over a specified range of the | peak..

The peak. The signal. The i 0. The i 1. status.

Positive negative pair.

The signal. The pk 1. The pk 2.

Process a Negative then Positive pair of peaks.

The signal. The first peak. The second peak

Find cluster peaks.

The cluster. The p count. The peak

Find highest peak.

The pk arr. The n peaks. The p signal. The highest peak.

Calculate weighted y.

The peak array. The number of peaks. The index. The tention. The wt m. The wt b. weighted y.

Auto calc integrator.

The info. The signal.

Setup local copies of the data arrays and detection parameters.

The original signal. The singal

Integrate the signal.

The info. The signal. Integration results

Make an integrator.

The event collection. Integrator information

Add back shoulder peak.

The psgnal. The pk. The i 0. The i 1.

Check for shoulders between peak apex and stop. .

The detector. The signal. The peak. The checked peak.

Add front shoulder peak.

The detector. The signal. The peak. The previous peak. The i 0. The i 1. The peak.

Check for shoulders between peak start and apex.

The detector. The signal. The pk. The prev pk.

This function returns arrays of first and second derivatives, _fx1 and _fx2 for an array of X and Y points. NOTES: 1. The derivatives are calculated using a 5 point window. 2. The first and last 2 derivatives are 0.0. 3. The second derivative is multiplied by 1000 to provide more reasonable human numbers.

The x. The y. The start. The points. The function returns true on success and false for a failure.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct integrator from integration settings

Settings for the Avalon integrator

The avalon detection.

Gets ConfirmThreshold.

Gets ShoulderThreshold.

Calculate an area slice.

The negative. The area slice.

Calculate areas.

The signal.

Remove references to tp int peaks.

Return the Signal index range to use in looking foward through the Signal to be used in determining the actual peak ending point.

The confirmed end distance.

Return the Signal index range to use in looking back through the Signal to be used in determining the actual peak starting point.

The confirmed start distance.

Unlink a tp integrator peak.

The peak to unlink.

Area reject tangent skim.

The cluster. Peak to use, after tests.

Remove empty peaks. That is, peaks with the same start and end points.

Cleanup state to start looking for another peak.

Set a timed event.

The timed event.

The set negative peak.

The timed event.

Set tangent skim.

The timed event.

Set force cluster on.

Set disable cluster on.

Set shoulders on.

The timed event.

Set bunch factor.

The timed event.

Set end threshold.

The timed event.

Set start threshold.

The timed event.

Setup initial values.

The event list.

Detect when we think another peak is starting. Return true if a peak has started, false otherwise. If a "start-of-peak" is found, then initialize _start and _position to that starting point. .

The status.

Tangent skim cluster. Code to assign peak baselines for tangent skimming within a peak cluster

The cluster. The signal. Peak with assigned baselines.

Check timed events.

Area reject.

The signal.

The baseline tension allows you to adjust the drop of baselines. That is, how well/fast the integrated peak baselines follow the chromatographic baseline. A high tension will give you a lot of baseline drops. A low tension will give you more valley-valley peaks.

The signal.

Check this peak against the previous peak (if any) to see if they overlap. If so, then set the overlap flag in the previous peak.

The signal.

Check one peak for overlap.

The signal. The peak. The times. The intensities. The peak start intensity. The peak Start Intensity.

Assign baseline.

The signal.

handle events affecting baseline.

The signal. The times.

The check baseline penetration.

The signal.

check start end points.

The intensities.

The adjust starting point for negative peaks.

The signal.

The allocate preliminary baseline.

The signal.

This is the main function used to detect shoulder peaks on the front | back of a peak.

The signal.

Get next point.

The signal. The get next point.

Confirm that this is a "real" peak and not just noise. Then find its| actual starting point.

The signal. The confirm peak.

Find peak apex.

The signal. The status.

Find peak end point.

The signal. The intensities. The end peak count.

Find peak starting point.

The signal.

Get first point.

The signal. The status.

Perform detection.

The signal.

Class to read a chromatogram and return the data as a signal. This is a worker class, and is intentionally not serializable

Gets or sets the definition of chromatogram (scan filter, mass ranges etc.)

Gets or sets an already opened raw file to read from

Gets or sets Mass tolerance options, to add tolerance band to the masses supplied. This is only used where mass chromatograms have a single value for "mass" instead of a range. If this is null, default options for the file system are used.

Gets or sets smoothing options, to smooth the chromatogram intensities. If this is null or a default constructed object, no smoothing is performed.

Apply a trace operator to two arrays, which must be same length

Intensities of first trace Intensities of second trace Operator, such as add or subtract

Create the list of chromatogram settings needed for 1 peak

Chromatograms needed for this peak Trace settings, ready to send to file

Read data from a raw file over a given time range, and return the data as a signal. Smooth the signal before returning if requested. The method selects the appropriate instrument from the raw file, and leaves this selected on exit.

Lowest time requested for chromatogram Highest time requested for chromatogram (optional) if set "true" base peak mass values are read for each scan. Only set if this data is needed, as this takes extra time The signal read from the raw file.

Read base peak masses from scan stats.

The chromatogram scans. The base peak vales for each scan.

Get the chromatogram data.

The count. The times. The intensities. The scans. the base peak masses The start scan. The end scan.

DetectionThresholdFlags flags based on threshold values.

Gets or sets a value indicating whether the Area Threshold passed.

true if [Area Threshold passed]; otherwise, false.

Gets or sets a value indicating whether the Height Threshold passed.

true if [Height Threshold passed]; otherwise, false.

Initializes a new instance of the class. Default constructor for serializer..

Initializes a new instance of the class. Copy constructor..

The access.

Initializes a new instance of the class.

if set to true [area threshold passed]. if set to true [height threshold passed].

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Detection threshold values

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Gets or sets the Area limit threshold.

The Area limit threshold.

Gets or sets the height limit threshold.

The height limit threshold.

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Calculate if the peak area and height above baseline pass threshold tests.

The peak to analyze flags from area and height tests

Class to read data for spectrum find algorithm

Set the input data stream for find algorithm

input data

provide spectral data to the find algorithm, for each supplied scan. Data is returned using a List of the SpecPoint objects.

A scan number (from a raw file) The mass and intensity data for the requested scan

resets the array of polynomial coefficents when a new value of time is used

returns the partial derivatives for all coefficients at the given time

the time value the list of adjustable parameters the value of GammaPeakShapeValue(time) the list of derivatives the number of parameters in the list

returns the value of the function at time t

the retention time amplitude of the peak there is no peak intensity before this time flow rate when not stuck on the column mixing parameter

LogGamma uses series expansion from Abramowitz and Stegun (6.1.41

double Digamma(x) uses series expansion from Abramowitz and Stegun (6.3.18) plus additional last term from derivative of 6.1.41

returns a good estimate for gamma_r

A point on the chromatogram, to detect

Time for this point on chromatogram, in minutes.

Intensity for this point on chromatogram

This class implements the Genesis peak detector, as first created in the LCQ data system

Gets or sets a value indicating whether valley detection is performed. This parameter must be set to true when performing base to base integration

Gets or sets a value indicating whether a peak's width (the tail) must be constrained. This flag allows you to constrain the peak width of a detected peak (remove tailing) width is then restricted by specifying a peak height threshold and a tailing factor.

Gets or sets a constraint on peak height. The percent of the total peak height (100%) that a signal needs to be above the baseline before integration is turned on or off. This applies only when the ConstrainPeak is true. The valid range is 0.0 to 100.0%.

Gets or sets the distance from a peak, for baseline analysis. The default is 2 minutes (peak time +/- 2 minutes)

Gets or sets the tolerance in minutes for using the same noise and baseline. When performing baseline analysis (using SurveyDistance from a peak) an analysis does not need to be repeated, when the peak is within this tolerance of the last analyzed peak. Default 0. Suggested application default 1 second NoiseAndBaselineTolerance = 1.0 / 60.0 Also: Since noise is calculated from the baseline window, the peak will be assigned the noise value of the previous peak. Setting this above zero can significantly improve performance.

Gets or sets the peak tailing factor. This controls how Genesis integrates the tail of a peak. This factor is the maximum ratio of the trailing edge to the leading side of a constrained peak. This applies only when the is true. The valid range is 0.5 through 9.0.

Gets or sets "half the width" of a typical peak. This controls the minimum width that a peak is expected to have (minutes) if valley detection is enabled. The property is expressed as a half window. With valley detection enabled, any valley points nearer than the expectedPeakHalfWidth (which is [expected width]/2) to the top of the peak are ignored. If a valley point is found outside the expected peak width, Genesis terminates the peak at that point. Genesis always terminates a peak when the signal reaches the baseline, independent of the value set for the expectedPeakHalfWidth.

Gets or sets a value indicating whether to enable RMS noise calculation. If not set, noise is calculated peak to peak. It is set by default.

Gets or sets a noise limit, where the code stops attempting to find a better baseline. controls how the baseline is drawn in the noise data. The higher the baseline noise tolerance value, the higher the baseline is drawn through the noise data. The valid range is 0.0 to 1.0.

Gets or sets the minimum number of scans that Genesis uses to calculate a baseline. A larger number includes more data in determining an averaged baseline. The valid range is 2 to 100.

Gets or sets the maximum number of scans that Genesis uses to calculate a baseline. A larger number can include more data in determining an averaged baseline. The baseline start and end times are determined by peak apex time +/- the SurveyDistance. If these times would include more than half of MaxScansInBaseline before or after the peak apex, then the baseline is restricted. The suggested valid range (if shown on UI) is 200 to 50,000. If this is not greater than "MinScansInBaseline" it is ignored. Default: 0. No limit.

Gets or sets a factor which controls the width of the RMS noise band above and below the peak detection baseline and is applied to the raw RMS noise values to raise the effective RMS noise during peak detection. The left and right peak boundaries are assigned above the noise and, therefore, closer to the peak apex value in minutes. This action effectively raises the peak integration baseline above the RMS noise level. Range: 0.1 to 10.0. Default: 2.0.

Gets or sets the minimum acceptable percentage of the largest peak. Do not return peaks which have a height less than this % of the highest peak above baseline.

Gets or sets the minimum acceptable signal to noise of a peak. Genesis ignores all chromatogram peaks that have signal-to-noise values that are less than the S/N Threshold value

Gets or sets a limit for the "baseline signal to noise ratio". A peak is considered ended if the following condition is met: height <= (BaseNoise * BaseSignalToNoiseRatio)) Where BaseNoise is the calculated noise on the fitted baseline, and height is the height above baseline.

Gets or sets the minimum peak width (in minutes) Default: 0 (no filtering) Suggested application default: 1/600 (tenth of a second). This setting can significantly reduce processing time, as the integrator does not need to calculate certain information about peaks (such as signal to noise ratio) which fail this test.

Gets or sets the multiplier of the valley bottom that the peak trace can rise above a baseline (before or after the peak). If the trace exceeds ValleyThreshold, Genesis applies valley detection peak integration criteria. This method drops a vertical line from the apex of the valley between unresolved peaks to the baseline. The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak. This test is applied to both the left and right edges of the peak. The ValleyThreshold criteria is useful for integrating peaks with long tails. Useful range: 1.001 to 1.5 Note: Appears on product UI converted from factor to percentage as "Rise percentage". For example: 1.1 = 10% Code tests similar to the following:


            if ((currentSignal-baseline) > ((valleyBottom-baseline) * ValleyThreshold))
            {
                side of peak has bottomed out, and risen above minimum
            }

Gets or sets the S/N range is 1.0 to 100.0. for valley detection. Technical equation:height(here +/- VALLEY_WIDTH) > ValleyDepth*SNR+height(here) => valley here

Gets or sets the Peak Signal ToNoise Ratio Cutoff. The peak edge is set to values below this defined S/N. This test assumes an edge of a peak is found when the baseline adjusted height of the edge is less than the ratio of the baseline adjusted apex height and the peak S/N cutoff ratio. If the S/N at the apex is 500 and the peak S/N cutoff value is 200, Genesis defines the right and left edges of the peak when the S/N reaches a value less than 200. Range: 50.0 to 10000.0. Technical equation:if height < (1/PeakSignalToNoiseRatioCutoff)*height(apex) => valley here

Gets or sets the number of minutes between background scan recalculations. Baseline is refitted each time this interval elapses.

Gets or sets a value indicating whether a manual region is used for noise measurement

Gets or sets the user entered time range

Gets the regression line from the last manual noise region. This will hold useful information only if: is true, has been set and a peak has been integrated, and a manual noise region was set

Ensure that the a value is in bounds.

The value to restrict. The low. The high. The bound restricted value.

Return the height above baseline of the chromatogram at the given index.

The index. The true height.

Initializes a new instance of the class. Default Constructor

Constructs a new Genesis integrator from qualitative settings. Currently uses access.GenesisSettings and access.ManualNoise. All interfaces other than "access" itself and "access.GenesisSettings" are permitted to be null. Future version may use more settings, to emulate more of the Xcalibur "qual processing" behavior. This method is suitable when working from an application like qual browser, as it sets all the values as shown on the genesis integrator tab (detection settings, advanced settings and manual baseline) TODO: Also support these settings? NoiseAndBaselineTolerance, MaxScansInBaseline,

Xcalibur (qual) settings Configured integrator

Construct an integrator from Raw settings (as in Xcalibur processing method file, PMD)

The settings (Xcalibur format) The integrator

Gets or sets a value indicating whether to use the binary search time finder. The binary search algorithm will be a more accurate comparison to Qual Browser and is recommended. The alternative is a linear search, present in legacy builds, which does not always return the nearest point.

Initialize fields.

Setup local copies of the data arrays and detection parameters.

The signal.

Detect all peaks in the chromatogram data, appending results to a linked list of peaks

The chromatogram to search A list of the detected peaks. If the signal is invalid, this is null

Find generic peaks.

The peak array. The peak limit.

Find highest peak.

The highest peak

Given a retention time, return the corresponding index in the chromatogram. if the retention time is beyond the end, return the end position.

The retention time to find. The index of the found retention time.

Find the index of the time value which is closest to a supplied time.

Time to search for The index of the nearest time in in the signal

Find the closest retention time.

The time. The index of the closest retention time.

Test a point in the chromatogram to see if it is a valley point.

The index to test. index of the valley point, or -1 for none. Note that the valley point returned can be different than 'position'.

Test a point in the chromatogram to see if it is a peak apex.

The index to test. peak : index of the peak point, or -1 for none. Note that the peak point returned can be different than 'position'.

Fill out 'peak' with default info for an invalid peak.

The peak to fill.

find left and right extents of peak at 'apex', then fill in the Peak struct for this peak.

The PeakInfo to fill in. index of the peak starting point. The peak left retention time limit. The first Noise Calculation. The previous Noise. The last Apex Time. The threshold.

Fill the peak noise.

The peak. The noise line.

Handle constrained peak boundaries.

The peak. The number of points.

Track the peak left side.

The apex. The peak. The valley. The index of the valley? The valley index.

Track the peak right side.

The apex. The peak. The number of points. The valley. The value of "here".

trapezoidal integration of the chromatogram from index first to last, fills in the appropriate bits of the Peak.

The peak to fill. The index of first scan in integration range. The index of last scan in integration range.

Return the height above baseline of a peak which includes the highest intensity in the chromatogram, For peak list height threshold purposes.

The base width. Class to quickly sum ranges of data The height above baseline.

The survey.

The peak. The location. The peak left retention time limit.

Initialize Maximizing Masses.

The start.

Find The next integrator peak.

The separation between peaks. The threshold. The next integrator peak.

Evaluate mx+b to find baseline at a ret. time..

The retention time of interest. The baseline height.

Initializes a new instance of the class. Construct integrator from integration settings

Genesis integration settings

Reset integrator with integration settings

Genesis integration settings

Get integrator settings. Converts from internal properties to "Settings"

The converted settings.

Gets or sets the uncertainty of the population count. the "RMS" noise is calculated as Sqrt(sumNoiseSquared/ Max(1, polulationCount - PopulationUncertainty)) For true RMS, this value is 0. For standard deviation, the value is 1. The default is 2, for "significant uncertainty"

Gets or sets a value indicating whether filtering of peaks is by relative signal height

Make initial approximation of baseline based on total energy and size of zero transitions in the chromatogram.

The line. The first. The last. The quick Sum.

Perform one step of the iterative process of finding a baseline.

The line. The first index of the baseline. The last index of the baseline. Set of this is the first call.

Calculate the baseline fit, and find the baseline data for the chromatogram.

The first. The last. determines which chromatogram points are included in the baseline Class to quickly sum ranges of data

Find The local baseline.

The center. The offset from the center, left and right, to the edge of the baseline. determines which chromatogram points are included in the baseline The quick Sum.

Set search range.

The expected. true if OK.

Find high peak.

The peak. The window.

Find near peak.

The initial peak. The lowest permitted signal to noise ratio. The peak found.

Sets up an integration range for Survey().

The survey center. The re center range.

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Integrator.

Integrate a peak based on manually set limits

Chromatogram Array - (containing time and intensity) Retention time of left side of manual peak Baseline of left side of manual peak Retention time of right side of manual peak Baseline of right side of manual peak The integrated manual peak

Calculate noise for manual peak.

The signal. The start. The stop. The minimum noise for MS. The manual peak.

The peak detection algorithm originally in the ICIS data system

Gets or sets a value indicating whether to report the peak's RT and intensity from the parabola curve's apex point. Default: false - means it will report the apex scan's RT. This is the existing behavior in QualBrowser. If it's set to true, a parabola is fitted through the apex scan, the previous scan and the next scan of the XIC, and the parabola curve's apex time and intensity will be reported as the peak's RT and intensity. The peak's ScanAtApex will still be the scan # of the apex scan.

Gets or sets a value which determines how the ICIS peak detector determines which signals are noise. The selected points can determine a noise level, or be fed into an RMS calculator, depending on the RMS setting.

Gets or sets noise level multiplier (a minimum S/N ratio). This determines the potential peak signal threshold. Range: 1 - 1000 Default multiplier: 10

Gets or sets a number of scans. Each scan is checked to see if it should be considered a baseline scan. This is determined by looking at a number of scans (BaselineWindow) before and after the a data point. If it is the lowest point in the group it will be marked as a "baseline" point. Range: 1 - 500 Default: 40

Gets or sets the minimum number of scans required in a peak. Range: 0 to 100. Default: 3.

Gets the minimum number of scans required in a peak. Range: 0 to 100. Default: 3.

Gets or sets the minimum separation in scans between the apexes of two potential peaks. This is a criterion to determine if two peaks are resolved. Enter a larger number in a noisy environment when the signal is bouncing around. Range: 1 to 500. Default: 10 scans.

Gets or sets the Noise level multiplier. This determines the peak edge after the location of the possible peak, allowing the peak to narrow or broaden without affecting the baseline. Range: 1 - 500 Default multiplier: 5

Gets or sets the number of scans on each side of the peak apex to be allowed. Range: 0 to 100. Default: 0 scans Note: 0 specifies that all scans from peak-start to peak-end are to be included in the area integration.

Gets or sets a value indicating whether you can constrain the peak width of a detected peak (remove tailing) width is then restricted by specifying a peak height threshold and a tailing factor.

Gets or sets the percent of the total peak height (100%) that a signal needs to be above the baseline before integration is turned on or off. This applies only when the ConstrainPeak is true. The valid range is 0.0 to 100.0%.

Gets or sets the peak tailing factor. This controls how ICIS integrates the tail of a peak. This factor is the maximum ratio of the trailing edge to the leading side of a constrained peak. This applies only when the ConstrainPeak is true. The valid range is 0.5 through 9.0.

Gets or sets the number of scans past the peak endpoint to use in averaging the intensity. Range: 0 to 100. Default: 5 scans.

Gets or sets a value indicating whether noise is calculated using an RMS method

Gets or sets a value indicating whether a manual region is used for noise measurement

Gets or sets a user entered time range for manual noise region. All signal within this range (based on the nearest points to the start end times) is considered to be noise.

Gets the regression line from the last manual noise region. This will hold useful information only if: is true, has been set and a peak has been integrated, and a manual noise region was set

Initializes a new instance of the class. Default construction of the ICIS peak detector

Initializes a new instance of the class. Construct integrator from integration settings

Integration settings

Reset integrator with integration settings

Integration settings

Get integrator settings. Converts from internal properties to "Settings"

The settings.

Detect peaks, using the ICIS algorithm.

The chromatogram to detect The list of peak found. If the signal is invalid, this is null

Get peak points.

The original signal. The peak Height. The left, apex, and right points (items 1,2,3)

Test for tailing.

The edge types. The updated edge types.

Find the apex baseline. Also updates "_peakHeight"

The original intensities. The peak Height at apex. The baseline.

Determine multiplet edge types.

The peak number in multiplet. The left and right edge types, as Item1 and Item2

The get parabola apex data.

The apex scan index. The new apex RT. The new apex intensity.

The setup threshold.

The noise factor.

The get noise factors.

The find peak end points.

The check for right tail.

The right edge type. The left side. The new integration end. The right edge type

The look to the right.

The peak intensity. The right edge type. the right edge type

Look to the left.

The peak intensity. The left edge type. the edge type

Setup the data.

The signal.

The noise factors.

The noise method. The noisel. The average signal.

Compute noise level from values in buffers intens and rettim noise-level is computed for the sequence : (intens(1),rettim(1)) (intens(2),rettim(2)) ... (intens(ninten -1),rettim(ninten -1)) which needs as starting-values (intens(1),rettim(1)) and as terminating values (intens(ninten),rettim(ninten)) NOTE: the noise for intens(ninten), rettim(ninten) has to be calculated in an additional step !

The noisel. The average signal.

The sort noise array.

The index. The noise a. The scans a.

The iterative noise evaluation.

The number of noise values. The total noise. The calculated noise. The sumint. The index. The a max. The a min. The intensities a. The noise a. The iterative noise evaluation.

The get initial noise points.

The intensity 2. The number of noise values. The total noise. The calculated noise. The sum Of Intensities. The index. The a max. The a min. The intensities a. The noise a. The scans a. The data to integrate. The number Of Noise Values.

calculate the noise in the data using the INCOS method.

The auto noise result. The average Baseline Signal.

The calculate auto noise.

The tim 1. The avesig. The anoise. The int 1. The noise list. The noise line. The tim 2. The int 2. The noise. The number of noise values. The calculate auto noise.

To determine the baseline scans. The baseline scans are marked by setting their intensities to the negative of their absolute value..

The window.

The examine scan.

The window. The scan. The current intensity. The large real 4. The min scan left. The min intensity left window. The min scan right. The min intensity right window. absolute intensity for each chromatogram point

The test if right is lower.

The min scan left. The min intensity left window. The min scan right. The start right window. The min intensity right window. The current intensity. The current time. The start left window. true if right is lower.

The search left side.

The large real 4. The scan. The window. The min scan left. The start left window. The end left window. The min intensity left window. absolute intensity of each point The new value of minScanLeft.

Find and subtract baseline (background). Background "Anchor" points are already set after the call to GetBaselineScans(). They are flagged as negative intensities

Flag local maxima by making its value negative.

The input (initial) minimum peak width. The multiplet resolution. The noise threshold.

Find next multiplet (part above noise level)

The offset. The qnoism. The bnoisl. The pptfst. The pptlst. The lpt 1 st. The lpt 2 nd. The mlabel. The minsc 1. The minsc 2.

Calculate baseline endpoints to use when calculating the area of a peak..

The pptfst. The pptlst. The tailex. The qnoism. The bnoisl. The cintb 1. The cintb 2.

Find the scan corresponding to the maximum peak within the supplied scan range.

The start scan. The end scan. The scan. The time.

Search for next labeled scan and the minimal scan before.

The count. The offset. The first labeled scan (returned). The scan which has the minimum absolute intensity.

Find height above baseline

index of data to measure (usually peak apex) RT at start of background line RT at end of background line intensity at start of background line intensity at end of background line The height above baseline, at the selected point in the chromatogram

Get slope of baseline from start and end points of the baseline

start RT end RT start intensity end intensity The slope

Get peak height above baseline from baseline start and end points using calculated slope

RT of given point intensity of given point RT of start point of baseline intensity of start point of baseline RT of end point of baseline intensity of end point of baseline height above baseline of given point

Find the minimum intensity in chro.

The intensities. The minimum intensity in chro.

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Integrator.

Tools to give a simple application interface to some common integration tasks

Find a peak in a raw file, based on identification settings (such as chromatogram specifications and integrator parameters). This method finds the expected time of the peak, using a reference peak to adjust the time, as specified in the location settings, then reads and smooths the chromatogram, then integrates and returns the best matching peak according to location settings.

The source of data to generate chromatograms How to read the chromatogram from the data file How to smooth the chromatogram How to integrate the smoothed chromatogram How to find a peak from the list of possible peaks in the chromatogram Peak of retention time reference compound The detected peak, its chromatogram and scan at apex

The source of data to generate chromatograms How to read the chromatogram from the data file tolerance to apply to mass chromatograms How to smooth the chromatogram How to integrate the smoothed chromatogram How to find a peak from the list of possible peaks in the chromatogram Peak of retention time reference compound The detected peak, its chromatogram and scan at apex

Find a peak in a chromatogram, based on identification settings (such as chromatogram specifications and integrator parameters). This method finds the expected time of the peak, using a reference peak to adjust the time, as specified in the location settings, then integrates and returns the best matching peak according to location settings.

A chromatogram (previously constructed from file) How to integrate the smoothed chromatogram How to find a peak from the list of possible peaks in the chromatogram Peak of retention time reference compound The detected peak, its chromatogram and scan at apex

Integrate a peak based on manually set limits

Chromatogram to integrate The new baseline of the peak Allow baselines below zero. Default: false chromatogram is null. The manually integrated peak.

Find a peak list in a raw file, based on identification settings (such as chromatogram specifications and integrator parameters) This method reads the chromatogram, smooths the chromatogram, then integrates and returns the list of peaks found.

The source of data to generate chromatograms How to read the chromatogram from the data file How to smooth the chromatogram How to integrate the smoothed chromatogram The detected peaks and chromatogram data is null.

Read a chromatogram from a file using such as chromatogram specifications This method reads the chromatogram, smooths the chromatogram, then returns it.

The source of data to generate chromatograms How to read the chromatogram from the data file How to smooth the chromatogram The chromatogram data is null.

Find a peak list in a chromatogram, based on integrator parameters This method integrates the chromatogram and returns the list of peaks found.

The chromatogram to integrate How to integrate the chromatogram The detected peaks chromatogram is null.

Create an integrator from settings

Integration settings True if negative values are permitted in the signal. An integrator to detect peaks If the peak integrator enum is not valid. integration is null.

Find the scan at the apex of a peak

How to peak was integrated. This determines the detector to read the scan from File to read scan. Peak who's apex scan is needed. The scan at the apex of the peak. chromatogramSettings is null.

Class for integrating peaks. This class provides a standard integration method for a detected peak. The class can be used alone, for basic manual integration using the ManualIntegrate method, or derived classes can provided a peak detection algorithm, then call the Integrate method.

Gets or sets the RT center of the search window.

Gets or sets a value indicating whether calculated values (such as height) may return negative numbers. If false: negative calculated numbers are returned as 0

Gets or sets a value which determines the method used to find peaks. Default is Generic.

Gets or sets the window considered for valid peaks, when looking for the highest peak, near an expected retention time. The highest peak in the RT range expected +/- window is found.

Integrate a peak based on manually set limits

Chromatogram Array - (containing time and intensity) Baseline of the peak to integrate Allow baselines below zero. Default: false The integrated manual peak

Make a parabola fit through three given points and determine the vertex point

x of point 1 y of point 1 x of point 2 y of point 2 x of point 3 y of point 3 return x of vertex point return y of vertex point

Detect peaks in the supplied signal

The chromatogram signal The list of detected peaks. The base version always returns null. A derived class of Integrator must be used.

Calculates slope and offset of baseline of manual peak.

Retention time of left side of manual peak. The Baseline of left side of manual peak. The Retention time of right side of manual peak. The Baseline of right side of manual peak. The calculated slope. The calculated offset.

Calculate manual noise.

The data to detect. The low index. The high index. The average noise. A noise line, containing the calculated noise

Get the array index in the array of the first point greater than or equal to the time.

The chromatogram times. The time we are trying to find index of The index of the requested time. 0 if time less than or equal to the first scan's Time -1 if time is greater than the last scan's Time. -1 if m_pTraceResult == 0.

Return the height above baseline of the chromatogram at the supplied index.

The data. The index into the chromatogram. The slope. The offset. The true height.

Calculate the baseline.

The retention time. The slope. The offset. The baseline.

trapezoidal integration of the mass chromatogram from first to last, fills in the appropriate bits of the Peak.

The chromatogram containing the peak The updated peak. Note that baseline information must be in the passed in this peak First chromatogram point to integrate Last chromatogram point to integrate if true, Baseline will not be calculated; instead slope and offset passed as arguments will be used Slope of baseline; value is ignored if is false Offset of baseline; value is ignored if is false

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Integrator.

Use this to create an object for fetching scans A derived class must be made, which implements "GetSpecData". Typically an application derived class would include an file stream field, so that the stream can remain open between calls. The GetSpecData will be called many times, to test if individual scans match the find target.

A real method must override this, to provide spectral data to the find algorithgm, for each supplied scan. Data is returned using a List of the SpecPoint objects.

A scan number (from a raw file) The mass and intensity data for the requested scan

Set the input data stream for find algorithm

Data source for find algorithm

Interface for generating signals, needed by the peak detection software. This can be used by applications to improve efficiency when reading data. Signals are required based on time windows, calculated during the peak location process. This interface allows reading of the signals to be delayed until the window is determined.

Return a signal based on a time range

Start of time range for generated signal End of time range for generated signal A signal created based on the requested time range

Create a signal with no limits

A signal with all available data

read only access to DetectionThresholdFlags flags based on threshold values.

Gets a value indicating whether the Area Threshold passed.

true if [Area Threshold passed]; otherwise, false.

Gets a value indicating whether the Height Threshold passed.

true if [Height Threshold passed]; otherwise, false.

Class to perform a list of ion ratio calculations on a detected peak. This class reads the ion chromatograms, and calculates the ratios. It keeps the chromatograms and results of the tests.

Gets or sets the tests to be performed

Gets or sets the tolerance settings

Gets or sets a value which determines if the peak's height or area is being used.

Gets the chromatograms for each tested Ion

Gets the pass/fail results for each tested ion

Gets a value indicating whether every test passes on all ions

Create a list of Irc tests, from chromatogram data. The chromatogram data is smoothed if needed, based on component settings.

The mass and expected ratio for each Irc test The chromatograms for each Irc Test A list of Irc tests, ready to run. Each test has the chromatogram and expected ratios attached

Initializes a new instance of the class. Constructor

Get the chromatogram data for each of the ions which need to be measured for Irc.

List of masses, to generate the chromatograms File to integrate Filter to use when reading IRC chromatograms The data for each chromatogram

Run a set of IRC tests, based on a list of chromatograms to test and IRC parameters from the component. Saves the results of each test.

The list of chromatograms and expected ratios for each chromatogram Expected location of the component peak The peak which is being checked True if all test pass

Perform ion ratio checks for a table of ions

The file needed to read ion chromatograms. method of locating a peak in the chromatogram The peak to compare ratios with Filer to use from the MS data for the ion chromatograms

Determines if ion rations are to be calculated based on peak area or peak height.

Calculate ratios using peak area

Calculate ratios using peak height

Class to perform Ion ratio Checks. To perform checks: Set the peak to test against construct an IonRatioCheckMember for each ion to be compared with the signal. Ensure that the signal and integrator (Locate information) have been set for all members Set the properties of this class for common detection settings Call the DoIRC method Inspect the individual member results

Gets or sets a value which determines if ratio tests are based on peak height or peak area

Gets or sets a value which determines if ion ratio checks are based on an absolute or relative window, from the expected percentage. For example: 50% +/- absolute 10% gives 40-60%. 50% +/ relative 10% gives 45%-55%.

Gets or sets the time the retention time can vary from the expected retention time for the ion to still be considered confirmed. Units: minutes Range: 0.000 - 0.100

Check if all ion ratio tests in the list have passed

A list of test results True if all tests pass

Check ion ratio, based on location information for a target compound. Data about the expected location (time and time adjustment, nearest, highest or spectral fit) is transferred from the target compound to each ion to be checked. To manually set all IRC setting, use the alternate form of this, which accepts a peak, and does not adjust the individual ion settings.

The list of individual ion chromatograms to perform ratio tests with Signal and integrator settings for the target compound. These settings are used to find a peak for the target compound Flag: when set all integration settings are shared from the target compound to the ions being checked The results for each test in the list. The results are in the same order as the original list of ions, and are also keyed by the "mass" from the ions to test

The list of individual ion chromatograms to perform ratio tests with integrator settings for the target compound Detected peak for the target compound Flag: when set all integration settings are shared from the target compound to the ions being checked The results for each test in the list. The results are in the same order as the original list of ions, and are also keyed by the "mass" from the ions to test

Check ion ratio, based on an already located targetPeak. Peaks are located in each ion Signal, and results are calculated

The list of individual ion chromatograms to perform ratio tests with The peak for the target compound to compare ion chromatograms against The results for each test in the list. The results are in the same order as the original list of ions, and are also keyed by the "mass" from the ions to test

Test the ion ratio

The current peak. The test to run. Test results

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current IonRatioChecks.

This class offloads the burden of fetching the chromatogram data from the RawFile.

Gets the ion signal remembered from the methods.

The ion signal.

Initializes a new instance of the class.

The chromatogram settings. The smoothing settings. The file.

Get a windowed chromatogram, based on an expected time. The window is converted to "nearest scan" based on the file system. Then the filtered chromatogram is generated from those scan numbers. This algorithm is intentional, to match Xcalibur, and can lead to data points being read outside the the supplied time window.

The start of the time window The end of the time window. The windowed chromatogram.

read chromatogram data.

The start time. The end time. The chromatogram data read from file

Create a signal with no limits

A signal with all available data

Class representing an individual ion to be tested, for ratio with the quan ion. Set the chromatogram signal and integration settings in the locate class. Set specific ion ratio settings for this chromatogram After testing is completed, check the results Use the IonRatioChecks class to perform a list of tests on a chromatogram

Gets parameters to the Ion Ratio confirmation algorithm, for one mass. Specifies the mass, expected ratio and window.

Gets or sets the peak locator. Provides the means of finding a peak in a chromatogram for this ion.

Gets or sets a value indicating whether the peak is manually integrated (do not locate the peak). For manual peaks, set PeakInfo for the manually marked peak. When this is not set, the peak will be automatically detected from the supplied chromatogram.

Gets or sets the peak detected for this ion.

Gets a value indicating whether a peak has been found for this ion

Gets or sets the apex time of the ion peak must be within this time (minutes) of the apex time of the target compound peak.

Check the ratio of this ion with the target compound peak

Peak who's height or area is checked Response is either area or height Measure window of tolerance as absolute % or relative % True if the test passes

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current IonRatioTest.

Class to find a single peak, from a list, using expected time, time window etc. This class uses expected time windowing to request a chromatogram over the correct time range, calls a supplied Integrator to find a collection of peaks, then locates a specific peak, usually by highest in window.

Gets or sets an interface for delayed reading of to a signal, called after windowing has been calculated for the signal. Note: Since the Signal class implements this interface, a caller can construct a signal with all available data, and it will be windowed as needed. In this case windowed data is defined as signals strictly inside the window time range. If the caller wishes to delay reading, then a class must be written implementing this interface.

Prepare an object to locate a single peak in a chromatogram.

How the peak will be found in the chromatogram (such as expected time, window) How the chromatogram will be integrated An object which can be used to Locate a peak

Create a peak finder.

The find settings.

Gets or sets the peak which is used for retention time reference adjustments. Typically: the peak detected for a reference compound.

Gets or sets the time before useful data (solvent time). Void time is is considered as "time zero" for retention time reference calculations. For example: In a 10 minute run, if the void time is 0 minute, and the reference peak is expected at 2 minutes, but occurs at 3 minutes, then all peaks relative to that reference are shifted by 50%. A peak expected at 1:30 becomes expected at 2:15 etc. If the void time is 1 minute, with the same reference shift (from expected 2 to actual 3 minutes), then the shift is "twice the distance from the void time" Therefore a peak expected at 1:30 (30s after void time) now expected at 2 minutes (1 min after void time). A peak originally expected a 3:00 (2 minutes after void) is now expected at 5:00. (4 minutes after void) Void time may be automatically set based on peaks found in a chromatogram. See

Gets or sets the chromatogram signal which can be used for void time calculations. The first detected peak in this chromatogram is used as a marker for the start of the sample data (possibly a solvent peak). For more information see and

Gets or sets the integrator to use. When peak detection has to be done on the chromatogram signal, this integrator is used.

Gets or sets the void method. Determines how is specified (either by a fixed value, or based on a detected peak in a )

Gets or sets a value which determines how the chromatogram data is restricted. Except when set to NoWindow, a sub-set of data is taken from the chromatogram.

Gets or sets an object to find spectra. When using spectra location, this object must be supplied, with matching thresholds set. Spectral and chromatogram data is automatically sent to this finder as needed

Gets or sets the expected time and window for the peak. Also, the method of finding a peak within the window.

If using spectrum , this call must be made to set the target compound spectrum.

The spectrum for the analyte to detect

Initializes a new instance of the class. Default constructor

Adjust the retention time, based on the time of a reference peak.

The reference peak.

Detect peaks in the supplied chromatogram, and find the peak which best matches the location criteria.

The peak which has been located. If no peak is found, then .DetectedPeak.Valid is false.

Perform a noise test.

The detected peak.

Perform window test.

The detected peak.

Perform a Peak search.

The peak found. The set of peaks to search in.

Find a peak.

The peak found. The searcher algorithm. The peak found

Find the nearest peak.

The peak found. The peaks to search.

Find the highest peak.

The found peak. The peaks to search.

Get a sub signal (part of the time range).

The sub signal

The setup void time.

Detect a peak by spectral fit

The peak which is found The peak which is found (updated)

Shallow Copy the means of finding a peak, so that peaks can be found in multiple chromatograms using the same criteria.

Source of the copy

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Locate.

The lorentz function.

returns the partial derivatives for all coefficients at the given time

the time value the list of adjustable parameters the y value produced by this function the list of derivatives the number of parameters in the list

Calculate the lorentz intensity at point.

The time. The adjustable parameters. The peak shape value. The number of parameters.

returns the value of the function at time t

the x value of the input point the scaling factor (intensity at resonance) offset from resonance linewidth The lorentz peak shape value.

Perform peak detection using the Marquardt Levenberg algorithm.

Gets or sets a value indicating whether to allow different fitting for protein-type TIC data

Gets or sets a value to choose the gamma fit even when it has a larger error. This occurs when there is a small peak in the near left side; can be resolved by multiple peak fitting to a data region

Gets or sets a value indicating whether to choose the gamma fit even when it has a larger error

Gets or sets values used in the BiasToSkewed case, which looks at a wider range of expermental values

Gets or sets the wider yrange.

Calculates an error result over a wider range of experimental data

number of peaks fitted - currently always 1 set '0' for gaussian, '1' for gamma

The noise line.

The noise line point.

Sets the uncertainty of the population count. the "RMS" noise is calculated as Sqrt(sumNoiseSquared/ Max(1, populationCount - PopulationUncertainty)) For true RMS, this value is 0. For standard deviation, the value is 1. The default is 2, for "significant uncertainty"

Gets or sets the base data.

Gets or sets the sum of x values

Gets or sets the sum of Y values

Gets or sets the sum of x squared

Gets or sets the sum of y squared

Gets or sets the sum of x*y

Gets or sets the accumulated baseline "error"

Gets or sets the sum of square 'error'.

Gets or sets the baseline offset

Gets or sets the baseline slope

Gets or sets the calculated noise

Gets or sets the low point of the baseData

Gets or sets the high point of the baseData

Gets or sets the count of baseline points

Gets or sets the set of baseline points which were included in sums.

Initializes a new instance of the class.

Initialize the stats.

Initialize only the noise stats.

Add noise points to the line.

The noise list. The point.

calculate the RMS noise.

Add to line within noise.

The first. The last. The chromatogram points. True if initial call.

Calculate a baseline regression on current statistics. Used only by Genesis algorithm

The noise minimum.

Calculate the true noise of a set of baseData.

The baseline noise rejection factor. The noise minimum. The min scans in baseline. The base noise limit. This method either calculates "MinMax" or "Noise" (RMS)

Drawing noise line.

The fitted line

The baseline sum. To sum baseline sections in parallel

Gets or sets the baseline offset

Gets or sets the baseline slope

Gets or sets the calculated noise

Sets the chromatogram points.

Gets or sets the first chromatogram point in the baseline

Gets or sets the last chromatogram point in the baseline.

Gets or sets the set of baseline points which were included in sums.

Gets the count of points added or removed.

Method executed in parallel

Gets or sets the sum of x values

Gets or sets the sum of Y values

Gets or sets the sum of x squared

Gets or sets the sum of y squared

Gets or sets the sum of x*y

Gets or sets the accumulated baseline "error"

Gets or sets the sum of square 'error'.

Gets or sets the block start.

Class to perform chromatographic peak checks

The concave limit.

Set the internal array of chromatogram points, this must be called before another method

an array of data points that make up a chromatogram

Depending on the threshold values, CalcPeakSymmetryParams can be used to determine if a peaks is symmetric, tailing or column overloaded. CalcPeakSymmetryParams will also return the right and left hand width so the Peak width threshold can be calculated. SetSignal must be called first

the retention time that the peak occurs at the percentage of the height the width is to be calculated at. SOP defines symmetry to be 50% of the height of the peak the pass mark threshold value, SOP defines Symmetry to be 70% The ratio calculated a reference to the right hand width a reference to the left hand width baseline height true if a result can be calculated

Get right width.

The i. The threshold intensity. The peak center retention time. The right width.

Get the left width.

The i. The threshold intensity. The peak center retention time. The left width.

Depending on the threshold value determines whether or not the resolution of a peak is OK. SetSignal must be called first

the retention time that the peak occurs at Intensity at baseline the retention time the valley occurs at The threshold value the determines if a peak's resolution or OK or not. Resolution threshold is defined as the ratio: 100 × V/P where: V = the horizontal asymptote extended from the target peak’s apex to the lowest point in the valley between the target peak and a neighboring peak P = the height of the target peak The calculated resolution value true if the resolution meets the test

Depending on the threshold values, CalcPeakSymmetryParams can be used to determine if a peaks is symmetric, tailing or column overloaded.

the retention time that the peak occurs at the percentage of the height the width is to be calculated at. SOP defines symmetry to be 50% of the height of the peak the pass mark threshold value, SOP defines Symmetry to be 70% baseline height The width ratio calculated true if the peak passes symmetry tests. Returns false if no signal has been set

Determines if a peak contains more than 3 identical consecutive points SetSignal must be called first

the retention time that the peak occurs at intensities are considered the same if within this % tolerance of the apex intensity. the found number of consecutive points is returned true if the signal indicates saturation

Determines if a peak width is greater or less than the given peak width threshold value SetSignal must be called first

the retention time that the peak occurs at the percentage of the height the width is to be calculated at the min value a width can be the max value a width can be Intensity at baseline The calculated width true if the width is within bounds

Determines if the peak has been baseline clipped or not. SetSignal must be called first

the start point of the peak the end point of the peak the decimal factor used to scale a peak's width (in time) in the test for clipping true if the peak is baseline clipped

Determines if a peak top is concave SetSignal must be called first

the retention time that the peak occurs at the window to look for a concave peak, value in seconds true if the peak is concave

Determines if a has a tail. SetSignal must be called first

The retention time that the peak occurs at The percentage of the height at which the width is to be calculated The largest tailing factor permitted (ratio of right width to left width) Baseline height true if the width is beyond bounds

Determine if peak has a left-tail (column overload)

the retention time that the peak occurs at the percentage of the height at which the width is to be calculated the tailing factor permitted (ratio of left width to right width) baseline height true if the column is overloaded. If no signal has been set, this returns false

Test if signal to noise is above threshold

Signal to noise to test Threshold (minimum signal to noise) true if this data passes the test. If no signal has be set, the test fails

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current PeakChecks.

internal Exception in peak detect code. These should all be handled in the code (never intentionally thrown to caller)

Initializes a new instance of the class. Basic analysis exception, no specified reason.

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception Trapped inner exception

Initializes a new instance of the class. Construct an exception, with serialization.

Data to serialize this object Stream for serializing

Create a peak envelope shape from a peak

Gets the calculated envelope for a peak

Gets or sets an over sampling rate. Sample the gaussian about this times as fast as the chromatographic sampling, to make smooth peaks.

Find the index of the last point before a given time (or 0 if no points before that time)

Signal to search Time to find The index of the last point before a given tim

Create the shape for one peak

The peak to "draw" Chromatogram signal

Create the shape for a peak merged from several peaks

The peak to "draw" The peak to "merge" Chromatogram signal

Create the shape for a peak merged from several peaks

The peak to "draw" The peak to "merge" Chromatogram signal

calculate contribution to intensity for an overlapped peak

The peak. The retention time. The overlapped peak. The Gamma Function. contribution to intensity from this peak.

Defines one line segment of a peak envelope

Gets or sets the start of line segment X coordinate

Gets or sets the start of line segment Y coordinate

Gets or sets the end of line segment X coordinate

Gets or sets the end of line segment Y coordinate

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

This class finds a single peak in a single data file.

Gets or sets the chromatogram data

Gets or sets the results of integrating this peak

Integrate a single peak from one raw file.

The file whose data is integrated Definition of how to construct a chromatogram tolerance to apply to mass chromatograms Determines how to smooth the chromatogram, after reading it Settings for integrating the chromatogram How to find a single peak from the integrated chromatogram Peak to use for retention time reference calculation If true, the chromatogram signal is kept. This can save re-reading the signal to display chromatograms. True if negative values are permitted in the signal. An integrated peak.

Integrate a single peak from one raw file.

The file whose data is integrated Definition of how to construct a chromatogram tolerance to apply to mass chromatograms Determines how to smooth the chromatogram, after reading it Tool to find a peak list from the chromatogram How to find a single peak from the integrated chromatogram Peak to use for retention time reference calculation If true, the chromatogram signal is kept. This can save re-reading the signal to display chromatograms. An integrated peak.

Integrate a single peak from a chromatogram.

The chromatogram where the peak must be found How to integrate the smoothed chromatogram How to find a peak from the list of possible peaks in the chromatogram Peak of retention time reference compound If set, the chromatogram is kept The peak integration results

Initializes a new instance of the class. default constructor to support serialize

Initializes a new instance of the class.

Class to read chromatogram data for the peak for the peak

Return the signal, with no retention time window applied

All possible chromatogram data

The start of the time window The end of the time window. The windowed chromatogram

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Calculate results.

The reference peak. True if the signal is to be kept in the results. The location settings. The integrator. The signal reader. The integrated results

Read the data.

The start time. The end time. The signal which has been read

Calculate results.

The integrator. The location settings. The reference peak. Store signal? The signal reader. The integrated peak

Locate the peak.

The location settings. The reference peak. The signal reader. The locate.

Filter a list of detected peaks, removing peaks which fail certain criteria, as set by the properties.

Gets or sets the minimum value of signal to noise, based on the peak height above baseline. Filter out peaks, where a noise value has been calculated, and the signal to noise (calculated from the peak height above baseline) is below this value

Gets or sets the minimum acceptable percentage of the highest peak. Filter out peaks, whose height is lower than this percent of the highest peak in the list.

Filter a list of peaks, returning those peaks which pass the criteria.

The peaks to be filtered The peaks which passed the filtering tests

Test if a peak passes filter.

The peak. The highest. True if the peak passes filter. Invalid "noise result" setting.

Class for Peak Purity.

The min coverage.

The max coverage.

The min correlation.

Prevents a default instance of the class from being created.

Correlate scans.

The scan a. The scan b. The correlation. The threshold. True, if successful.

Computes peak purity based on Peak Information.

PEAKINFO Array for processing. RawFile Object. Threshold info. Desired Coverage. Purified PEAKINFO Array

Provides the basic parameters of a peak - RT, width, and intensity, regardless of peak type

Return the Retention Time, independent of peak shape function

The peak whose RT is needed

Return something related to the Intensity at peak maximum. For the actual intensity, use the function 'IntensityAtApex'.

The peak whose intensity is needed

Return the Intensity at peak maximum, independent of peak shape function

The peak whose intensity is needed

For Gaussian peaks, returns the peak width parameter 'c' in the equation f(x) = a * exp((x-b)/2c), For gamma peaks it returns the same value as the 'Width' function

The peak whose width is needed

Return the peak width (as FWHH), independent of peak shape function

The peak whose width is needed

The parameter less peak detection algorithm

Gets or sets safety limit on when to stop

Gets or sets a value indicating whether, if merging is turned on, after peak detection and merging, stop at this number of peaks

Every peak that is detected in PPD shows up here, even the ones that are ultimately rejected. Examination of the conditions under which the peak is reject should be useful in correcting the condition.

The location of the peak of the fitted data

The intensity of the peak of the fitted data

The calculated width

The quality of the fitted data

The calculate S/N value. Since the noise is re-computed right at the end, this value will probably be different from the value in the peak array (if this peak is ultimately accepted)

the fitting function used

The index of the (supposed) peak maximum

The number of points used in the fitting process

When a peak is rejected, this parameter explains the exit condition hit

In contrast to the exit code, there can be multiple warning conditions, so this is a bitfield

This is the current position in the 'found peaks' array. (Without it, it can be difficult to figure out where we are in that list when a peak is rejected. When a peak is accepted, of course, we can find it in both lists.)

get nearest detected peak signal 2 noise.

The .

Gets or sets a value indicating whether to sort debug info. The peak info array contains useful info about every peak rejected. However, sorting it takes finite time; for performance reasons don't do it automatically

Gets or sets a value indicating whether or not to adjust the fitting data points to minimize negative residual

Gets or sets a value indicating whether or not to merge adjacent peaks

The designer can control, at run-time, which model functions are used in the fitting process. The choices are 'All' functions in the library, 'GammaOnly' and 'GaussianOnly'

The default. All functions in the library are tried in the fitting process

Only a Gamma function fit is attempted.

Only a Gaussian fit is attempted

Gets or sets which model functions are used in the fitting process. The choices are 'All' functions in the library, 'GammaOnly' and 'GaussianOnly'

When to replace the model function area (the one derived from the analytic solution to the area of the model function) with numerical integration from the start to stop scans

Never use non-model peak integration. Always use the area computed from the formula for the model peak shape function. This is the default setting

Replace the model peak area with numerical integration of the data when the fit of the data to the model shape is lower than the threshold value set by 'NonModelPeakShapeIntegrationLimit'

Always replace the model function area (the one derived from the analytic solution to the area of the model function) with numerical integration from the start to stop scans

Gets or sets a rule about when to replace the model function area (the one derived from the analytic solution to the area of the model function) with numerical integration from the start to stop scans

Gets or sets a value which controls whether or not to merge adjacent peaks

Gets or sets a value indicating whether to change the detection rules to favor typical protein TIC lineshapes - broad, mostly Gaussian, but with a more rapid LHS rise

Gets or sets a value indicating whether to choose the gamma fit even when it has a larger error

Use this flag in conjunction with the target time and window width to find the nearest peak to the time

Peaks that are close to the Nyquist limit and near other peaks may choose a poor set of initial conditions and never find a good fit. This flag turns on oversampling for such peaks, but it is only attempted when the number of non-zero points in the data stream are less than 100

Look thru the input signal for data points that exceed the noise level. If the calling function tends to send a lot of signals that are just noise, this is a useful feature that prevents spending a lot of time looking for peaks in noise. If, on the other hand. the signal can pretty much be expected to contain a peak, setting this option true is a performance hit.

Gets or sets The time where a peak should be found - return the closest peak

Gets or sets The window width to use when searching for a peak at time TargetTime

When using the feature 'FindPeakAtTime', the largest detected peak that is within a window of twice this value, is returned. The default value is suitable for all normal situations, but for special cases the designer may want a smaller or larger value

When a model baseline is computed, it should not have gigantic values of polynomial order. Sensible values will be very small (1-5), but one can imagine a chro with a big lump might have a much higher- order curve describing the baseline. This max value is the highest value allowed, and the default setting is 20. That means that a baseline of order 16 !! (max value of 20 - 4) may be used for really unusual data. This parameter is exposed only because legacy code corrected for the older value of 30, and still needs it. New applications should not set this parameter.

PPD stops detection when the 'on the fly' noise, and the new peak's intensity, fall below the SNR limit. However, this is not very accurate, and sometimes PPD does not even start detecting when the first peak's SNR is (wrongly) computed as too low. This flag lowers the 'on the fly' determination and then trims to the correct limit at the end.

The maximum polynomial order for baseline correction can either be a static value, or computed from the number of data points. This flag sets the algo to use a dynamic calculation

This is the error string supplied when the math functions in the MLA used to just crash but now throw an exception

Gets or sets the value of the residual noise

Method to create a line shape

the time value the list of adjustable parameters the value of GammaPeakShapeValue(time) the list of derivatives the number of parameters in the list

Initializes a new instance of the class. default constructor

Sets the signal to noise limit

the value of SNR where peak detection stops. Default value is 1.0

SetRememberHistory - compare each peak with the average result for previous peaks - reject them if they are 'much' worse

Default value is true. Set to 'false' to judge each peak on it's own. (Usually a bad idea.)

Sets a "warning" code where PPD will stop. Warning codes include "code 8" Polynomial too high "code 512" Peak too small (Should be a flags enumeration?)

If you want PPD to quit when a warning condition is hit, set it here

Returns the 'y' value for the given 'x'. Currently doens't handle any merged peaks contained in the object

additional peaks that are merged into the total the 'y' value for the given 'x'

returns the data left over after Peak Detection is done

The data left over after Peak Detection is done.

constructor with slide factor and other parameters

whether to use sliding fits The upper limit for a possible polynomial baseline correction can by computed from the number of points in the data by setting this param to 'true'. If it is false, a static value, set by 'MaximumPolynomialBaselineCoefficient', is used. The calculated limit is zero for 5-point data and increases as the number of data points increase. PPD uses a fraction of the S/N limit (the limit default is 1) to determine when to stop detecting peaks. The reason for this is that the computed noise can be too large and consequently the reported signal/noise too small, and you may wish to re-compute it later by some other means. However, if you wish to trim the output list to a specific S/N limit, set this flag to 'true'. If peak merging is turned on, merging is performed before the S/N trimming happens Look through the input signal for data points that exceed the noise level. If the calling function tends to send a lot of signals that are just noise, this is a useful feature that prevents spending a lot of time looking for peaks in noise. If, on the other hand. the signal can pretty much be expected to contain a peak, setting this option true is a performance hit.

constructor with slide factor parameter

whether to use sliding fits flag to look for peak at target time the target time so find a peak at the window to use in searching for a peak at time target time

Primary entry point for feature

The positions. The intensities. The start MZ. The end MZ.

Primary entry point for feature

The signal.

Detect peaks, using the PPD algorithm.

The mass values of the spectrum The intensity values of the spectrum to detect The list of peak found. If the signal is invalid, this is null

Detect peaks, using the PPD algorithm, over a mass range

The mass values of the spectrum The intensity values of the spectrum to detect The starting M/Z value in the spectral data The ending M/Z value in the spectral data The list of peak found. If the signal is invalid, this is null

Detect peaks, using the PPD algorithm, over a mass range, and using the width of the first for all peaks

Detect peaks, using the PPD algorithm.

The chromatogram to detect The list of peak found. If the signal is invalid, this is null

Determine whether peaks are too narrow for standard ppd.

The signal. whether peaks are too narrow for standard ppd

Detect peaks, using the PPD algorithm, and simple second order baseline correction.

The chromatogram to detect The list of peak found. If the signal is invalid, this is null

Detect peaks, using the PPD algorithm, but without first performing baseline correction

The chromatogram to detect The list of peak found. If the signal is invalid, this is null

Estimate peaks, using the PPD algorithm.

The chromatogram to detect The number of peaks found. If the signal is invalid, this is null

Estimate peaks2, using the PPD algorithm.

The chromatogram to detect The list of peaks found. If the signal is invalid, this is null

SubtractSecondOrderBaselineAndDetectPeaks - internal function to make a second order baseline correction and then detect peaks

Find and subtract baseline, then estimate number of peaks by regular PPD algorithm, but assuming that all peaks have the shape of the first peak

ChangeDomainOfFitParameter - Changes the domain of this parameter from 0 to negative infinity to 1 to 0

UnChangeDomainOfFitParameter - Changes the domain of this parameter from 0 to negative infinity to 1 to 0

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Integrator.

Class to calculate sum and max values more quickly, when many sub-ranges are to be summed of the same data. works by knowing results for all blocks of 10 samples.

Initializes a new instance of the class.

The points.

Get the sum and max

The from index. The to index. a Tuple with Item1 as sum, Item2 as max.

Line fitted through manual noise region

Gets or sets the X coordinate at start of line

Gets or sets the X coordinate at end of line

Gets or sets the Y coordinate at start of line

Gets or sets the Y coordinate at end of line

Calculator for retention time windows. This object manages the expected retention time of a peak. It can determine if a peak is within a window, or search through a collection of peaks, finding the highest peak in a window, or the nearest to the centre of the window. Expected times can be adjusted by retention time reference peaks, and by a void time.

Gets or sets the time when the peak is expected, after making adjustments

Gets or sets the peak for relative retention time adjustment. This adjustment is made based on the shift from expected time to the found time of the reference peak. The following formula is used to calculate the time, based on reference peak and void times, from "userEnteredRT", the users original expected time of a peak: double slope = (ReferencePeak.Apex.RetentionTime - VoidTime)/(ReferencePeak.ExpectedRT - VoidTime); ExpectedRT = VoidTime + (userEnteredRT - VoidTime)*slope;

Gets or sets area and height thresholds. When searching for peaks in a window, peaks must pass the area and height thresholds. By default these are 0.

Calculate the expected retention time, using the user entered RT, and adjustments

If true, make adjustments to the users entered RT The originally expected retention time (before adjustments) True if the "ExpectedRT" is valid. It wall be always true when no adjustments are needed. If adjustments are needed, it will be true if the ReferencePeak has been set

Test is a specific time is within the RT window of the expected time

time to test width of the window true if the time is within +/- half of the window of the expected time

Find the peak which has the largest "Height above baseline" within the search window.

The collection of peaks to search Peak must be within +/- half of the window of the expected time The highest peak in the window, or null of no peaks are in the window

Test if the peak passes thresholds.

The peak. True if the peak passes thresholds.

Find the nearest peak to the given time

The collection of peaks to search Peak must be within +/- half of the window of the expected time The nearest peak to the centre of the window, or null of no peaks are in the window

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Class to represent a signal, to be detected. Use the method to construct this, or: or The static construction methods described above need to have the same number of elements in each array. The minimum information in the signal is time and intensity values. The other possible values per point (scan number and base peak mass) are optional, and remain as "null" fields in the object when not supplied.

Convert from data type "ChromatogramSignal". Does not move any data.

Signal to convert The converted signal

Create a peak detector signal, from time and intensity arrays

array of retention times array of intensities at each time The constructed signal, or null if either of the inputs are null, or the inputs are not the same length

Create a peak detector signal, from time, intensity, scan number and base peak mass arrays

array of retention times array of intensities at each time array of scan numbers for each time array of base peak masses The constructed signal, or null if any of the inputs are null, or the inputs are not the same length

Create a peak detector signal, from time, intensity and scan arrays

array of retention times array of intensities at each time array of scan numbers for each time The constructed signal, or null if either of the inputs are null, or the inputs are not the same length

Create an array of signals from . The Interface describes data read from a file (if using IRawData). This constructor converts to an array of type Signal, simplifying use of individual chromatograms with Peak integration.

data (usually read from file) to convert into signals The constructed signals, or null if the input is null

Create an array of signals from chromatogram signals.

data to convert into signals The constructed signals, or null if the input is null

Create a signal from a set of signals. This merges the signals, summing intensities of all signals at each time point. Times for each point are found by the following rule: Choose the next time which will include not more than 1 data point from each signal in the list. The returned point will have the intensity weighted average of all times of contributed signals, and the summed intensity. The most abundant scan contributing to each point is returned as that point's scan number.

Signals to merge The merged signal

Sum intensity from all signals before time.

The next time index. The signals. The time. the weighted average time (item1), the summed intensity (item2) and the most abundant scan (item3)

Hind highest start time in all signals.

The next time index. The signals. The highest start time.

Find smallest second time.

The next time index. The signals. The smallest "second time" in any of the signals

Initializes a new instance of the class.

The times. The intensities.

Initializes a new instance of the class.

The times. The intensities. The scans.

Initializes a new instance of the class.

The times. The intensities. The scans. The base peaks.

Gets an Array of x (time in minutes) values.

Gets an Array of y (abundance) values.

Gets the times.

The signal times.

Gets the intensities.

The signal intensities.

Gets the signal scans.

The signal scans.

Gets a value indicating whether this signal has the (optional) base peak data. Tests that the base peak data is set, and has the correct length.

Gets the base peak masses.

Gets the Array of base peak masses.

Gets the Array of scan numbers..

Gets the time at the end of the signal.

Gets the time at the start of the signal..

Gets the number of points in the signal.

Create a Signal from a

A chromatogram to create the signal from The constructed signal

Initializes a new instance of from a Signal object. This permits Signal to be efficiently converted where or are needed

The chromatogram signal.

Construct a sub-signal from a time range

lowest scan in sub-signal highest scan in sub-signal The sliced signal, including only the scans indicated. null if the signal does not contain scan numbers

Construct a sub-signal from a time range

lowest time in sub-signal highest time in sub-signal If this is true, then the signal returned starts from the nearest data point to the start time, and ends at the nearest point to the end time. If it is not set, the signal returns the largest set of points which are strictly within the sub range The sliced signal, between the times indicated

Get a copy of the scan data for the signal

A copy of the scan numbers from this signal

Get a copy of the time data for the signal

A copy of the time information from this signal

Get a copy of the intensity data for the signal

A copy of the intensity information from this signal

Test if the data is contained in valid arrays of the same size

The times. The intensities. True if both times and intensities have been set, and are the same length

Test if the data is contained in valid arrays of the same size

The times. The intensities. The scans. True if all of times intensities and scans have been set, and are the same length

Test if the data is contained in valid arrays of the same size

The times. The intensities. The scans. The base Peaks. True if all of times intensities and scans have been set, and are the same length

Get a copy of the base peak masses for the signal

A copy of the base peak masses for the signal

Test if the signal is valid

True if both times and intensities have been set, and are the same length

Calculate the average change in Y from one point to the next.

The first point. The last point. the average change in Y

Find the index of the time value which is closest to a supplied time.

Time to search for The index of the nearest time in the signal

Find the index of the time value which is at or after the supplied "staring time". That is, the first point in range.

The time to search for the index of the time value in the times array which is at or after the parameter "time"

Find the index of the scan value which is at or after the supplied "staring scan". That is, the first point in range.

The scan number to search for The index of the scan in the scans array which is at or after the parameter "scan"

Find the index of the time value which is at or before the supplied "ending time". That is, the last point in range.

The time to search for the index of the time (in the times array) which is at or before the parameter "time"

Find the index of the scan value which is at or before the supplied "ending scan". That is, the last point in range.

The scan number to search for The index of the scan (in the scans numbers array) which is at or before the parameter "scan"

Returns the first scan number

First scan

GetNthScan - Returns the Nth scan for this filter

If all the scans for this filter are listed in an array, this is the index of the scan to return Nth scan

GetScanIndex -return the index into the signal for this scan

The scan whose index is desired The index for this scan number. If there is no data, the return is 0. If there are scans in the array, but this does not match a specific scan, the index of the next point in the chromatogram is returned. If there are scans, but this is beyond all scans, the index of "one beyond the data" is returned. This is equivalent rule to the return of 0, when there is an empty chromatogram

Search for a particular scan number

The scan number. The index of the found scan

GetNextScan - get the next scan from a given scan

The current scan The next scan, or -1 if there are no more scans in the chromatogram

Gets the previous scan from given scan

The current scan The previous scan

Determines if two scans are adjacent. That is: They are the scan numbers of consecutive points in the signal. Scan numbers may be presented in any order. A scan is not adjacent to itself.

the first scan the second scan true if the scans are adjacent

Counts the number of scans in the signal between the start and stop, including the start and stop scans. It is expected that the start and stop numbers will be valid scan numbers from the signal points.

First scan number Last scan number the scans in this interval. E.g., if there is only one filter type, returns stop-start+1. For these unexpected cases: The method will return 0 if the scans numbers are out of order. If the start is not a scan of a point in the signal, then counting begins at the first signal point after the start. If the end is beyond the end of the signal, then the "index of the end scan" is considered to be one beyond the end of the signal so the count would be 1 higher.

Find the scan number of the point in the signal, which is nearest to the number of the scan passed in.

Scan number to search for Closest scan number in the signal

Count the number of above zero points

the number of above zero points

Trivial integration: Sum all absolute intensities of points which lie between start time and end time. For example: Intensities 1,2,-4 give a total of 7. For a more sophisticated "area" integration (using both time and intensity), use Integrator.ManualIntegrate or Integrator.Integrate

Start of peak to integrate. Times greater or equal to this included. End of peak to integrate. Times less than or equal to this included The sum of all absolute values whose time is within the range.

Find the location of the maximum point for the specified signal in the specified range.

The start index. The end index. index of max

Find the location of the minimum point for the specified signal in the specified range.

The start index. The end index. index of min

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Signal.

Return a signal based on a time range

Start of time range for generated signal End of time range for generated signal A signal created based on the requested time range

Create a signal with no limits

A signal with all available data

Smooth data, where the data is an array of doubles. This offers multiple algorithms for "FIR filtering". This class uses FIR methods, where the taps are calculated based on an envelope shape. Various methods permit different handling of "baseline" before and after the selected signal. Such as: Considering that the fits and last values continue before and after the data. Using a value "0" as the bassline before and after the data (or any other specific value) Generating a "virtual baseline" before and after the data, correcting for the issue that the first and last values are underrepresented, such that the total of the smoothed data values is closer to the original total. If wishing to preserve total signal after a smooth, "

Initializes a new instance of the class. Construct a smoother with a selected smooth envelope

Smoothing envelope shape Length of envelope

Initializes a new instance of the class. Make a copy of the smoothing object

Object to copy

smooth the supplied data with a repeated moving mean method. This algorithm assumes that the signal is extended backwards by the first data point repeated and forwards by the final data point repeated. This permits smoothing points to be as much as twice the data length. For example, 4 data points can be smoothed by a "9 point smooth" since "(int)(9/2) = 4". However, 4 data points will not be smoothed by an 11 point smooth.

the data to smooth The number of points in the smoothing window. Even values are increased to the next odd number. The number times to smooth The smoothed data

Smooth the supplied data. The data is assumed to extend infinitely before the first data value, repeating the baseline value. The data is assumed to extend infinitely after the final data value, repeating the baseline value. For example: A 9 point Moving Mean smooth of (1000, 0, 0, 1000) with the default baseline of 0.0 sees: (0, 0, 0, 0, 0, 0 [1000, 0, 0, 1000] 0, 0, 0, 0, 0, 0) So: each smoothing step will see "2 entries of 1000 plus 7 of 0", which divides by 9 to give 222.222. To auto extend the first and last data points, instead of supplying a baseline value, see "Smooth".

Smoothing parameters the data to smooth The baseline value, repeated before and after the supplied data The smoothed data

Smooth the supplied data. The data is assumed to extend infinitely before the first data value, repeating the baseline left value. The data is assumed to extend infinitely after the final data value, repeating the baseline right value. For example: A 9 point Moving Mean smooth of (1000, 0, 0, 2000) with the baselines of 100, 200: (100, 100, 100,100, 100, 100 [1000, 0, 0, 2000] 200, 200, 200, 200, 200, 200) To auto extend the first and last data points, instead of supplying a baseline value, see "Smooth".

Smoothing parameters the data to smooth The baseline value, repeated before the supplied data The baseline value, repeated after the supplied data The smoothed data

The internal version of smooth with baseline extension. Does not need "null checks"

The smoothing parameters The data to be smoothed The baseline left. The baseline right. The smoothed data

smooth with smart tailing. This recognizes that the first and final values are not represented fully in the smoothed result. For example: a 9 point smooth, starting with value "1000", this value would be counted in 5 times, smoothing the first 5 points, then divided by 9 at each use of the value so: only 5*1000/9 would be included and 4*1000/9 would be lost. This algorithm creates an artificial baseline left and right of the data which corrects for this. Similar issues for "second values" or "second to last" are addressed by this algorithm. Such that: When used with a moving mean smooth, the "total abundance" is always preserved (except in rare cases where the data length is smaller than the smooth length, where this algorithm cannot be fully applied)

The smoothing settings. The data to be smoothed The smoothed data for null parameters

create data with auto baseline.

The smoothing settings. The data to smooth. The smoothed data.

Smooth the supplied data. The data is assumed to extend infinitely before the first data value, repeating the first value. The data is assumed to extend infinitely after the final data value, repeating the final value. For example: A 9 point Moving Mean smooth of [1000, 0, 0, 1000] sees: (1000, 1000, 1000, 1000, 1000, 1000 [1000, 0, 0, 1000] 1000, 1000, 1000, 1000, 1000, 1000) So: each smoothing step will see "7 entries of 1000 plus 2 of 0", which divides by 9 to give 777.77. Calling code which needs a different behavior (such as "all prior values are 0") can achieve this by inserting the data to be smoothed into an array 2 elements larger, where the first and last values are 0. The method "SmoothWithBaselineExtension" can be used for this

Smoothing parameters the data to smooth The smoothed data

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Replicate.

Smooth an array of doubles

The data to smooth (unchanged) A new array containing a smoothed copy of data

Average smooth results.

The smooth less. The smooth more. A combination of the two smoothing operations

Set up a equal weighting smoother.

number of filter taps

Set up a Gaussian smoother.

width of filter, must be odd. fraction of Center value at cutoff, e.g. 0.05 for 5%.

Set the FIR "finite impulse response" filter coefficients.

pointer to list of filter values, count: number of filter values.

Find a peak based on spectral matching. This class includes algorithms to match an expected scan against scans found at detected peaks. From time to time the algorithm needs scan data to compare against. To avoid tie in with any particular file system, an abstract class is used to delegate that work to the caller. The callers derived object deals with any file system specific information (such as open files or database, data filtering mechanisms) FIX: This class is incomplete and not tested. DO not use!

The match range.

The max spectrum points.

Gets or sets the chromatogram which is peak detected

Gets or sets the end of valid retention time range for finding peaks

Gets or sets the forward find threshold: TODO: May Need Fix: needs definition

Gets or sets the match threshold: TODO: May Need Fix needs definition

Gets or sets the reverse find threshold FIXFOXFIX needs definition

Gets Object for fetching scans from a raw file (IRawData) Calling code should call "Source.SetRawFile(myFile)" to set the input data for the finder

Gets or sets start of valid retention time range for finding peaks

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current .

Find peaks with matching spectrum

The spectrum to search for. Spectrum of analyte Predicted scan time Integrator, to detect peaks Returned: time of best match Table of results

Match the spectrum with the analyte spectrum

Spectrum from file Spectrum from analyte definition Returned sum of intensity products, from matching peaks Returned sum of square roots of intensity products, from matching peaks

Compare candidates.

The c 1. The c 2. 1 if C2 is better. -1 if C1 is better.

Compare spec points highest intensity.

The c 1. The c 2. 1 if c2 is greater than c1 -1 if c1 is greater than c2. 0 if the same.

Compare spec points lowest mass.

The c 1. The c 2. 1 if c1 mass is greater than c2 mass -1 if c2 mass is greater than c1 mass 0 if the same.

Get the top peaks in a scan, and sum the intensities

Scan to analyze Sum of intensities

Peak detect the find trace.

The find results. The find peak detection. The peaks found.

Go through all scans in the window, calculating match values.

Target (analyte) spectrum Results of matches, added to this list First scan Last scan Where this spectrum is expected to be Sum of intensities ion spectrum spectrum

Peak detect quan mass trace.

The integrator. The integrated peaks

Class to perform system suitability calculations. These calculations check the shape of detected peaks

Run the system suitability tests.

Algorithm parameters (from UI) Chromatogram signal containing the peak Peak to analyze the window to look for a concave peak, value in seconds The results of all tests

Run peak classification tests.

The peak. The results. The settings. The checks. The search window.

Test if peak edge passed a threshold (going down from the apex). For "valley" peaks, the peak drops below a calculated valley level (based on peak integration settings). For "stripe" peaks, the peak drops below a calculated threshold based on a peak tailing constraint (using PeakHeightPercentage) . For "tail" peak has a tail, causing the peak to end early (above the constraint threshold) and is possibly not resolved (from it's tail). For other edge types, there is no defined "end intensity". The peak may end, for example, at the end of the signal.

The edge type. The .

test if always resolved.

The edge type. The .

Run resolution checks.

The peak. The results. The settings. The checks.

Get valley retention time.

The peak. valley retention time.

This class was originally: Thru-put (Target) data system integrated peak.

Initializes a new instance of the class.

Gets or sets Next integrated peak.

Gets or sets Parent for Tangent Skimming.

Gets or sets XStart.

Gets or sets XTop.

Gets or sets XEnd.

Gets or sets a value indicating whether a Shoulder was Detected.

Gets or sets a value indicating whether peaks Overlap.

Gets or sets PeakType.

Gets or sets StartBaselineType.

Gets or sets EndBaselineType.

Gets or sets Area.

Gets or sets Height.

Gets or sets Start.

Gets or sets Top.

Gets or sets End.

Gets or sets a value indicating whether NegativePeak.

Gets or sets YStart.

Gets or sets YEnd.

Calculate the raw area of the specified peak. This calculation takes the baseline into account, but does not include removal of any extra area from tangent skim (child) peaks that may be present..

The signal. The calculated peak area.

Calculate the baseline corrected peak height. This the raw peak height minus the baseline height at "iTop" point of the peak.

The signal. The calculated peak height.

Test if the next peak not negative.

True if the next peak not negative.