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MQScript Auxiliary Functions |
| double | length (VariantArray array) |
| | Returns the length of an array.
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| double | verbose (void) |
| | Toggles the verbose mode.
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| double | Number_Save (double number, char *filename) |
| | Saves a number to a file.
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MQScript Map2D Input/Output Functions |
| Map2D | Map_Load (char *mqf_map) |
| | Loads and returns a data structure of a 2D-map (Map2D).
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Map2D | lmap (char *mqf_map) |
| | Short-hand version of Map_Load.
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| double | Map_Save (Map2D map, char *mqf_map) |
| | Saves a 2D-map (Map2D) at the location filename.
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double | smap (Map2D map, char *mqf_map) |
| | Short-hand version of Map_Save.
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| double | Map_Remove (char *mqf_map) |
| | Deletes a 2D-map file at the location mqf_map.
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double | rmmap (char *mqf_map) |
| | Short-hand version of Map_Remove.
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MQScript Map2D Get Functions |
| double | Map_GetArea (Map2D map) |
| | Calculates and returns the area of the 2D-map.
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| double | Map_GetMedian (Map2D map, double mode) |
| | Calculates and returns the median of the abundance values for all the points in a 2D-map.
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| double | Map_GetAvgAbsDevFromValue (Map2D map, double value, double mode) |
| | Calculates and returns the average absolute deviation from a given value for all the abundance values of the points in a 2D-map.
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| double | Map_GetMedianAbsDevFromValue (Map2D map, double value, double mode) |
| | Calculates and returns the median absolute deviation from a given value for all the abundance values of the points in a 2D-map.
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| double | Map_GetMean (Map2D map, double mode) |
| | Calculates and returns the mean of the abundance values for all the points in a 2D-map.
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| double | Map_GetSD (Map2D map, double mean, double mode) |
| | Calculates and returns the standard deviation of the abundance values for all the points in a 2D-map.
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| VariantArray | Map_GetSegmentArray (Map2D map) |
| | Returns all the segments of a segmented map in an array.
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| VariantArray | Map_GetSegmentArrayContainingPeaks (Map2D map, VariantArray peaks, double dMZTolerance, double nScanTolerance) |
| | Returns only the segments of a segmented map that contain the peaks of interest.
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MQScript Map2D Processing Functions |
| Map2D | Map_ApplyFilter (Map2D map, char *filter, double dim) |
| | Applies a convolution filter to a 2D-map (Map2D).
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Map2D | filtermap (Map2D map, char *filter, double dim) |
| | Short-hand version of Map_ApplyFilter.
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| Map2D | Map_Segment (Map2D map, double bin_size) |
| | Applies the watershed algorithm to a 2D-map (Map2D).
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Map2D | segmap (Map2D map, double bin_size) |
| | Short-hand version of Map_Segment.
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| Map2D | Map_ApplyOpening (Map2D map, char *structel) |
| | Applies a morphological opening to the 2D-map (Map2D).
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Map2D | openmap (Map2D map, char *structel) |
| | Short-hand version of Map_ApplyOpening.
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| Map2D | Map_ApplyClosing (Map2D map, char *structel) |
| | Applies a morphological closing to the 2D-map (Map2D).
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Map2D | closemap (Map2D map, char *structel) |
| | Short-hand version of Map_ApplyClosing.
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| Map2D | Map_ApplyLinearInterpolation (Map2D map) |
| | Applies a linear interpolation for each mass chromatogram.
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Map2D | linintermap (Map2D map) |
| | Short-hand version of Map_ApplyLinearInterpolation.
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| Map2D | Map_RemoveStreaks4 (Map2D map) |
| | Removes the streaks from a map.
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Map2D | rstreaks4 (Map2D map) |
| | Short-hand version of Map_RemoveStreaks4.
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| VariantArray | Map_FindPeaks (Map2D source, char *structel, double abuthr) |
| | Finds peaks in a map.
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VariantArray | findpk (Map2D source, char *structel, double abuthr) |
| | Short-hand version of Map_FindPeaks.
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| Map2D | Map_Extract (Map2D source, Map2D stencil, Segment segment) |
| | Extracts a segment map.
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Map2D | extractmap (Map2D source, Map2D stencil, Segment segment) |
| | Short-hand version of Map_Extract.
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MQScript Peak Related Functions |
| VariantArray | PeakArray_Load (char *mqf_pk) |
| | Loads a peak series.
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VariantArray | lpk (char *mqf_pk) |
| | Short-hand version of PeakArray_Load.
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| double | PeakArray_Print (VariantArray array) |
| | Prints a peak series.
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| double | PeakArray_Save (VariantArray array, char *mqf_pk) |
| | Saves a peak series.
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| double | PeakArray_SaveWithMapValue (VariantArray array, Map2D map, char *mqf_pk) |
| | Saves a peak series with value in map.
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| double | PeakArray_SavePhysQuantWithMapValue (VariantArray array, Map2D map, char *mqf_pk) |
| | Saves a peak series using their physical quantity values (time and m/z) and the intensity value.
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| double | PeakArray_SaveWithBaseline (VariantArray array, Map2D map, char *mqf_pk) |
| | Saves a peak series with baseline values.
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MQScript FPeak Related Functions |
| VariantArray | FPeakArray_Load (char *mqf_fpk) |
| | Loads a fpeak series.
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VariantArray | lfpk (char *name) |
| | Short-hand version of FPeakArray_Load.
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| double | FPeakArray_Print (VariantArray array) |
| | Prints an array of type FPeak2i to standard output.
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| VariantArray | FPeakArray_GetPeaksNotInPeakGroup (VariantArray pFPeaksAll, PeakGroup peakgroup) |
| | Returns the subset of fpeaks from a set of fpeaks, that do not belong to a particular peakgroup.
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| VariantArray | FPeakArray_GetPeakArray (VariantArray array) |
| | Converts an array of type FPeak2i to an array of type Peak2i.
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| Map2D | FPeakArray_CreateMapFrom (VariantArray array, Map2D template_map) |
| | Creates a map from an array of peaks of type FPeak2i.
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MQScript Segment Related Functions |
| Segment | Segment_FindAndFitPeaks (Segment segment, Map2D map, char *structel, double abuthr, char *curve) |
| | Finding and fitting peaks in a 2D-map.
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| Map2D | Segment_GetMap (Segment segment, Map2D source, Map2D mask) |
| | Extracts a segment map.
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| double | Segment_Save (Segment segment, char *mqf_fpk) |
| | Saves a Segment in a file mqf_fpk.
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| double | Segment_Print (Segment segment) |
| | Prints a Segment to standard output.
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| VariantArray | Segment_GetFPeaks (Segment segment) |
| | Gets the FPeak2i array from a Segment.
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| VariantArray | SegmentArray_Load (char *mqf_fpk) |
| | Loads an array of type Segment.
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| double | FPeakFile_WriteHeader (char *szFilename, Map2D source, char *curve, double nsegments) |
| | Saves the header of a fpeaks file.
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| double | FPeakFile_CalcStatAndSave (char *mqf_fpk) |
| | Calculates and saves the statistics of attributes of the fpeaks.
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MQScript PeakGroup Related Functions |
| VariantArray | PeakGroupArray_Load (char *mqf_pgr) |
| | Loads a peakgroup array from a pgroups file.
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VariantArray | lpg (char *mqf_pgr) |
| | Short-hand version of PeakGroupArray_Load.
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| double | PeakGroup_Print (PeakGroup peakgroup) |
| | Prints a PeakGroup in standard out.
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| double | PeakGroup_Save (PeakGroup peakgroup, char *filename, double type) |
| | Saves a PeakGroup in a file.
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| VariantArray | PeakGroup_GetFPeaks (PeakGroup peakgroup) |
| | Gets the FPeak2i array from a PeakGroup.
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VariantArray | getfpk (PeakGroup peakgroup) |
| | Short-hand version of PeakGroup_GetFPeaks.
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| PeakGroup | PeakGroup_Create (VariantArray array) |
| | Creates a peakgroup.
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PeakGroup | mkpg (VariantArray array) |
| | Short-hand version of PeakGroup_Create.
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| VariantArray | PeakGroupArray_GetFPeaks (VariantArray pg_array) |
| | Gets the FPeak2i array from a PeakGroup array.
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VariantArray | vgetfpk (VariantArray pg_array) |
| | Short-hand version of PeakGroupArray_GetFPeaks.
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| Map2D | getpgmap (PeakGroup peakgroup, Map2D source, Map2D stencil) |
| | Returns the peakgroup map of a peakgroup.
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| VariantArray | getpgmappeaks (PeakGroup peakgroup, char *mqf_fpk) |
| | Returns the fpeaks that are found in a peakgroup map.
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| double | PeakGroupFile_WriteHeader (char *mqf_fpk, char *type, char *curve, double npg, double npeaks) |
| | Saves the header of a pgroups file.
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MQScript FPeak Clustering Related Functions |
| double | FPeakFile_ClusterAndSave (char *mqf_fpk_in, char *mgf_pgr_out, double scan_thr, double mz_thr, double abund_thr, double nLinkageType) |
| | Clusters fpeaks (FPeak2i) into co-eluting peakgroups (PeakGroup).
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| double | PeakGroupFile_ClusterAndSave (char *mgf_pgr_in, char *mgf_pgr_out, double scan_thr, double mz_thr, double abund_thr, double nLinkageType) |
| | Clusters fpeaks (FPeak2i) iteratively in each PeakGroup of a PeakGroup array.
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MQScript SegmentHandler Related Functions |
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SegmentHandler | SegmentHandler_Init (char *peakgroupfilename) |
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SegmentHandler | SegmentHandler_Set (SegmentHandler seghand, PeakGroup peakgroup) |
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Map2D | SegmentHandler_GetMap (SegmentHandler seghand, PeakGroup peakgroup) |
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VariantArray | SegmentHandler_GetMapPeaks (SegmentHandler seghand, PeakGroup peakgroup) |
MQScript PeakGroup Refining/Deconvolving Functions |
| PeakGroup | PeakGroup_Refine7 (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char *struct_elem, double abu_thr, char *curve, double scan_window, double mz_overlap_thr) |
| | Deconvolves overlapping fpeaks in a PeakGroup.
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PeakGroup | refine7 (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char *struct_elem, double abu_thr, char *curve, double scan_window, double mz_overlap_thr) |
| | Short-hand version of PeakGroup_Refine7.
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| PeakGroup | PeakGroup_Deconv3 (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char *curve) |
| | Deconvolves the PeakGroup into IsotopicClusters using fitting.
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PeakGroup | deconv3 (PeakGroup peakgroup, Map2D PGMap, VariantArray pPGOutFPeaks, char *curve) |
| | Short-hand version of PeakGroup_Deconv3.
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| PeakGroup | PeakGroup_Deconv4 (PeakGroup peakgroup) |
| | Deconvolves the PeakGroup into IsotopicClusters without using fitting.
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PeakGroup | deconv4 (PeakGroup peakgroup) |
| | Short-hand version of PeakGroup_Deconv4.
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MQScript Manual/Visual Fitting Related Functions |
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double | fixmz (void) |
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double | fixz (void) |
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double | fixc (void) |
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double | fixsmz (void) |
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double | setsmz (double index, double value) |
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double | clrfitter (void) |
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double | commonsmz (void) |
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VariantArray | fit (double init_sigma_rt, double init_sigma_mz) |
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VariantArray | fitsmz (double init_sigma_rt, double smz_begin, double smz_end, double delta_sigma_mz) |
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VariantArray | fitpep (double charge, double carbons) |
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double | sfpk (VariantArray array, char *mqf) |
MQScript Visualization Related Functions |
| double | plotmap (Map2D map) |
| | Plots a variable of type Map2D.
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| double | overlaymap (Map2D map) |
| | Overlays the segment boundaries of a labelled map on a grayscale map.
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| double | plotpk (VariantArray array) |
| | Plots an array of peaks, either of type Peak2i or FPeak2i.
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| double | plotpg (VariantArray array) |
| | Plots an array of peakgroups.
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| double | plotseqsum (char *filename, char *which) |
| | Plots the sequest hits summarized in a seqsum file.
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| double | movepk (double handle, double dx) |
| | Moves the rendering of the peaks stored at the given handle position.
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| double | plotmqsqmap (char *filename) |
| | Plots the contents of an mqsqmap file.
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| double | plotms2 (char *ms2_exp_name) |
| | Plots all the ms/ms (sequencing events) on the map.
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| double | coversegments (VariantArray peak_array, double mz_threshold, double scan_theshold) |
| | Covers the segments that overlap with any of the rectangles surrounding the array of peaks.
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| double | coversegmentsonedge (void) |
| | Covers the segments that touch the top and bottom edges of a Map2D.
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| double | showlabels (void) |
| | Plots the label number of each segment.
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| double | axes (void) |
| | Toggles the values of the axes from sampling coordinates to physical quantities.
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| double | grid (void) |
| | Toggles the view of the grid.
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| double | zoomin (double x1, double x2, double y1, double y2) |
| | Zooms in the required rectangle.
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| double | setgraylevel (char *level) |
| | Sets the graylevel of the map.
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| double | goscan (double scan) |
| | Displays the mass spectrum of that scan.
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| double | show (double handle, char *field) |
| | Shows.
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| double | hide (double handle) |
| | Hides.
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| double | clear (double handle) |
| | Clears.
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MQScript Other Functions |
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Map2D | extractseam (Map2D smap1, Map2D smap2, Map2D lmap1, Map2D lmap2) |
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double | tilefpeakfile (char *mqf_fpk, char *mqf_pgf) |
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char * | print (char *string) |
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char * | int2str (double number, double width) |
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double | setfilter (char *filter) |
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double | createMS2table (char *expmntname) |
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double | printZoomBoundaries (void) |
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double | auxExtractMapShown (char *filename) |
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double | auxExtractMap (Map2D map, double x1, double x2, double y1, double y2, char *filename) |
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double | PrintFPeaksArrayInfo (VariantArray fpeaks, double parameter) |
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double | PeakArray_SaveDTAPositionsWithSequence (char *szSequestSummaryName, char *szSExperimentName, char *szQExperimentName, char *szOutputfile) |
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VariantArray | PeakArray_GetDTAPositions (char *szSequestSummaryName, char *szSExperimentName, char *szQExperimentName) |
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double | MS2GuidedQuantitation (Map2D map, double bin_width) |
![\[f(m, r; A, r_o, m_o, \sigma_m, \sigma_r) = \frac{A}{2\pi\sigma_m\sigma_r}e^{\frac{(r-r_o)^2}{2\sigma_r^2}}e^{\frac{(m-m_o)^2}{2\sigma_m^2}}\]](form_0.png)
