#include "allheaders.h"
#include "gelinfo.h"
#include "anacutoff.h"
Go to the source code of this file.
Defines | |
#define | SIGMA_CUTOFF 4 |
sigma value used for peak finding | |
#define | FWHM_FACTOR 5.0/9.0 |
factor used to estimate the width of a peak based on generic spacing | |
#define | ZONE_PROJECTION_FACTOR 3 |
determines the number of zones to include in border finding | |
#define | BORDERTOLERANCEFACTOR 0.4 |
factor used to calculate the tolerance we allow from the expected spacing between lanes | |
#define | OFFSETFACTOR 40 |
factor used to determine along lane (x) offset allowed for correlation calculation | |
Functions | |
void | findBorder (FILE *FLAGOUT_FILE, PIX *pixGel, INT32 **ZoneProjection, struct GelInfo *GelInfo, struct AnaCutoff *AnaCutoff, int *ToneAdjusted, int Verbose) |
finds the outer most lanes by extrapolating from the outermost marker lanes. | |
float | correlation (PIX *pixGel, int row1, int row2, int start, int stop, int maxoffset) |
float | roughness (PIX *pixGel, int row, int start, int stop) |
calculates a roughness measure in a row in a PIX, defined as the sum of the absolute difference between neighbouring points normalized by the dynamic range of the pix |
These are tested for similary and roughness before accepted. Correlation and roughness code are also found here, which is also used for result checking.
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factor used to estimate the width of a peak based on generic spacing
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factor used to determine along lane (x) offset allowed for correlation calculation
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sigma value used for peak finding
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brief calculates the uncentered correlation between two rows in a PIX while allowing for a offset.
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finds the outer most lanes by extrapolating from the outermost marker lanes. Using the generic spacing, we estimate the distance between the outermost markers. A number of the first zones after the first data zone is chosen. Tone adjusted zones are not included, unless all zones considered have been tone adjusted From the sum of zone projection of these zones, we find two peaks close to the estimated distance apart. The data in these two rows are check for correlation with each other (with translational offset allowed) and with their respective neighbour marker lanes. The data is also checked for roughness. The results will be stored in GelInfo->LowYBorder and GelInfo->HighYBorder
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calculates a roughness measure in a row in a PIX, defined as the sum of the absolute difference between neighbouring points normalized by the dynamic range of the pix
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