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LaneRuler File List

Here is a list of all documented files with brief descriptions:
trunk/anacutoff.h [code]Defines a struct to hold cutoffs and constants for the program, and define their default values as well
trunk/asymmetry.cFunction to calculate, sort and evaluate the asymmetry score in each lane
trunk/asymmetry.h [code]Header file for asymmetry.c, contains functions for calculating and evaluating the asymmetry in each lane
trunk/border.cFunction to find the outer most lanes by first finding the outer most marker lanes
trunk/border.h [code]Header file for border.c, contains function to find the outer most lanes by first finding the outer most marker lanes
trunk/checknogrowths.cFunctions to extract the median row for each lane and outputs the thresholded roughness and maxdiff to a file
trunk/checknogrowths.h [code]Header file for checknogrowths.c, contains functions to extract the median row for each lane and outputs the thresholded roughness and maxdiff to a file
trunk/checkresult.h [code]
trunk/diagnostic.cFunction to write a PNG of the gel with node and peak position information overlaid. Interpolated peaks are shown in red for diagnostic purposes
trunk/diagnostic.h [code]Header file for diagnostic.c, contains function to write a PNG of the gel with node and peak position information overlaid. Interpolated peaks are shown in red for diagnostic purposes
trunk/fftw3.h [code]
trunk/findlanes.cFile holding the main for findlanes
trunk/findlanes.h [code]Header file for findlanes.c holds the default gel parameters
trunk/gelinfo.h [code]
trunk/mapto8bits.cFunctino to map a 16 bit image to 8 bit and stretches its dymanic range to be full scale
trunk/mapto8bits.h [code]Header file for mapto8bits.c, maps a 16 bit image to 8 bit and stretches its dymanic range to be full scale
trunk/medianfilter.cImplements a 3x3 then 1x9 median filter for a PIX
trunk/medianfilter.h [code]Header file for medianfilter.c, implements a 3x3 then 1x9 median filter for a PIX
trunk/node.cImplements functions for extrapolating nodes to the edge, adjusting the boundary nodes, and writing lanes information to file
trunk/node.h [code]Header file for node.c, implements functions for extrapolating nodes to the edge, adjusting the boundary nodes, and writing lanes information to file
trunk/noisedetect.cFunctions to find multi-lane noise
trunk/noisedetect.h [code]Header file for noisedetect.c, contains functions to find multi-lane noise
trunk/peaks.cFunction for finding guassian-like peaks in a vector of intensity
trunk/peaks.h [code]Header file for peak.c, contains function for finding guassian-like peaks in a vector of intensity
trunk/position.cFunctions for peak matching and curvature calculations and output
trunk/position.h [code]Header file for position.c, contains functions for peak matching and curvature calculations and output
trunk/readlanes.cRead and parse lanes file in gel directory for node and peak positions for generation of traces16 without re-lanetracking
trunk/readlanes.h [code]Header file for readlanes.h, read and parse lanes file in gel directory for node and peak positions for generation of traces16 without re-lanetracking
trunk/readtiff.cHolds function to read in 16bit tiff file (image.tif)
trunk/readtiff.h [code]Header file for readtiff.c, holds function to read in 16bit tiff file (image.tif)
trunk/spacing.cAlgorithm for finding the dominant lane spacing in the gel as well as the dominant spacing of each zone
trunk/spacing.h [code]Header file for spacing.c, contains algorithm for finding the dominant lane spacing in the gel as well as the dominant spacing of each zone
trunk/toneadjust.cHolds functions for tone mapping for contrast enhancement using a bezier curve
trunk/toneadjust.h [code]Header file for toneadjust.c, has function for tone mapping for contrast enhancement using a bezier curve
trunk/traces16.cFunction to write lane straightened image to traces16 file
trunk/traces16.h [code]Header file for traces16.c, contains function to write lane straightened image to traces16 file
trunk/zone.cFunctions related to the initialization operations of zone boundary, nodes, and zoneprojection
trunk/zone.h [code]Header file for zone.c, contains functions related to the initialization operations of zone boundary, nodes, and zoneprojection

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