% Formerly CBT.Hca.Settings.set_fast_sets
%
%
%
minLen = 0; % minimum length of barcodes for comparison
timeFramesNr = 0; % 0 - take all timeframes
alignMethod = 1; % 1 - nralign, 2 - ssdalign, 3 - ssg
genConsensus = 0; % generate consensus
plotallmatches = 0;
adddefaulttheorysets = 0;
  
skipEdgeDetection = 0; % skip edge detection
edgeSettings = 1;
skipDoubleTanhAdjustment = 1;
comparisonMethod = 'mass_pcc'; % method for comparison of exp vs theory, alt 'unmasked_pcc_corr', 'mass_pcc', 'mp', and less tested onces, such as 'spearman'..
w = 200; %
displayResults = 1;
saveinfoscores = 1; % if to save infoscores

skipPrechoice = 1;
prestretchMethod = 0; % 0 - do not prestretch % 1 - prestretch to common length
theories = 'theories_2020-03-13_15_17_22_.txt'; % theories either as mat or directly txts
userDefinedSeqCushion = 20;
useGUI = 1; % whether to use GUI
[subfragment]
askForSubfragmentSettings = 1; % whether to ask for subfragment settings (to be implemented)
generate = 1; % whether to generate subfragments
numberFragments = 4; % how many subfragments to generate
%randomPosition = 1; % if position should be random
%fragmentLength = 200; % otherwise splits the length of barcode into totalLength/numberFragments

[filterSettings]
filter = 0; % filter
% filter settings. For one timeframe, refer to P.Torche paper for best
filterMethod = 0; % 0 - filter after stretching, 1 - before
filterSize = 2.3;
  
[kymosets]
askforkymos = 1; % sould we ask for kymos  
% sample filename, comment out for the release version
kymoFile = 'kymos_2020-03-13_14_26_49_.txt'; % if file with kymograph txt's was generated before, this is the name of the folder
% all the different setting choices
askforsets = 1; % should we ask for settings
[random]
generate = 0; % generate random
noOfCutouts = 2; % number of random cutouts from the input set
cutoutSize = 200; % size of region to be cut out (units: pixels)

% bitmask settings
[bitmasking]
prestretchPixelWidth_nm = 130; % camera nm/px
psfSigmaWidth_nm = 300; % psf in nanometers
deltaCut = 3; % how many delta's should we take
%untrustedPx = sets.bitmasking.deltaCut*sets.bitmasking.psfSigmaWidth_nm/sets.bitmasking.prestretchPixelWidth_nm;

[consensus]
barcodeNormalization = 'bgmean';
promptForBarcodeClusterLimit = 1;
threshold = 0.75;

% import OptMap.MoleculeDetection.EdgeDetection.get_default_edge_detection_settings;
%  sets.edgeDetectionSettings = get_default_edge_detection_settings(sets.skipDoubleTanhAdjustment);

[export]
savetxt = 1;

[theory]
askfortheory = 1;
precision = 5;  %default is 5;
askfornmbp = 1;
nmbp = 0.225;
skipStretch = 1;
stretchFactors = [0.95 0.96 0.9700    0.9800    0.9900    1.0000    1.0100    1.0200    1.0300 1.04 1.05];
theoryDontSaveTxts = 0;
%    sets.theory.askfortheory = 1;
% 	sets.theoryFileFold{1} = '/home/albyback/rawData/dnaData/humanData/';
%     sets.theoryFile{1}= 'ncbi_chromosomes_181022_130nmPixel_0.3nmPERbp.mat';
%   sets.theoryFileFold{1} = '';
%   sets.theoryFile{1} = '';
%  sets.theory.askfornmbp = 1;
%  sets.theory.nmbp = 0.225;
%sets.theory.skipStretch = 1; %0 - do not stretch,  1 - stretch
%	sets.theory.stretchFactors = [0.95 0.96 0.9700    0.9800    0.9900    1.0000    1.0100    1.0200    1.0300 1.04 1.05];
%         % 
    

[pvalue];    
file = ''; 
promtforparams = 0;
len2 = 5000000;
pixelWidth_nm = 130;
lenMin = 100;
lenMax = 1000;
numRnd = 1000;
psfSigmaWidth_nm = 300;
    
[output]
matDirpath = ''
askforoutputdir = 1;

