removed files that are now in main MATLAB

matlabcode/FCS/getAllFiles.m

-function fileList = getAllFiles(dirName, extension, file_pattern_matching, recursive)
-% GETALLFILES Recursively finds all the files in a folder and its subfolder with 'extension'
-% extension specified by the 3 digit string 'extension'
-%     dirName - root directory name
-%     extension - string for extension
-%     file_pattern_matching - a string contained in filename
-% Moshir Harsh, EMBL, November 2016
-% Antonio Politi, EMBL, January 2017 added file_patter_matching
-if nargin < 3
-    file_pattern_matching = [];
-end
-if nargin < 4
-    recursive = 1;
-end
-%TODO: Add a pattern matching clause to match file names
-dirData   = dir(dirName);      %# Get the data for the current directory
-dirIndex  = [dirData.isdir];   %# Find the index for directories
-dirData2 = dir(fullfile(dirName, ['*.' extension])); %Find only the files with the specific extension
-
-%dirData2 = dirData2(~cellfun('isempty', {dirData2.name})); %To remove the invalid output of dir if the folder is found empty of reqd files
-fileList = {dirData2.name}';  %'# Get a list of the files
-% perform pattern matching
-if ~isempty(file_pattern_matching)
-    idx = [];
-    for i=1:length(fileList)
-        if ~isempty(regexp(fileList{i}, file_pattern_matching, 'match'))
-            idx = [idx;i];
-        end
-    end
-    fileList = fileList(idx);
-end
-if ~isempty(fileList)
-    fileList = cellfun(@(x) fullfile(dirName,x),...  %# Prepend path to files
-        fileList,'UniformOutput',false);
-end
-subDirs    = {dirData(dirIndex).name};             %# Get a list of the subdirectories
-validIndex = ~ismember(subDirs,{'.','..'});     %# Find index of subdirectories
-%#   that are not '.' or '..'
-if recursive
-    for iDir = find(validIndex)                     %# Loop over valid subdirectories
-        nextDir = fullfile(dirName,subDirs{iDir});    %# Get the subdirectory path
-        fileList = [fileList; getAllFiles(nextDir, extension, file_pattern_matching, recursive)];  %# Recursively call getAllFiles
-    end
-end
-
-end
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matlabcode/FCS/getAllFolders.m

-function [folderList, level] = getAllFolders(dirName, file_pattern_matching)
-% GETALLFOLDERS Recursively finds all folders in a folder and its subfolder
-% that match/cotain file_pattern_matching
-%     dirName - root directory name
-%     file_pattern_matching - a string contained in filename
-% Antonio Politi, EMBL, January 2017 added file_patter_matching
-
-dirData   = dir(dirName);                                             % Get the data for the current directory
-dirIndex  = [dirData.isdir].*(~ismember({dirData.name}, {'.','..'}));   % index of valid subdirectories 
-dirData = dirData(find(dirIndex));                                          
-
-dirList = {dirData.name}';  % name of valid subdirectorues
-% perform pattern matching
-idx = [];
-for i=1:length(dirList)
-    if ~isempty(regexp(dirList{i}, file_pattern_matching, 'match'))
-        idx = [idx;i];
-    end
-end
-folderList = dirList(idx);
-if ~isempty(folderList)
-    folderList = cellfun(@(x) fullfile(dirName,x),...  %# Prepend path to files
-        folderList,'UniformOutput',false);
-end
-
-for i = 1:length(dirList)                  %# Loop over valid subdirectories
-    nextDir = fullfile(dirName, dirList{i});    %# Get the subdirectory path
-    folderList = [folderList; getAllFolders(nextDir, file_pattern_matching)];  %# Recursively call getAllFiles
-end
-
-end
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