From b18a1c76652df93b1155b56ccc6eb115340c2e31 Mon Sep 17 00:00:00 2001
From: Alan Race <alan.m.race@gmail.com>
Date: Tue, 28 Jul 2020 09:28:21 +0200
Subject: [PATCH] Reorganised starting of software to be a function

This will allow generation of App and Standalone installers
---
 src/SpectralAnalysis.m => SpectralAnalysis.m  | 21 +++----------------
 docs-src/content/installation/_index.md       |  4 +---
 files/README                                  |  2 --
 runSpectralAnalysis.m                         |  1 +
 .../peakfilter}/PeakThresholdFilterMedian.m   |  0
 src/{ => util}/strsplit.m                     |  0
 6 files changed, 5 insertions(+), 23 deletions(-)
 rename src/SpectralAnalysis.m => SpectralAnalysis.m (52%)
 delete mode 100644 files/README
 rename src/processing/{preprocessing => peakdetection/peakfilter}/PeakThresholdFilterMedian.m (100%)
 rename src/{ => util}/strsplit.m (100%)

diff --git a/src/SpectralAnalysis.m b/SpectralAnalysis.m
similarity index 52%
rename from src/SpectralAnalysis.m
rename to SpectralAnalysis.m
index f00b8a2..ed1b19e 100644
--- a/src/SpectralAnalysis.m
+++ b/SpectralAnalysis.m
@@ -1,5 +1,6 @@
 %% SpectralAnalysis
 % Spectral Imaging analysis software
+function spectralAnalysis = SpectralAnalysis()
 
 % Get location of current m-file
 if(isdeployed())
@@ -23,27 +24,11 @@
 if ~exist(spectralAnalysisHome, 'file')
     mkdir(spectralAnalysisHome);
     
-    copyfile([path filesep '..' filesep 'files' filesep 'profiles'], [spectralAnalysisHome filesep 'profiles'])
+    copyfile([path filesep 'files' filesep 'profiles'], [spectralAnalysisHome filesep 'profiles'])
 end
 
 % TODO: Check version on github to see if update available
 
 % Launch spectral analysis interface
-try 
-    spectralAnalysis = SpectralAnalysisInterface();
-catch err
-    if((strcmp(err.identifier, 'MATLAB:class:undefinedMethod') || strcmp(err.identifier, 'MATLAB:class:InvalidSuperClass')) ...
-            && ~isempty(strfind(err.message, 'Figure')))
-        disp('ERROR: Missing MOOGL. Download from https://github.com/AlanRace/MOOGL and place in src/gui/MOOGL folder');
-        
-        return;
-    else
-        throw(err);
-    end
-end
-
+spectralAnalysis = SpectralAnalysisInterface();
 
-% Check that a valid licence exists, otherwise show the 
-if(~isValidLicence())
-    MissingLicenceFigure();
-end
\ No newline at end of file
diff --git a/docs-src/content/installation/_index.md b/docs-src/content/installation/_index.md
index ad0452f..0d79a3a 100644
--- a/docs-src/content/installation/_index.md
+++ b/docs-src/content/installation/_index.md
@@ -20,12 +20,10 @@ The source code version requires a valid MATLAB licence.
 
 #### Installation with Git
 
-1. Clone the repository and initialise the submodules
+1. Clone the repository
 
 ```bash
 git clone https://github.com/AlanRace/SpectralAnalysis
-cd SpectralAnalysis
-git submodule update --init
 ```
 
 2. Open MATLAB and navigate to the folder containing the source code 
diff --git a/files/README b/files/README
deleted file mode 100644
index 640ff6a..0000000
--- a/files/README
+++ /dev/null
@@ -1,2 +0,0 @@
-                    SpectralAnalysis 0.75
-                         Alan Race
\ No newline at end of file
diff --git a/runSpectralAnalysis.m b/runSpectralAnalysis.m
index fd6b40b..01837dd 100644
--- a/runSpectralAnalysis.m
+++ b/runSpectralAnalysis.m
@@ -2,6 +2,7 @@
 path = [fileparts(mfilename('fullpath')) filesep 'src'];
 
 % Ensure all folders are on the path
+addpath(fileparts(mfilename('fullpath')));
 addpath(genpath(path));
 
 SpectralAnalysis
\ No newline at end of file
diff --git a/src/processing/preprocessing/PeakThresholdFilterMedian.m b/src/processing/peakdetection/peakfilter/PeakThresholdFilterMedian.m
similarity index 100%
rename from src/processing/preprocessing/PeakThresholdFilterMedian.m
rename to src/processing/peakdetection/peakfilter/PeakThresholdFilterMedian.m
diff --git a/src/strsplit.m b/src/util/strsplit.m
similarity index 100%
rename from src/strsplit.m
rename to src/util/strsplit.m