Merge pull request #71 from RNA-FRETools/MASH-FRET-1.3.1-doc

MASH-FRET-1.3.1 Documentation update

Author: pflanzenhueter

MASH-FRET/.release_version.json

@@ -1,4 +1,4 @@
 {
-"tag" : "1.3.0",
-"prev_commit_hash" : "1aa5eac8"
+"tag" : "1.3.1",
+"prev_commit_hash" : "48221723"
 }

MASH-FRET/source/extern/README-MEX-FILES.txt

@@ -20,8 +20,8 @@ If working with Windows 32bit:
 
 	3) move the new .mexw32 files to MASH-FRET\source\extern\ITALS\runtime32
 
-If you have the MATLAB error message about a msising compiler (like I do), go to MATLAB menu "Environment"/"Add ons" and search for "mingw-w64".
-Then, apparently, you should follow the prompt instruction (which I can't access).
+If you have the MATLAB error message about a msising compiler, go to MATLAB menu "Environment"/"Add ons" and search for "mingw-w64".
+Then follow the prompt instruction.
 
 Once installed, try again steps 2) and 3).
 To be sure, test by add the "Gaussian filter (sensitive)".

docs/transition-analysis/workflow.md

@@ -124,7 +124,7 @@ To build the TDP:
    [Include last states](panels/panel-transition-density-plot.html#include-last-states)  
 
 1. Update the TDP and display by pressing 
-   ![Update](../../assets/images/gui/TA-but-update.png "Update").
+   ![Update](../assets/images/gui/TA-but-update.png "Update").
 
 
 ---
@@ -154,7 +154,7 @@ The number
 An example for 
 [*J*](){: .math_var } = 4 and for each cluster configuration is given below:
 
-<img src="../../assets/images/figures/TA-panel-state-configuration-clusters-config.png">
+<img src="../assets/images/figures/TA-panel-state-configuration-clusters-config.png">
 
 In the case of well-separated transition clusters, 
 [*K*](){: .math_var } is easily determined by eye, where a simple partition algorithm, like k-mean or manual clustering, can be used to cluster data.
@@ -290,7 +290,7 @@ To export data to files:
    [Molecule subgroup list](panels/panel-transition-density-plot.html#molecule-subgroup-list)  
 
 1. Open export options by pressing 
-   ![Export](../../assets/images/gui/TA-but-export.png "Export") and set the options as desired; please refer to 
+   ![Export](../assets/images/gui/TA-but-export.png "Export") and set the options as desired; please refer to 
    [Set export options](functionalities/set-export-options.html) for help.
 
 1. Press 

docs/video-processing/panels/panel-molecule-coordinates.md

@@ -158,9 +158,10 @@ It identifies bright spots considering:
 
 The Schmied2012 algorithm was written in C and was compiled to .mex file via the `mex` function of MATLAB. 
 The .mex file may work with certain MATLAB versions and lead to errors with others. 
-If the use of Schmied2012 gives an error, please recompile the .mex file by typing in MATLAB's command window:
+If the use of Schmied2012 gives an error, please recompile the .mex file by entering in MATLAB's command window the following:
 
 ```matlab
+cd 'xxxxx\MASH-FRET\source\extern\schmied2012'
 mex 'xxxxx\MASH-FRET\source\extern\schmied2012\forloop.c'
 ```