Merge pull request #74 from RNA-FRETools/MASH-FRET-1.3.2

Estimation of state degeneracy - panel "Kinetic model" - 2D-vbFRET - Linux compatibility - divers bug fixes

Author: pflanzenhueter

.githooks/pre-commit

@@ -1,4 +1,4 @@
 {
 "tag" : "1.3.1",
-"prev_commit_hash" : "48221723"
+"prev_commit_hash" : "e0bc2229"
 }

MASH-FRET/.release_version.json

@@ -1,13 +1,19 @@
-function h_fig = MASH(varargin)
+function varargout = MASH(varargin)
 
 % add source folders to MATLAB search path
+disp('set MATLAB search path...')
 codePath = fileparts(mfilename('fullpath'));
 addpath(genpath(codePath));
 
 % set MATLAB's character encoding
 feature('DefaultCharacterSet','windows-1252');
 
-% get MATLAB version
+% compile C functions
+disp('checking mex files...');
+checkMASHmex
+
+disp('build GUI...')
+% get MASH version
 version_str = getMASHversion(codePath);
 
 % define figure name from MASH-FRET version
@@ -17,8 +23,15 @@
 h_fig = buildMASHfig(figName);
 
 % initialize main figure
+disp('initialize GUI..')
 initMASH(h_fig);
 
 % make main figure visible
 set(h_fig,'visible','on');
 
+if nargout==1
+    varargout = h_fig;
+end
+
+disp('MASH-FRET is ready !')
+

MASH-FRET/MASH.m

@@ -0,0 +1,42 @@
+function h = buildMenuKineticAnalysis(h)
+% Creates sub-menus of "Standard kinetic analysis" menu in menubar.
+%
+% h = buildMenuKineticAnalysis(h);
+%
+% h: structure to update with handles to new UI components and that must contain fields:
+%  h.menu_kineticAnalysis: handle to menu "Standard kinetic analysis"
+%  h.figure_MASH: handle to main figure
+
+% Last update by MH, 21.12.2020: remove useless step 4 (back-simulation)
+% created by MH, 3.3.2020
+
+% default
+lbl0 = 'Import analysis file...';
+lbl1 = 'All steps';
+lbl2 = 'Step 1: Determine number of states';
+lbl3 = 'Step 2: Determine FRET states & deviations';
+lbl4 = 'Step 3: Determine transition rates';
+% lbl5 = 'Step 4: Back-simulation';
+
+% parents
+h_fig = h.figure_MASH;
+h_men = h.menu_kineticAnalysis;
+
+% GUI
+h.menu_kinAna_import = uimenu(h_men,'label',lbl0,'callback',...
+    {@menu_kinAna_import_Callback,h_fig});
+
+h.menu_kinAna_allSteps = uimenu(h_men,'label',lbl1,'callback',...
+    {@menu_kinAna_Callback,0,h_fig});
+
+h.menu_kinAna_step1 = uimenu(h_men,'label',lbl2,'callback',...
+    {@menu_kinAna_Callback,1,h_fig});
+
+h.menu_kinAna_step2 = uimenu(h_men,'label',lbl3,'callback',...
+    {@menu_kinAna_Callback,2,h_fig});
+
+h.menu_kinAna_step3 = uimenu(h_men,'label',lbl4,'callback',...
+    {@menu_kinAna_Callback,3,h_fig});
+
+% h.menu_kinAna_step4 = uimenu(h_men,'label',lbl5,'callback',...
+%     {@menu_kinAna_Callback,4,h_fig});

MASH-FRET/source/GUI/bar_menu/buildMenuKineticAnalysis.m

@@ -11,7 +11,7 @@
 
 % default
 lbl0 = 'Test interface';
-lbl1 = 'Kinsoft challenge';
+lbl1 = 'Standard kinetic analysis';
 
 % parents
 h_men = h.menu_routine;
@@ -20,6 +20,6 @@
 h.menu_testInterface = uimenu(h_men,'label',lbl0);
 h = buildMenuTestInterface(h);
 
-h.menu_kinsoftChallenge = uimenu(h_men,'label',lbl1);
-h = buildMenuKinsoftChallenge(h);
+h.menu_kineticAnalysis = uimenu(h_men,'label',lbl1);
+h = buildMenuKineticAnalysis(h);
 

MASH-FRET/source/GUI/bar_menu/buildMenuKinsoftChallenge.m

@@ -13,7 +13,8 @@
 lbl1 = 'project management area';
 lbl2 = 'panel "Transition density plot"';
 lbl3 = 'panel "State configuration"';
-lbl4 = 'panel "State transition rates"';
+lbl4 = 'panel "State lifetimes"';
+lbl5 = 'panel "Kinetic model"';
 
 % parents
 h_fig = h.figure_MASH;
@@ -33,4 +34,7 @@
     {@menu_routineTest_Callback,'ta','state configuration',h_fig});
 
 h.menu_TA_stateTranditionRatesTest = uimenu(h_men,'label',lbl4,'callback',...
-    {@menu_routineTest_Callback,'ta','state transition rates',h_fig});
+    {@menu_routineTest_Callback,'ta','state lifetimes',h_fig});
+
+h.menu_TA_kineticModelTest = uimenu(h_men,'label',lbl5,'callback',...
+    {@menu_routineTest_Callback,'ta','kinetic model',h_fig});

MASH-FRET/source/GUI/bar_menu/buildMenuRoutine.m

@@ -17,7 +17,8 @@
 %   p.fntclr2: text color in special pushbuttons
 %   p.tbl: reference table listing character's pixel dimensions
 
-% Last update by MH, 19.3.2020: increase speed by replacing wrapStrToWidth by wrapHtmlTooltipString
+% Last update by MH, 22.12.2020: add vFRET 2D
+% update by MH, 19.3.2020: increase speed by replacing wrapStrToWidth by wrapHtmlTooltipString
 % created by MH, 19.10.2019
 
 % default
@@ -34,7 +35,7 @@
 str5 = 'refine';
 str6 = 'binning';
 str7 = 'deblurr';
-str8 = {'Thresholds','vbFRET','One state','CPA','STaSI'};
+str8 = {'Thresholds','vbFRET-1D','vbFRET-2D','One state','CPA','STaSI'};
 str9 = {'bottom','top','all'};
 str10 = {'Select a trace'};
 str11 = 'Results (states):';

MASH-FRET/source/GUI/bar_menu/buildMenuTransitionAnalysisTest.m

@@ -1,7 +1,7 @@
 function h = buildPanelTA(h,p)
 % h = buildPanelTA(h,p);
 %
-% Builds "Transition analysis" module including panels "Transition density plot", "State configuration" and "State transition rates".
+% Builds "Transition analysis" module including panels "Transition density plot", "State configuration", "Dwell time histograms" and "Kinetic model".
 %
 % h: structure to update with handles to new UI components and that must contain fields:
 %   h.figure_MASH: handle to main figure
@@ -34,7 +34,8 @@
 str4 = 'Save';
 ttl0 = 'Transition density plot';
 ttl1 = 'State configuration';
-ttl2 = 'State transition rates';
+ttl2 = 'Dwell time hisotgrams';
+ttl3 = 'Kinetic model';
 ttstr0 = wrapHtmlTooltipString('Open <b>import options</b> to configure how state sequences are imported from ASCII files.');
 ttstr1 = wrapHtmlTooltipString('<b>Import state sequences</b> from a .mash file or from a set of ASCII files.');
 ttstr2 = wrapHtmlTooltipString('<b>Close selected project</b> and remove it from the list.');
@@ -56,6 +57,8 @@
 wedit0 = poslst0(3);
 wpan1 = (pospan(3)-4*p.mg-poslst0(3))/2;
 hpan1 = pospan(4)-2*p.mg;
+hpan2 = (pospan(4)-2*p.mg-p.mg/2)/2;
+hpan3 = pospan(4)-2*p.mg-p.mg/2-hpan2;
 
 % GUI
 h.pushbutton_TDPimpOpt = uicontrol('style','pushbutton','parent',h_pan,...
@@ -110,10 +113,18 @@
 h = buildPanelTAstateConfiguration(h,p);
 
 x = x+wpan1+p.mg;
+y = pospan(4)-p.mg-hpan2;
 
-h.uipanel_TA_stateTransitionRates = uipanel('parent',h_pan,'units',p.posun,...
+h.uipanel_TA_dtHistograms = uipanel('parent',h_pan,'units',p.posun,...
     'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',...
-    [x,y,wpan1,hpan1],'title',ttl2);
-h = buildPanelTAstateTransitionRates(h,p);
+    [x,y,wpan1,hpan2],'title',ttl2);
+h = buildPanelTAdtHistograms(h,p);
+
+y = y-p.mg/2-hpan3;
+
+h.uipanel_TA_kineticModel = uipanel('parent',h_pan,'units',p.posun,...
+    'fontunits',p.fntun,'fontsize',p.fntsz1,'fontweight','bold','position',...
+    [x,y,wpan1,hpan3],'title',ttl3);
+h = buildPanelTAkineticModel(h,p);