Merge pull request #85 from RNA-FRETools/MASH-FRET-1.3.3-doc

Documentation updates

MASH-FRET/.release_version.json

@@ -1,4 +1,4 @@
 {
 "tag" : "1.3.2",
-"prev_commit_hash" : "8fcf5539"
+"prev_commit_hash" : "849a07f1"
 }

MASH-FRET/source/GUI/figure_MASH_CloseRequestFcn.m

@@ -23,6 +23,9 @@ function figure_MASH_CloseRequestFcn(obj, evd)
     delete(h.figure_dummy)
 end
 
+setContPan('save interface parameters in default_param.ini file ...',...
+    'process',obj);
+
 p = h.param;
 if ~isempty(p.proj) && isfield(p.ttPr,'defProjPrm')
     % remove background intensities
@@ -40,4 +43,6 @@ function figure_MASH_CloseRequestFcn(obj, evd)
 [mfile_path,o,o] = fileparts(which('MASH'));
 save([mfile_path filesep 'default_param.ini'], '-struct', 'p');
 
+setContPan('closing MASH-FRET ...','process',obj);
+
 delete(obj);

MASH-FRET/source/GUI/mod-histogram-analysis/buildHAtabPlotHist.m

@@ -34,7 +34,7 @@
 ylabel(h_axes,ylbl0);
 tiaxes = get(h_axes,'tightinset');
 posaxes = getRealPosAxes([x,y,waxes0,haxes0],tiaxes,'traces');
-set(h_axes,'position',posaxes);
+set(h_axes,'position',posaxes,'nextplot','replacechildren');
 
 if ~isempty(p.fname_boba)
     x = posaxes(1)+posaxes(3)-waxes1;
@@ -47,7 +47,8 @@
     ico_boba = repmat(ico_boba, [1,1,3]);
     image(ico_boba,'parent',h.axes_hist_BOBA);
     axis(h.axes_hist_BOBA,'image');
-    set(h.axes_hist_BOBA,'xtick',[],'ytick',[]);
+    set(h.axes_hist_BOBA,'xtick',[],'ytick',[],'nextplot',...
+        'replacechildren');
 end
 
 x = p.mg;
@@ -62,5 +63,5 @@
 ylabel(h_axes,ylbl1);
 tiaxes = get(h_axes,'tightinset');
 posaxes = getRealPosAxes([x,y,waxes0,haxes0],tiaxes,'traces');
-set(h_axes,'position',posaxes);
+set(h_axes,'position',posaxes,'nextplot','replacechildren');
 

MASH-FRET/source/GUI/mod-histogram-analysis/buildHAtabPlotMdlSlct.m

@@ -25,14 +25,13 @@
 y = postab(4)-p.mgtab-haxes0;
 
 h.axes_thm_BIC = axes('parent',h_tab,'units',p.posun,'fontunits',p.fntun,...
-    'fontsize',p.fntsz0,'position',[x,y,waxes0,haxes0],'xticklabelmode',...
-    'manual');
+    'fontsize',p.fntsz1,'position',[x,y,waxes0,haxes0]);
 h_axes = h.axes_thm_BIC;
 xlim(h_axes,xlim0);
 ylim(h_axes,ylim0);
 ylabel(h_axes,ylbl0);
 xlabel(h_axes,xlbl0);
 tiaxes = get(h_axes,'tightinset');
 posaxes = getRealPosAxes([x,y,waxes0,haxes0],tiaxes,'traces');
-set(h_axes,'position',posaxes);
+set(h_axes,'position',posaxes,'nextplot','replacechildren');
 

MASH-FRET/source/GUI/mod-histogram-analysis/buildPanelHAstateConfiguration.m

@@ -45,7 +45,7 @@
 ttstr2 = wrapHtmlTooltipString('<b>Model selection:</b> overfitting is penalized using a <b>minimum improvement</b> in likelihood (the model is selected if further increase in complexity does not sufficiently improve the likelihood).');
 ttstr3 = wrapHtmlTooltipString('<b>Improvement factor:</b> multiplication factor that expresses the minimum improvement in likelihood (example: 1.2 set a minimum improvement of 20%).');
 ttstr4 = wrapHtmlTooltipString('<b>Model selection:</b> overfitting is penalized using the <b>BIC</b> (the selected model minimizes the BIC).');
-ttstr4b = wrapHtmlTooltipString('<b>Likelihood calculation:</b> <u>complete data:</u> each transition is associated to one and only Gaussian; <u>incomplete data:</u> transitions have a non-null probability to belong to each Gaussian (subject to overestimation of model complexity).');
+ttstr4b = wrapHtmlTooltipString('<b>Likelihood calculation:</b> <u>complete data:</u> each bin is associated to one and only Gaussian; <u>incomplete data:</u> bins have a non-null probability to belong to each Gaussian (subject to overestimation of model complexity).');
 ttstr5 = wrapHtmlTooltipString('Select an inferred <b>state configuration</b> to show on the histogram plot: configurations are labelled with the corresponding number of Gaussians.');
 ttstr6 = wrapHtmlTooltipString('<b>Export Gaussian parameters</b> of the selected state configuration to panel "State populations" as starting guesses for state population analysis.');
 

MASH-FRET/source/GUI/mod-trace-processing/buildPanelTPfindStates.m

@@ -35,7 +35,8 @@
 str5 = 'refine';
 str6 = 'binning';
 str7 = 'deblurr';
-str8 = {'Thresholds','vbFRET-1D','vbFRET-2D','One state','CPA','STaSI'};
+str8 = {'Thresholds','vbFRET-1D','vbFRET-2D','One state','CPA','STaSI',...
+    'Imported'};
 str9 = {'bottom','top','all'};
 str10 = {'Select a trace'};
 str11 = 'Results (19 states):';

MASH-FRET/source/GUI/mod-trace-processing/buildPanelTPsampleManagement.m

@@ -31,7 +31,7 @@
 str6 = 'label';
 str7 = {'Selecte a label'};
 str8 = 'Del.';
-str9 = 'Add>';
+str9 = '<Add';
 ttstr6 = wrapHtmlTooltipString('Open the <b>Trace manager</b> to visualize the ensemble and sort single molecules.');
 ttstr7 = wrapHtmlTooltipString('<b>Clear excluded molecules</b> off the list: excluded molecules appear in black in the list.');
 ttstr8 = wrapHtmlTooltipString('<b>Molecule selection</b>: when activated, the current molecule is included in the refined sample, otherwise, molecule is considered excluded and appear in black in the list.');
@@ -91,24 +91,25 @@
     p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,'position',...
     [x,y,wpop0,htxt0],'string',str6);
 
-y = y-hpop0;
+x = p.mg;
+y = y-hpop0+(hpop0-hedit0)/2;
 
-h.popupmenu_TP_molLabel = uicontrol('style','popupmenu','parent',h_pan,...
+h.togglebutton_TP_addTag = uicontrol('style','togglebutton','parent',h_pan,...
     'units',p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,'position',...
-    [x,y,wpop0,hpop0],'string',str7,'tooltipstring',ttstr9);
+    [x,y,wbut5,hedit0],'string',str9,'tooltipstring',ttstr11,'callback',...
+    {@togglebutton_TP_addTag_Callback,h_fig});
 
-x = x+wpop0+p.mg/fact;
-y = y+(hpop0-hedit0)/2;
+x = x+wbut5+p.mg/fact;
 
 h.pushbutton_TP_deleteTag = uicontrol('style','pushbutton','parent',h_pan,...
     'units',p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,'position',...
     [x,y,wbut4,hedit0],'string',str8,'tooltipstring',ttstr10,'callback',...
     {@pushbutton_TP_deleteTag_Callback,h_fig});
 
 x = x+wbut4+p.mg/fact;
+y = y-(hpop0-hedit0)/2;
 
-h.togglebutton_TP_addTag = uicontrol('style','togglebutton','parent',h_pan,...
+h.popupmenu_TP_molLabel = uicontrol('style','popupmenu','parent',h_pan,...
     'units',p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,'position',...
-    [x,y,wbut5,hedit0],'string',str9,'tooltipstring',ttstr11,'callback',...
-    {@togglebutton_TP_addTag_Callback,h_fig});
+    [x,y,wpop0,hpop0],'string',str7,'tooltipstring',ttstr9);
 

MASH-FRET/source/GUI/mod-transition-analysis/buildPanelTAselectTool.m

@@ -23,7 +23,7 @@
 file_icon1 = 'icon_zoom.png';
 file_icon2 = 'icon_crosshair.png';
 file_icon3 = 'icon_clear.png';
-str0 = char(9668);
+str0 = char(9650);
 ttstr0 = wrapHtmlTooltipString('Switch to <b>cluster selection</b> mode');
 ttstr1 = wrapHtmlTooltipString('<b>Clear</b> current selection');
 ttstr2 = wrapHtmlTooltipString('Switch to <b>zoom</b> mode');
@@ -35,9 +35,9 @@
 
 % dimensions
 pospan = get(h_pan,'position');
-hpan = p.mg/2+hedit0+p.mg/2;
+hpan = p.mg/2+3*hedit0+2*p.mg/fact+p.mg/2+hedit0+p.mg/2;
 wbut0 = getUItextWidth(str0,p.fntun,p.fntsz1,'normal',p.tbl)+p.wbrd;
-wpan = p.mg/2+3*hedit0+2*p.mg/fact+p.mg/2+wbut0+p.mg/2;
+wpan = p.mg/2+wbut0+p.mg/2;
 
 % set panel dimensions
 set(h_pan,'position',[pospan(1:2),wpan,hpan]);
@@ -48,29 +48,30 @@
 img3 = imread(file_icon3);
 
 % GUI
-x = p.mg/2;
-y = p.mg/2;
+x = p.mg/2+(wbut0-hedit0)/2;
+y = hpan-p.mg/2-hedit0;
 
 h.tooglebutton_TDPselectZoom = uicontrol('style','togglebutton','parent',...
     h_pan,'units',p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,...
     'position',[x,y,hedit0,hedit0],'tooltipstring',ttstr2,'callback',...
     {@tooglebutton_TDPselect_Callback,h_fig,1},'cdata',img1);
 
-x = x+hedit0+p.mg/fact;
+y = y-hedit0-p.mg/fact;
 
 h.tooglebutton_TDPselectCross = uicontrol('style','togglebutton','parent',...
     h_pan,'units',p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,...
     'position',[x,y,hedit0,hedit0],'tooltipstring',ttstr0,'callback',...
     {@tooglebutton_TDPselect_Callback,h_fig,2},'cdata',img2);
 
-x = x+hedit0+p.mg/fact;
+y = y-hedit0-p.mg/fact;
 
 h.pushbutton_TDPselectClear = uicontrol('style','pushbutton','parent',...
     h_pan,'units',p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,...
     'position',[x,y,hedit0,hedit0],'tooltipstring',ttstr1,'callback',...
     {@tooglebutton_TDPselect_Callback,h_fig,3},'cdata',img3);
 
-x = x+hedit0+p.mg/2;
+x = x-(wbut0-hedit0)/2;
+y = y-hedit0-p.mg/2;
 
 h.pushbutton_TDPmanStart = uicontrol('style','pushbutton','parent',...
     h_pan,'units',p.posun,'fontunits',p.fntun,'fontsize',p.fntsz1,...

MASH-FRET/source/GUI/mod-transition-analysis/buildPanelTAstateConfiguration.m

@@ -153,7 +153,7 @@
 posbut = get(h.tooglebutton_TDPmanStart,'position');
 pospan1 = get(h.uipanel_TA_clusters,'position');
 pospan2 = get(h.uipanel_TA_selectTool,'position');
-pospan2(1) = pospan1(1)+posbut(1)+posbut(3);
-pospan2(2) = pospan1(2)+posbut(2)-(pospan2(4)-posbut(4))/2;
+pospan2(1) = pospan1(1)+posbut(1)+(posbut(3)-pospan2(3))/2;
+pospan2(2) = pospan1(2)+posbut(2)-pospan2(4);
 set(h.uipanel_TA_selectTool,'position',pospan2);
 

MASH-FRET/source/mod-histogram-analysis/plotHist.m

@@ -74,6 +74,7 @@ function plotHist(h_axes, P, lim, start, res, clr, boba, intUnits, h_fig)
             ylabel(h_axes(3),'Improvement factor');
             set(h_axes(3),'nextplot','replacechildren');
         end
+        set(h_axes(3),'xtick',1:Jmax);
     else
         cla(h_axes(3));
         set(h_axes(3),'visible','off');
@@ -167,7 +168,7 @@ function plotHist(h_axes, P, lim, start, res, clr, boba, intUnits, h_fig)
             end
             plot(h_axes(1), P(:,1), y_all, 'Color', [0.5 0.5 0.5], ...
                 'LineWidth', 2);
-            set(h_axes, 'NextPlot', 'replacechildren');
+            set(h_axes(1), 'NextPlot', 'replacechildren');
 
         % plot most probable configuration
         elseif ~isempty(res{3,1})
@@ -226,7 +227,7 @@ function plotHist(h_axes, P, lim, start, res, clr, boba, intUnits, h_fig)
             plot(h_axes(1), [thresh(k) thresh(k)], y_lim, '-k', ...
                 'LineWidth', 2);
         end
-        set(h_axes(1),'NextPlot','replace');
+        set(h_axes(1),'NextPlot','replacechildren');
 
         if numel(h_axes)>1
             plot(h_axes(2), P(:,1), P(:,3), '+k');
@@ -236,7 +237,7 @@ function plotHist(h_axes, P, lim, start, res, clr, boba, intUnits, h_fig)
                 plot(h_axes(2), [thresh(k) thresh(k)], y_cumlim, '-k', ...
                     'LineWidth', 2);
             end
-            set(h_axes(2),'NextPlot','replace');
+            set(h_axes(2),'NextPlot','replacechildren');
         end
 end
 

MASH-FRET/source/mod-simulation/export-options/exportResults.m

@@ -19,8 +19,6 @@
 h = guidata(h_fig);
 p = h.param;
 proj = p.curr_proj;
-inSec = p.proj{proj}.time_in_sec;
-perSec = p.proj{proj}.cnt_p_sec;
 prm = p.proj{proj}.sim.prm;
 
 % check simulated state sequences
@@ -93,6 +91,7 @@
 L = size(Idon,1);
 dat = p.proj{proj};
 dat.FRET_DTA = discr;
+dat.FRET_DTA_import = discr;
 dat.intensities = NaN(L,2*N);
 
  % check for file overwriting (one file exported per format)
@@ -341,15 +340,16 @@
         if isPresets && isfield(presets,'stateVal')
             states = presets.stateVal(n,:);
         end
+        statevals = dt(:,[2,3]);
         for j = 1:J
-            dt(dt(:,2)==j,2) = states(j);
-            dt(dt(:,3)==j,3) = states(j);
+            statevals(dt(:,2)==j,1) = states(j);
+            statevals(dt(:,3)==j,2) = states(j);
         end
 
         f = fopen(fname_dt,'Wt');
-        fprintf(f,cat(2,'dwell-time (second)\tstate\tstate after ',...
-            'transition\n'));
-        fprintf(f,'%d\t%d\t%d\n',dt');
+        fprintf(f,cat(2,'dwell-time (second)\tstate\t',...
+            'state after transition\tFRET\tFRET after transition\n'));
+        fprintf(f,'%d\t%d\t%d\t%d\t%d\n',[dt,statevals]');
         fclose(f);
     end
 
@@ -415,7 +415,7 @@
 dat.ES = {};
 dat.intensities_DTA = nan(L,2*N);
 dat.S_DTA = [];
-dat.bool_intensities = true(L,N);
+dat.bool_intensities = discr>0;
 
 dat.molTag = false(N,numel(dat.molTagNames));
 
@@ -435,6 +435,19 @@
 p = importHA(p,proj);
 p = importTA(p,proj);
 
+% set photobleaching cutoff
+for m = 1:numel(p.proj{proj}.TP.curr)
+    id = find(discr(:,m)>0);
+    if isempty(id)
+        cutoff = 1;
+    else 
+        cutoff = id(end);
+    end
+    p.proj{proj}.TP.curr{m}{2}{1}(1) = 1; % apply cutoff
+    p.proj{proj}.TP.curr{m}{2}{1}(2) = 1; % manual method
+    p.proj{proj}.TP.curr{m}{2}{1}(5) = cutoff; % cutoff frames
+end
+
 % save modifications
 h = guidata(h_fig); % recover file overwrite options
 p.proj{proj}.sim.prm = prm;

MASH-FRET/source/mod-trace-processing/_callbacks/popupmenu_TP_states_applyTo_Callback.m

@@ -16,8 +16,12 @@ function popupmenu_TP_states_applyTo_Callback(obj, evd, h_fig)
 val = get(obj, 'Value');
 if meth==3 && val~=1
     val = 1;
-    disp(['2D analysis is available for intensity ratio (bottom)',...
-        ' traces only.']);
+    disp(['2D analysis is available for intensity ratio  traces (bottom) ',...
+        'only.']);
+elseif meth==7 && val~=1
+    disp(['"Imported" is available for FRET state sequences (bottom) ',...
+        'only.']);
+    val = 1;
 end
 
 switch val

MASH-FRET/source/mod-trace-processing/_callbacks/popupmenu_TP_states_method_Callback.m

@@ -4,17 +4,32 @@ function popupmenu_TP_states_method_Callback(obj, evd, h_fig)
 p = h.param;
 proj = p.curr_proj;
 mol = p.ttPr.curr_mol(proj);
-
 meth = get(obj, 'Value');
-p.proj{proj}.TP.curr{mol}{4}{1}(1) = meth;
-
-h.param = p;
-guidata(h_fig, h);
 
 if meth==3 % 2D-vbFRET discretize bottom traces only
+    p.proj{proj}.TP.curr{mol}{4}{1}(1) = meth;
+    h.param = p;
+    guidata(h_fig, h);
+
     set(h.popupmenu_TP_states_applyTo,'value',1);
     popupmenu_TP_states_applyTo_Callback(h.popupmenu_TP_states_applyTo,...
         [],h_fig)
+
+elseif meth==7 % Imported
+    if ~(isfield(p.proj{proj},'FRET_DTA_import') && ...
+            ~isempty(p.proj{proj}.FRET_DTA_import))
+        setContPan(['"Imported" method can not be used for this project: ',...
+            'no imported FRET state sequences were found.'],'warning',...
+            h_fig);
+    else
+        p.proj{proj}.TP.curr{mol}{4}{1}(1) = meth;
+        h.param = p;
+        guidata(h_fig, h);
+
+        set(h.popupmenu_TP_states_applyTo,'value',1);
+        popupmenu_TP_states_applyTo_Callback(h.popupmenu_TP_states_applyTo,...
+            [],h_fig)
+    end
 end
 
 ud_DTA(h_fig);

MASH-FRET/source/mod-trace-processing/_callbacks/pushbutton_TTrem_Callback.m

@@ -50,6 +50,11 @@ function pushbutton_TTrem_Callback(obj, evd, h_fig)
 if nFRET > 0
     incl_f = reshape(repmat(incl, [nFRET,1]),1,nFRET*numel(incl));
     p.proj{proj}.FRET_DTA = p.proj{proj}.FRET_DTA(:,incl_f);
+    if isfield(p.proj{proj},'FRET_DTA_import') && ...
+            ~isempty(p.proj{proj}.FRET_DTA_import)
+        p.proj{proj}.FRET_DTA_import = ...
+            p.proj{proj}.FRET_DTA_import(:,incl_f);
+    end
 end
 
 if nS > 0

MASH-FRET/source/mod-trace-processing/background/background_analyzer/GUI/build_BA_panelMethodSettings.m

@@ -9,6 +9,7 @@
 % h_fig: handle to main figure
 
 % defaults
+file_icon0 = 'view.png';
 str0 = 'data';
 str1 = 'method';
 str2 = 'param.';
@@ -18,7 +19,7 @@
 str6 = 'XXXXX at 999nm';
 str7 = 'Most frequent value';
 str8 = 'auto';
-str9 = 'Show';
+str9 = 'Opt.';
 str10 = 'current molecule';
 str11 = 'BG value';
 str12 = char(9668);
@@ -42,6 +43,10 @@
 % parent
 h_pan = q.uipanel_determine_bg;
 
+% images
+pname = [fileparts(mfilename('fullpath')),filesep,'..',filesep,'..',filesep,'..',filesep,'..',filesep,'GUI',filesep];
+img0 = imread([pname,file_icon0]);
+
 % dimensions
 pospan = get(h_pan,'position');
 wpop0 = getUItextWidth(str6,p.fntun,p.fntsz,'normal',p.tbl) + p.warr;
@@ -157,7 +162,7 @@
 
 q.pushbutton_show = uicontrol('style','pushbutton','parent',h_pan,'units',...
     p.posun,'fontunits',p.fntun,'fontsize',p.fntsz,'position',...
-    [x,y,wbut0,p.hbut],'string',str9,'tooltipstring',ttstr6,'callback',...
+    [x,y,wbut0,p.hbut],'cdata',img0,'tooltipstring',ttstr6,'callback',...
     {@pushbutton_BA_show_Callback,h_fig});
 
 x = p.mg;