Merge pull request #51 from RNA-FRETools/MASH-code-10

Mash code 10

MASH-FRET/.release_version.json

@@ -1,4 +1,4 @@
 {
 "tag" : "1.1.2",
-"prev_commit_hash" : "07c398e"
+"prev_commit_hash" : "6bc4127"
 }

MASH-FRET/source/mod-trace-processing/management/traceManager.m

@@ -612,7 +612,10 @@ function setDataPlotPrm(h_fig)
 
 function openMngrTool(h_fig)
 
-% Last update by MH, 24.4.2019
+% Last update by MH, 24.8.2019
+% >> solve issue in "View of video": video was shown upside down.
+%
+% update by MH, 24.4.2019
 % >> add toolbar and empty tools "Auto sorting" and "View of video"
 % >> rename "Overview" panel in "Molecule selection"
 %
@@ -1533,9 +1536,12 @@ function openMngrTool(h_fig)
 xNext = w_cb + 3*mg;
 yNext = h_pan_tool - h_pop - mg - h_axes4;
 
+% modified by MH, 24.8.2019
 h.tm.axes_videoView = axes('parent',h.tm.uipanel_videoView,'units',...
     'pixels','fontunits','pixels','fontsize',fntS,'activepositionproperty',...
-    'outerposition','gridlineStyle',':','nextPlot','replacechildren');
+    'outerposition','gridlineStyle',':','nextPlot','replace');
+%     'outerposition','gridlineStyle',':','nextPlot','replacechildren');
+
 ylim(h.tm.axes_videoView,[0 10000]);
 ylabel(h.tm.axes_videoView,'x-position (pixel)');
 xlabel(h.tm.axes_videoView,'y-position (pixel)');
@@ -1888,6 +1894,10 @@ function switchPan_TM(obj,evd,h_fig)
 
 function plotDataTm(h_fig)
 
+% Last update by MH, 26.7.2019
+% >> handle error occurring when changing molecule in display before plot 
+%    is completed
+
 h = guidata(h_fig);
 p = h.param.ttPr;
 proj = p.curr_proj;
@@ -1921,6 +1931,12 @@ function plotDataTm(h_fig)
 drawnow;
 
 for i = 1:nDisp
+
+    % MH, 26.7.2019
+    if ~ishandle(h.tm.checkbox_molNb(i))
+        break;
+    end
+
     mol_nb = str2num(get(h.tm.checkbox_molNb(i), 'String'));
 
     axes.axes_traceTop = h.tm.axes_itt(i);
@@ -2514,6 +2530,9 @@ function drawMask_subpop(h_fig,molIncl)
 
 function plotData_videoView(h_fig)
 
+% Last update: 24.8.2019 by MH
+% >> adjust axes limits
+
 % defaults 
 mg_top = 0.4;
 mkSize = 10;
@@ -2633,8 +2652,11 @@ function plotData_videoView(h_fig)
 set(h.tm.axes_videoView,'nextplot','replacechildren');
 
 % set image limits
-xlim(h.tm.axes_videoView,[0,size(img,2)+1]);
-ylim(h.tm.axes_videoView,[0,size(img,1)+1]);
+% modified by MH, 24.08.2019
+xlim(h.tm.axes_videoView,[0,size(img,2)]);
+ylim(h.tm.axes_videoView,[0,size(img,1)]);
+% xlim(h.tm.axes_videoView,[0,size(img,2)+1]);
+% ylim(h.tm.axes_videoView,[0,size(img,1)+1]);
 
 end
 

MASH-FRET/source/project/openItgExpOpt.m

@@ -5,7 +5,7 @@ function openItgExpOpt(obj, evd, h)
 %          has been called (usually empty)
 % "h" >> main data structure stored in figure_MASH's handle
 
-% Last update: 3rd of April 2019 by MH
+% Last update: 3.4.2019 by MH
 % --> Add project's labels to default labels (FRET and S popupmenus were 
 %     updated with project's labels and channel popupmenu with defaults
 %     that are different when importing ASCII traces)
@@ -19,7 +19,7 @@ function openItgExpOpt(obj, evd, h)
 % --> avoid exporting empty parameters with non-zero dimensions, correct 
 %     typos and remove caps-lock in message boxes 
 %
-% update: 4th of February 2019 by Mélodie Hadzic
+% update: 4.2.2019 by Mélodie Hadzic
 % --> remove "file options" panel (displaced in an other option window
 %     created by function openItgExpOpt.m, called by control 
 %     pushbutton_TTgen_FileOpt)
@@ -71,6 +71,10 @@ function openItgExpOpt(obj, evd, h)
 
 
 function buildWinOpt(p, nExc, nChan, obj, h_fig)
+
+% Last update: 26.7.2019 by MH
+% >> reduce height of panel "color code" by removing extra space
+
 h = guidata(h_fig);
 nPrm = size(p{1},1);
 nFixPrm = 4 + nExc;
@@ -161,7 +165,10 @@ function buildWinOpt(p, nExc, nChan, obj, h_fig)
 h_pan_fret = 10 + h_lb + h_edit + 3*mg;
 h_pan_S = 10 + h_lb + h_edit + 3*mg;
 h_pan_chan = 10 + h_txt + 3*h_edit + h_but + big_mg + 4*mg;
-h_pan_clr = 10 + h_txt + h_edit + h_but + 3*mg;
+
+% 26.7.2019, MH: remove extra space
+% h_pan_clr = 10 + h_txt + h_edit + h_but + 3*mg;
+h_pan_clr = 10 + h_edit + h_but + 3*mg;
 
 w_pan = w_full + 2*mg;
 wFig = 2*w_pan + 3*mg;
@@ -555,7 +562,6 @@ function buildWinOpt(p, nExc, nChan, obj, h_fig)
         p{7}{2}, 'Value', val_FRETprm(2));
 end
 
-
 if isS
     %% Stoichiometry parameters