Who even knows at this point

workflow/apps/matlab/easy/DMPexcel2mat.m

@@ -129,7 +129,7 @@ try
       %   MP(numb).specifics2=' ';
       % end
       excLnNum=excLnNum+385;
-      msg=strcat('NumberOfMP = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));
+      msg=strcat('NumberOfMP=',num2str(numb), '   lastLineNo.=',num2str(excLnNum));
     end
   else 
     excLnNum=1;
@@ -157,7 +157,7 @@ try
         MP(numb).specifics= ' ';
       end
       excLnNum=excLnNum+385;
-      msg=strcat('NumberOfMP = ',num2str(numb), 'lastLineNo. = ',num2str(excLnNum));
+      msg=strcat('NumberOfMP=',num2str(numb), 'lastLineNo.=',num2str(excLnNum));
     end
   end
 catch ME
@@ -261,7 +261,7 @@ if isequal(Linked,1) % Drugs and Media are linked 1 to 1; else they are combinat
       DM.mod2(numb)={raw(excLnNum,7)};
       DM.conc2(numb)={raw(excLnNum,8)};
       excLnNum=excLnNum+1;
-      msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));
+      msg=strcat('NumberOf1:1DrugMediaPlates=',num2str(numb), '   lastLineNo.=',num2str(excLnNum));
     end
   else
     clear DM
@@ -283,7 +283,7 @@ if isequal(Linked,1) % Drugs and Media are linked 1 to 1; else they are combinat
       DM.conc2(numb)={DMtbl(excLnNum,8)};
       DM.conc2(numb)=table2cell(DM.conc2{numb});
       excLnNum=excLnNum+1;
-      msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));
+      msg=strcat('NumberOf1:1DrugMediaPlates=',num2str(numb), '   lastLineNo.=',num2str(excLnNum));
     end
   end
 end
@@ -321,7 +321,7 @@ if isequal(Linked,0) % 0 indicates Drugs and Media are combinatorial
       excLnNum=excLnNum+1;
     end
   end
-  msg=strcat('NumberOfDrugs = ',num2str(drgCnt), '     NumberOfMedias = ',num2str(medCnt)  );
+  msg=strcat('NumberOfDrugs=',num2str(drgCnt), '     NumberOfMedias=',num2str(medCnt)  );
 end
 
 save(mpdmFile, 'fields','MP','DM','Linked');

workflow/apps/matlab/easy/DgenResults.m

@@ -281,7 +281,7 @@ for s=1:size(scan,2)
           outIntens=[];
           outIntens=zeros(384,dataLength);
           intensBlob='';
-          tmBlob ='';
+          tmBlob='';
         
           for j=1:dataLength  %size(RawIntens,2)  %size(outTseries,1)
             if Ag(n)==0,Ag(n)=scan(s).Awindow;end
@@ -565,7 +565,7 @@ try
             outIntens=[];
             outIntens=zeros(384,dataLength);
             intensBlob='';
-            tmBlob ='';
+            tmBlob='';
 
             for j=1:dataLength  %size(RawIntens,2)  %size(outTseries,1)
               if Ag(n)==0,Ag(n)=scan(s).Awindow;end

workflow/apps/matlab/easy/EASYconsole.m

@@ -293,7 +293,7 @@ function NewExpDat_Callback(~, ~, ~)
 
     % create supporting dirs
     % this is also in the workflow script but here for standalone mode
-    dirs={'PrintResults', 'CFfigs', 'Fotos', 'Fotos/BkUp'};
+    dirs={'PrintResults', 'CFfigs', 'Fotos'};
     for i=1:length(dirs)
       d=dirs{i};
       if ~exist(fullfile(easyResultsDir, d), 'dir')
@@ -335,7 +335,7 @@ function LoadDatFile_Callback(~, ~, ~)
   global fhconsole
 
   try
-    questdlg('Load results .mat from ../ExpJobs/YourJob/Results/matResults/','File Creation','OK', struct('Default','OK','Interpreter','tex'));
+    questdlg('Load results .mat from ../out/project/','File Creation','OK', struct('Default','OK','Interpreter','tex'));
     [inputFile,inputPath]=uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
     matDir=fullfile(inputPath);
     matFile=fullfile(inputPath,inputFile);
@@ -370,11 +370,6 @@ function LoadDatFile_Callback(~, ~, ~)
       disp('WARNING: cannot find project scans');
     end
 
-    bkupDir=fullfile(matDir,'BkUp');
-    if ~exist(bkupDir, 'dir')
-      mkkdir(bkupDir);
-    end
-
     % Create supporting dirs
     dirs={'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'};
     for i=1:length(dirs)

workflow/apps/matlab/easy/par4Gbl_Main8c.m

@@ -48,7 +48,7 @@ end
 % EASYconsole
 
 if exist(matFile, 'file')
-  bkUpMatFile=fullfile(matDir,'BkUp',matFile);
+  bkUpMatFile=fullfile(matFile, '.bk');
   copyfile(matFile,bkUpMatFile);
 end
 
@@ -67,7 +67,7 @@ catch
   load(fullfile(pointMapsResultsDir,'Nbdg')); %Left in to accomodate loads of work before 20_0819
 end
 % Load Fotos stored data
-fotosToLoad = {'Coordinates', 'BGatTpts', 'anlZones', 'NCFparms'};
+fotosToLoad={'Coordinates', 'BGatTpts', 'anlZones', 'NCFparms'};
 for i=1:length(fotosToLoad)
   try
     load(fullfile(fotosResultsDir, fotosToLoad{i}));

workflow/apps/matlab/ezview/Axes2FigPrint.m

@@ -1,6 +1,6 @@
 close all
 figure('units','pix','pos',[200 200 850 750])
-ax = axes;
+ax=axes;
 plot((1:10).^2)
 set(ax,'units','pix')
 legend('x^2')
@@ -10,11 +10,11 @@ title('Title','fontsize',24)
 drawnow
 
 % Now capture the axes and labels.
-P = get(ax,'pos');
+P=get(ax,'pos');
-T = get(ax,'tightinset');
+T=get(ax,'tightinset');
-h = [P(1)-T(1)-5 P(2)-T(2)-5 P(3)+P(1)/2+T(3)+15 P(4)+P(2)/2+T(4)+10];
+h=[P(1)-T(1)-5 P(2)-T(2)-5 P(3)+P(1)/2+T(3)+15 P(4)+P(2)/2+T(4)+10];
-F = getframe(gcf,h);
+F=getframe(gcf,h);
-[X,Map] = frame2im(F);
+[X,Map]=frame2im(F);
 % I put the funny background color so the captured area stands out. 
 figure('color',[.6 .2 .2],'units','pix','pos',[26  33 1184 925])
 image(X)

workflow/apps/matlab/ezview/EZcompositePlot.m

@@ -69,17 +69,17 @@ if AddCplot==1,
 %******MEAN calculation Plot********************    
 %try
        
-  l= Exp(expN).cLmean(cTraceN); 
+  l=Exp(expN).cLmean(cTraceN); 
-  r= Exp(expN).cRmean(cTraceN);
+  r=Exp(expN).cRmean(cTraceN);
-  K= Exp(expN).cKmean(cTraceN);
+  K=Exp(expN).cKmean(cTraceN);
-  lslow= l + Exp(expN).cLstd(cTraceN); lfast= l - Exp(expN).cLstd(cTraceN); 
+  lslow=l + Exp(expN).cLstd(cTraceN); lfast= l - Exp(expN).cLstd(cTraceN); 
-  rl= r - Exp(expN).cRstd(cTraceN); ru= r + Exp(expN).cRstd(cTraceN);
+  rl=r - Exp(expN).cRstd(cTraceN); ru= r + Exp(expN).cRstd(cTraceN);
-  Kl= K - Exp(expN).cKstd(cTraceN); Ku= K + Exp(expN).cKstd(cTraceN);
+  Kl=K - Exp(expN).cKstd(cTraceN); Ku= K + Exp(expN).cKstd(cTraceN);
  clear g; 
  t=1:200;
- g =  K ./ (1 +  exp(-r.* (t - l )));
+ g=K ./ (1 +  exp(-r.* (t - l )));
-gSlow= Kl ./ (1 +  exp(-rl.* (t - lslow )));
+gSlow=Kl ./ (1 +  exp(-rl.* (t - lslow )));
-gFast= Ku ./ (1 +  exp(-ru.* (t - lfast )));
+gFast=Ku ./ (1 +  exp(-ru.* (t - lfast )));
 if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
        
 Exp(expN).hCmean(cTraceN)=plot(OLaxes,t,g);hold on;  %PLOT the composit mean of traces

workflow/apps/matlab/ezview/EZdestComp.m

@@ -309,11 +309,11 @@ intLadj=(deltaXR);
 Exp(expN).Trace(tracN).Dexp(DexpN).UsrIntL= intL;
 
 %{
-intNormL =   (intL) ./ Rn(1)
+intNormL=(intL) ./ Rn(1)
 intNormLadj= ((deltaXR)./ Rn(1))
-proGrIntL = -(intL) 
+proGrIntL=-(intL) 
-proGrIntLadj =  -(deltaXR)
+proGrIntLadj=-(deltaXR)
-proGrIntNormL = -(intL ./ Rn(1))
+proGrIntNormL=-(intL ./ Rn(1))
 proGrIntNormLadj=  -((deltaXR)./ Rn(1))
 %find where Xn(j)==0 and set interactL to a fixed Max interaction value
 intNormL(find(Xn==0))=2
@@ -365,7 +365,7 @@ end
      %Plot new intL  
      try 
          % zeroCLn= zeros(1,destPerMP)
-         % Exp(zoneSel).hzeroCLn = plot(DNLaxes,zeroCLn,1:destPerMP,'y');
+         % Exp(zoneSel).hzeroCLn=plot(DNLaxes,zeroCLn,1:destPerMP,'y');
           Exp(zoneSel).hintL(tracN)=  plot(DNLaxes,intL,1:destPerMP); Exp(zoneSel).hintLb(tracN)= plot(DNLaxes,intL,1:destPerMP,'rs');
           Exp(zoneSel).hintLadj(tracN)=  plot(DNLaxes,intLadj,1:destPerMP,'g'); Exp(zoneSel).hintLadjb(tracN)= plot(DNLaxes,intLadj,1:destPerMP,'gs');
       catch, 

workflow/apps/matlab/ezview/EZdiagRFsSheet.m

@@ -11,7 +11,7 @@ try %Try the whole routine
     cnames={'RF Name','Median','Mean','STD','Minimum','Maximum'};
     rCnt=0;
     RFfilename= fullfile(Exp(expN).Dexp(DexpN).resDir,'PrintResults','!RFsDiagnostics.txt');
-    fid = fopen(RFfilename,'w');  %('RFdiagnostic.txt','w');
+    fid=fopen(RFfilename,'w');  %('RFdiagnostic.txt','w');
     ftitle= strcat(ExpPath,':::Reference Diagnostic Values');
     try
       fprintf(fid,'%s\n',ftitle);

workflow/apps/matlab/ezview/EZdiagRFsSheetwImport.m

@@ -1,8 +1,8 @@
 %Diagnostic sheet called by EZvInitLoad.m, EZexpSel.m ?EZinteractDev_.m?
 global Exp
 
-intLfilename1= fullfile(Exp(expN).resDir,'PrintResults','!RFsDiagnostics.txt');
+intLfilename1=fullfile(Exp(expN).resDir,'PrintResults','!RFsDiagnostics.txt');
-fid = fopen(RFdiagnostic,'w');
+fid=fopen(RFdiagnostic,'w');
 ln=1;
 fprintf(fid,'%d\t',ln);
 fprintf(fid,'%s\ExpName:::','Reference Diagnostic Values');

workflow/apps/matlab/ezview/EZexpSel.m

@@ -570,7 +570,7 @@ else
   Exp(expN).Dexp(1).RFmd1pltN= RF1mp; 
     
    try medValList1{d+1}= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt; 
-   catch, catcherror = 'Ln356',
+   catch, catcherror='Ln356',
    end
      
 end  %~isempty(nonZeroIndx) && length(medianIndx) > (.15*384)
@@ -853,8 +853,8 @@ uu= horzcat(uu,vv);
 for d=1:DMnum
     medianIndxG=[];
     NZrfIndxG=[];
-    minG = min(nonzeros(vv(:,d)));
+    minG=min(nonzeros(vv(:,d)));
-    maxG = max(nonzeros(vv(:,d)));
+    maxG=max(nonzeros(vv(:,d)));
     RFmeanG= mean(nonzeros(vv(:,d)));
     RFstdG= std(nonzeros(vv(:,d)));
     NZrfIndxG= find(vv(:,d));  %find(nonzeros(vv(:,d)));  WWRONG FOR A WHILE! 
@@ -976,7 +976,7 @@ if expN==1
    set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
   end
   DNLaxes1= handles.DNLaxes1; %ZoneRelated
-  Exp(1).hzeroCLn(expLdCnt) = plot(DNLaxes1,zeroCLn,1:DMnum,'y');
+  Exp(1).hzeroCLn(expLdCnt)=plot(DNLaxes1,zeroCLn,1:DMnum,'y');
 end
 
 if expN==2
@@ -993,7 +993,7 @@ if expN==2
    set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtGnLst)
   end
   DNLaxes2= handles.DNLaxes2;  %ZoneRelated
-  Exp(2).hzeroCLn(expLdCnt) = plot(DNLaxes2,zeroCLn,1:DMnum,'y');
+  Exp(2).hzeroCLn(expLdCnt)=plot(DNLaxes2,zeroCLn,1:DMnum,'y');
   
 end
 
@@ -1011,7 +1011,7 @@ if expN==3
    set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtGnLst)
   end
   DNLaxes3= handles.DNLaxes3; %ZoneRelated
-  Exp(3).hzeroCLn(expLdCnt) = plot(DNLaxes3,zeroCLn,1:DMnum,'y');
+  Exp(3).hzeroCLn(expLdCnt)=plot(DNLaxes3,zeroCLn,1:DMnum,'y');
 end
 
 if Exp(4).interacPBsel==0  %if interaction "raw" don't show a center line
@@ -1126,11 +1126,11 @@ elseif expType==2  %Multiple Experiment from in one Folder extraction
 %*************************************************
        ww=pwd;
        try EZmultiDayGui; catch ME
-       msg = ME.message, cd(ww); end     %*            %*
+       msg=ME.message, cd(ww); end     %*            %*
        try EZmultiDay; catch ME
-       msg = ME.message, cd(ww); end       %*
+       msg=ME.message, cd(ww); end       %*
        try EZmultiExLoad; catch ME
-       msg = ME.message, cd(ww); end     %*
+       msg=ME.message, cd(ww); end     %*
       %*********************
 elseif expType==3
     Exp(expN).DexpType= 'multi';
@@ -1148,11 +1148,11 @@ elseif expType==3
 %*************************************************
        ww=pwd;
        try EZmultiDayGui; catch ME
-       msg = ME.message,cd(ww); end     %*            %*
+       msg=ME.message,cd(ww); end     %*            %*
        try EZmultiDay; catch ME
-       msg = ME.message, cd(ww); end        %*
+       msg=ME.message, cd(ww); end        %*
        try EZmultiExLoad;  catch ME
-       msg = ME.message, cd(ww); end   %*
+       msg=ME.message, cd(ww); end   %*
       %*********************
 else
     disp('Cancel Load Exp')
@@ -1205,12 +1205,12 @@ end
 
 %User Reference Input Dialog Box used in the multiExperiment Chrono setup
 
-   prompt = {'Enter GeneName to use as Reference:',...
+   prompt={'Enter GeneName to use as Reference:',...
        'Enter Specifics Term if used to futher specify Reference '}       
-    dlg_title = 'User Reference Input';
+    dlg_title='User Reference Input';
-    num_lines = 1;
+    num_lines=1;
-    def = {'RF1','None'};
+    def={'RF1','None'};
-    answer = inputdlg(prompt,dlg_title,num_lines,def);
+    answer=inputdlg(prompt,dlg_title,num_lines,def);
     rfGene= cell2mat(answer(1));
     if ~strcmpi(rfGene,'RF1')|| ~strcmpi(rfGene,'RF2'), usrRefFg=1; end
     rfSpec= answer(2); %if strcmpi(answer(2),'None'), rfSpec= ''; end
@@ -1220,12 +1220,12 @@ end
 %+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 %First user input prototype code
 if ~exist('RF1scanN','var') && ~exist('RF2scanN','var')  %change || &&
-    prompt = {'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
+    prompt={'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
               'Enter GeneName of Your Reference:'};
-    dlg_title = 'User Reference Input';
+    dlg_title='User Reference Input';
-    num_lines = 1;
+    num_lines=1;
-    def = {'Ref MP(s)','USRrefGeneName'};
+    def={'Ref MP(s)','USRrefGeneName'};
-    answer = inputdlg(prompt,dlg_title,num_lines,def);
+    answer=inputdlg(prompt,dlg_title,num_lines,def);
     rfMPstr= cell2mat(answer(1));
     rfMPcomas=strfind((cell2mat(answer(1))),',');
     n=0;

workflow/apps/matlab/ezview/EZfigTrendOL.m

@@ -206,19 +206,19 @@ sh= userPars.BPlblShft;
 fontSize= userPars.BPfontSz;
 rotation= userPars.BProt;
 
-%fontSize = 8;    
+%fontSize=8;    
-    %tickLabelStr = {'Label alpha','Label beta','Label chi','Label delta',...
+    %tickLabelStr={'Label alpha','Label beta','Label chi','Label delta',...
     %                    'Label epsilon','Label fish','Label gamma','Label hallo','Label ingo'}
     % generate data
     if size(BPvals,1)==1, BPvals(2,1:maxCols)= nan; end
-    final_res = BPvals;   %10*randn(300,9)+10;
+    final_res=BPvals;   %10*randn(300,9)+10;
     
     % group boxes
-    %sh = 0.3;  %sh is shift value
+    %sh=0.3;  %sh is shift value
-    width = .5*sh;  
+    width=.5*sh;  
      
     
-    %pos = [1+sh 2-sh 3+sh 4-sh 5+sh 6-sh 7+sh 8-sh 9+sh];
+    %pos=[1+sh 2-sh 3+sh 4-sh 5+sh 6-sh 7+sh 8-sh 9+sh];
     bpn=1;
     if strcmp(Exp(expN).DexpType, 'chrono')
         ticDim= length(Exp(expN).Dexp);
@@ -235,7 +235,7 @@ rotation= userPars.BProt;
           end
         end
     end
-    wid = width * ones(1,length(pos));
+    wid=width * ones(1,length(pos));
     
     % boxplot
     figure
@@ -257,10 +257,10 @@ rotation= userPars.BProt;
     ylabel('L in Hours', 'FontSize', fontSize)
     
     %x-labels
-    text_h = findobj(gca, 'Type', 'text');
+    text_h=findobj(gca, 'Type', 'text');
-    %rotation = 45;
+    %rotation=45;
     
-    for cnt = 1:length(text_h)
+    for cnt=1:length(text_h)
         set(text_h(cnt),    'FontSize', fontSize,...
                             'Rotation', rotation, ...
                             'String', tickLabelStr{length(tickLabelStr)-cnt+1}, ...
@@ -270,16 +270,16 @@ rotation= userPars.BProt;
     % 'VerticalAlignment', 'cap', ...
     
     % smaller box for axes, in order to un-hide the labels
-    squeeze = 0.2;
+    squeeze=0.2;
-    left = 0.02;
+    left=0.02;
-    right = 1;
+    right=1;
-    bottom = squeeze;
+    bottom=squeeze;
-    top = 1-squeeze;
+    top=1-squeeze;
     set(gca, 'OuterPosition', [left bottom right top])
         
     % remove outliers
-    hout = findobj(gca,'tag','Outliers');
+    hout=findobj(gca,'tag','Outliers');
-    for out_cnt = 1 : length(hout)
+    for out_cnt=1 : length(hout)
          if strcmpi(BPoutliers,'on'), 
              set(hout(out_cnt), 'Visible', 'on')
          elseif strcmpi(BPnotch,'off'), 

workflow/apps/matlab/ezview/EZhtMap.m

@@ -284,7 +284,7 @@ elseif htTog==3
     Xhn{m,j,:}=Exp(expN).Dexp(DexpN).scan(scnN).plate(1).CFout(:,12);  %Exp(expN).Dexp(DexpN).scan(DM{j}(m)).plate(1).CFout(:,12);
     
     %*********************************************************
-    %intL{m,j,:} =  ((Xn{m,j,:} - Xn{m,1,:}) - (Rn(j)-Rn(1)));
+    %intL{m,j,:}= ((Xn{m,j,:} - Xn{m,1,:}) - (Rn(j)-Rn(1)));
    intL= ((Xn{m,j,:} - Xn{m,1,:}) - (Rn(j)-Rn(1)));
     Exp(expN).HtMpIntN2=intL;  %ZoneRelated
     %{

workflow/apps/matlab/ezview/EZintPrint.m

@@ -27,7 +27,7 @@ userInputs=cell2mat(strcat( 'ExpZone:',num2str(expN), '; LeftPercent',answer(1),
 
 %********************11111111111111111111111111111111111111111****************************************************************************************************************
 %Interaction Printout for Positive (longer L interaction values) Non-Adjusted for Ref std and curve fit boundaries              
-fid = fopen(intLfilename1,'w');
+fid=fopen(intLfilename1,'w');
 ln=1;
 fprintf(fid,'%d\t',ln);
 fprintf(fid,'%s\userInputs',strcat('AggrevatingInteractionResults for User Input: ',userInputs));
@@ -63,7 +63,7 @@ end
 fclose(fid)
 %********************222222222222222222222222222222222222222222222****************************************************************************************************************
 %Interaction Printout for Negative (shorter L interaction values) Non-Adjusted for Ref std and curve fit boundaries
-fid = fopen(intLfilename2,'w');
+fid=fopen(intLfilename2,'w');
 ln=1;
 fprintf(fid,'%d\t',ln);
 fprintf(fid,'%s\userInputs',strcat('AlleviatingInteractionResults for User Input: ',userInputs));  %fprintf(fid,'%s\userInputs',userInputs);
@@ -96,7 +96,7 @@ end
 fclose(fid)
 %********************3333333333333333333333333333333333333333333333****************************************************************************************************************
 %Interaction Printout for Positive (longer L interaction values) "ADJUSTED" for Ref std and curve fit boundaries
-fid = fopen(intLfilename3,'w');
+fid=fopen(intLfilename3,'w');
 ln=1;
 fprintf(fid,'%d\t',ln);
 fprintf(fid,'%s\userInputs',strcat('Adjusted AggrevatingInteractionResults for User Input: ',userInputs));
@@ -128,7 +128,7 @@ fclose(fid)
 
 %********************44444444444444444444444444444444444444444444****************************************************************************************************************%Interaction Printout for Negative (shorter L interaction values) Non-Adjusted for Ref std and curve fit boundaries
 
-fid = fopen(intLfilename4,'w');
+fid=fopen(intLfilename4,'w');
 ln=1;
 fprintf(fid,'%d\t',ln);
 fprintf(fid,'%s\userInputs',strcat('AlleviatingInteractionResults for User Input: ',userInputs));  %fprintf(fid,'%s\userInputs',userInputs);

workflow/apps/matlab/ezview/EZlstBoxCmpExt.m

@@ -54,16 +54,16 @@ ru= r + Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
 lfast= l - Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
 lslow= l + Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).std;
 end
-try Kstr=Ks(1:5); catch, Kstr = Ks(1:length(Ks)); end
+try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
-try rstr=rs(1:5); catch, rstr = rs(1:length(rs)); end
+try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
-try Lstr=Ls(1:5); catch, Lstr = Ls(1:length(Ls)); end
+try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
 
 
 t=1:200;
 clear g;
 
 %try
-g =  K ./ (1 +  exp(-r.* (t - l )));
+g= K ./ (1 +  exp(-r.* (t - l )));
 gSlow= Kl ./ (1 +  exp(-rl.* (t - lslow )));
 gFast= Ku ./ (1 +  exp(-ru.* (t - lfast )));
 if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end

workflow/apps/matlab/ezview/EZlstBoxExt.m

@@ -132,9 +132,9 @@ try
 K=scan(1,plateNum).plate(1).CFout(indx,3); Ks= num2str(K);
 r=scan(1,plateNum).plate(1).CFout(indx,4); rs= num2str(r);
 l=scan(1,plateNum).plate(1).CFout(indx,5); Ls= num2str(l);
-try Kstr=Ks(1:5); catch, Kstr = Ks(1:length(Ks)); end
+try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
-try rstr=rs(1:5); catch, rstr = rs(1:length(rs)); end
+try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
-try Lstr=Ls(1:5); catch, Lstr = Ls(1:length(Ls)); end
+try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
 
 Kl=scan(1,plateNum).plate(1).CFout(indx,7);
 Ku=scan(1,plateNum).plate(1).CFout(indx,8);
@@ -147,7 +147,7 @@ t=1:200;
 clear g;
 
 try
-g =  K ./ (1 +  exp(-r.* (t - l )));
+g= K ./ (1 +  exp(-r.* (t - l )));
 gSlow= Kl ./ (1 +  exp(-rl.* (t - lslow )));
 gFast= Ku ./ (1 +  exp(-ru.* (t - lfast )));
 if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end

workflow/apps/matlab/ezview/EZmDayPlotUcmp.m

@@ -23,11 +23,11 @@ else
 end
 
 
-   prompt = {'Enter Specifics Term if used to futher specify selection '}       
+   prompt={'Enter Specifics Term if used to futher specify selection '}       
-    dlg_title = 'User Specifics Term for Refinement Composite';
+    dlg_title='User Specifics Term for Refinement Composite';
-    num_lines = 1;
+    num_lines=1;
-    def = {'None'};
+    def={'None'};
-    answer = inputdlg(prompt,dlg_title,num_lines,def);
+    answer=inputdlg(prompt,dlg_title,num_lines,def);
     usrSpec= cell2mat(answer(1)); 
     if strcmpi(usrSpec,'None'), usrGnSp= {strcat(usrGene,'-')}; 
     elseif length(usrSpec)> 8, 
@@ -190,9 +190,9 @@ lfast= l - Lstd;
 lslow= l + Lstd;
 end
     
-try Kstr=Ks(1:5); catch, Kstr = Ks(1:length(Ks)); end
+try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
-try rstr=rs(1:5); catch, rstr = rs(1:length(rs)); end
+try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
-try Lstr=Ls(1:5); catch, Lstr = Ls(1:length(Ls)); end
+try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
 
             
             pertSel=Exp(zoneSel).Dexp(DexpN).pertSel;  %floor(get(handles.DMsldr1,'value'));
@@ -205,7 +205,7 @@ t=1:200;
 clear g;
 
 try
-g =  K ./ (1 +  exp(-r.* (t - l )));
+g= K ./ (1 +  exp(-r.* (t - l )));
 gSlow= Kl ./ (1 +  exp(-rl.* (t - lslow )));
 gFast= Ku ./ (1 +  exp(-ru.* (t - lfast )));
 if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end

workflow/apps/matlab/ezview/EZmDayPlotUcomposite.m

@@ -18,11 +18,11 @@ selStrNm= char(selGnOrf)
 usrGene= selStrNm(1:(patrnN(1)-1))
 
 
-   prompt = {'Enter Specifics Term if used to futher specify selection '}       
+   prompt={'Enter Specifics Term if used to futher specify selection '}       
-    dlg_title = 'User Specifics Term for Refinement Composite';
+    dlg_title='User Specifics Term for Refinement Composite';
-    num_lines = 1;
+    num_lines=1;
-    def = {'None'};
+    def={'None'};
-    answer = inputdlg(prompt,dlg_title,num_lines,def);
+    answer=inputdlg(prompt,dlg_title,num_lines,def);
     %usrGene= cell2mat(answer(1));
     usrSpec= answer(1); 
     usrGnSp= strcat(usrGene,usrSpec);
@@ -150,8 +150,8 @@ uu= horzcat(uu,vv);
 for d=dmSel:dmSel
     medianIndxG=[];
     NZusrIndxG=[];
-    minG = min(nonzeros(vv(:,d)));
+    minG=min(nonzeros(vv(:,d)));
-    maxG = max(nonzeros(vv(:,d)));
+    maxG=max(nonzeros(vv(:,d)));
     usrmeanG= mean(nonzeros(vv(:,d)));
     usrStdG= std(nonzeros(vv(:,d)));
     NZusrIndxG= find(vv(:,d));   
@@ -192,9 +192,9 @@ ru= r + std(vvr(medianIndxG,dmSel));   %r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).
 lfast= l - std(vv(medianIndxG,dmSel)); %l - Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
 lslow= l + std(vv(medianIndxG,dmSel)); %l + Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
 
-try Kstr=Ks(1:5); catch, Kstr = Ks(1:length(Ks)); end
+try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
-try rstr=rs(1:5); catch, rstr = rs(1:length(rs)); end
+try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
-try Lstr=Ls(1:5); catch, Lstr = Ls(1:length(Ls)); end
+try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
 
             
             pertSel=Exp(zoneSel).Dexp(DexpN).pertSel;  %floor(get(handles.DMsldr1,'value'));
@@ -208,7 +208,7 @@ t=1:200;
 clear g;
 
 try
-g =  K ./ (1 +  exp(-r.* (t - l )));
+g= K ./ (1 +  exp(-r.* (t - l )));
 gSlow= Kl ./ (1 +  exp(-rl.* (t - lslow )));
 gFast= Ku ./ (1 +  exp(-ru.* (t - lfast )));
 if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
@@ -451,16 +451,16 @@ ru= r + std(vvr(medianIndxP,dmSel));   %r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).
 lfast= l - std(vv(medianIndxP,dmSel)); %l - Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
 lslow= l + std(vv(medianIndxP,dmSel)); %l + Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
 
-try Kstr=Ks(1:5); catch, Kstr = Ks(1:length(Ks)); end
+try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
-try rstr=rs(1:5); catch, rstr = rs(1:length(rs)); end
+try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
-try Lstr=Ls(1:5); catch, Lstr = Ls(1:length(Ls)); end
+try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
 
 
 t=1:200;
 clear g;
 
 try
-g =  K ./ (1 +  exp(-r.* (t - l )));
+g= K ./ (1 +  exp(-r.* (t - l )));
 gSlow= Kl ./ (1 +  exp(-rl.* (t - lslow )));
 gFast= Ku ./ (1 +  exp(-ru.* (t - lfast )));
 if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end

workflow/apps/matlab/ezview/EZmDayTrend.m

@@ -373,7 +373,7 @@ end
      %Plot new intL  
      try 
          % zeroCLn= zeros(1,days)
-         % Exp(zoneSel).hzeroCLn = plot(DNLaxes,zeroCLn,1:days,'y');
+         % Exp(zoneSel).hzeroCLn=plot(DNLaxes,zeroCLn,1:days,'y');
           Exp(zoneSel).hintL(tracN)=  plot(DNLaxes,intL,1:days); Exp(zoneSel).hintLb(tracN)= plot(DNLaxes,intL,1:days,'rs');
           Exp(zoneSel).hintLadj(tracN)=  plot(DNLaxes,intLadj,1:days,'g'); Exp(zoneSel).hintLadjb(tracN)= plot(DNLaxes,intLadj,1:days,'gs');
       catch, 

workflow/apps/matlab/ezview/EZmultiDay.m

@@ -3,17 +3,16 @@ global exp
 global exDlst
 global exFolder
 
-c= strfind(exDlst,' ');
+c=strfind(exDlst,' ');
-d= strfind(exDlst,'_');
+d=strfind(exDlst,'_');
 clear expDlstS
 ii=0;
 for n=1:(size(c,1))
-   if ((sum(ismember(cell2mat(c(n)),[3,4]))==1 && ~isempty(ismember(cell2mat(c(n)),[3,4])))||...
+  if ((sum(ismember(cell2mat(c(n)),[3,4]))==1 && ~isempty(ismember(cell2mat(c(n)),[3,4]))) ||...
   (sum(ismember(cell2mat(d(n)),[3,4]))==1 && ~isempty(ismember(cell2mat(d(n)),[3,4]))))
-      ii= ii+1;
+    ii=ii+1;
-       expDlst(ii)= exDlst(n);
+    expDlst(ii)=exDlst(n);
   end
-    
 end
 
 clear matFile
@@ -21,27 +20,25 @@ ii=0;
 for m= 1:size(expDlst,2)
   exD=fullfile(exFolder,cell2mat(expDlst(m)))
   dirLst=dir(exD);
-
   clear matFlst
   clear resF
   clear resMatF
     
   for n=1:size(dirLst,1)
     if sum(ismember('Results2', dirLst(n).name))==8
-   resF= dirLst(n).name
+      resF=dirLst(n).name
-   resMatF= fullfile(exFolder,cell2mat(expDlst(m)),resF,'matResults')
+      resMatF=fullfile(exFolder,cell2mat(expDlst(m)),resF,'matResults')
-   matFlst= dir(resMatF)
+      matFlst=dir(resMatF)
       for o=1:size(matFlst,1)
         if sum(ismember('.mat', matFlst(o).name))==4
           ii= ii+1; 
-          resDir{ii}= fullfile(exFolder,cell2mat(expDlst(m)),resF)
+          resDir{ii}=fullfile(exFolder,cell2mat(expDlst(m)),resF)
-          matFile(m)= cellstr(fullfile(resMatF,matFlst(o).name))
+          matFile(m)=cellstr(fullfile(resMatF,matFlst(o).name))
         end
-   end   %for o=1:size(matFlst,1)
+      end
-   
+    end
-   end  %if sum(ismember('Results2', dirLst(n).name))
+  end
-  end  %for n=1:size(dirLst,1)
+end
-end   %for m= 1:size(expDlst,2)
 
 Exp(expN).DexpLength= size(matFile,2);
 Exp(expN).DexpN= size(matFile,2);

workflow/apps/matlab/ezview/EZmultiDayExp.m

@@ -21,8 +21,8 @@ exDirs=dir(exFolder)
  exFs= {exDirs.name}
 
 
-f = figure('Menubar','none','Position',[1000 100 640 750],'Name','Select Exp Folders' ); 
+f=figure('Menubar','none','Position',[1000 100 640 750],'Name','Select Exp Folders' ); 
-hListbox = uicontrol(...
+hListbox=uicontrol(...
       'Style', 'listbox',...
       'String',sort(exFs),...
       'value',[],...
@@ -36,8 +36,8 @@ function load_listbox(source,eventdata)
     
     %global CSrchRng
     %global CSrearchRange
-userIndx = (get(source,'value'))
+userIndx=(get(source,'value'))
-userStr = (get(source,'string'))
+userStr=(get(source,'string'))
 %scLstIndx= str2num(char(strrep(userStr(userIndx), 'Scan', '')))
 
 user_entry=userStr(userIndx)
@@ -51,7 +51,7 @@ user_entry=userStr(userIndx)
    yPos=0.85-(btnNumber-1)*(btnHt+spacing);
    btnPos=[xPos yPos-spacing btnWid btnHt];
 
-hedit8 = uicontrol(...
+hedit8=uicontrol(...
       'Style', 'pushbutton',...
       'String',{'Continue'},...
       'Units','normalized',...   

workflow/apps/matlab/ezview/EZmultiDayGui.m

@@ -50,7 +50,7 @@ function EZmultiDayGui
 
   f=figure('Menubar','none','Position',[1000 100 640 750],'Name','Select Exp Folders' );
 
-  hListbox = uicontrol(...
+  hListbox=uicontrol(...
     'Style', 'listbox',...
     'String',ExpOrderByExp,...
     'value',[],...
@@ -72,7 +72,7 @@ function EZmultiDayGui
   yPos=0.85-(btnNumber-1)*(btnHt+spacing);
   btnPos=[xPos yPos-spacing btnWid btnHt];
 
-  hedit8 = uicontrol(...
+  hedit8=uicontrol(...
     'Style', 'pushbutton',...
     'String',{'Continue'},...
     'Units','normalized',...   

workflow/apps/matlab/ezview/EZmultiExLoad.m

@@ -173,12 +173,12 @@ EZVimDisplay  %*
 %*********************
    
    usrRefFg=0;
-   prompt = {'Enter GeneName to use as Reference:',...
+   prompt={'Enter GeneName to use as Reference:',...
        'Enter Specifics Term if used to futher specify Reference '}       
-    dlg_title = 'User Reference Input';
+    dlg_title='User Reference Input';
-    num_lines = 1;
+    num_lines=1;
-    def = {'RF1','None'};
+    def={'RF1','None'};
-    answer = inputdlg(prompt,dlg_title,num_lines,def);
+    answer=inputdlg(prompt,dlg_title,num_lines,def);
     if iscell(answer(1))
     rfGene= cell2mat(answer(1));
     else
@@ -266,7 +266,7 @@ if expN==1  %Adapted to accomodate AppDesigner 230821
    set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
   end
   DNLaxes1= handles.DNLaxes1;
-  Exp(1).hzeroCLn(expLdCnt) = plot(DNLaxes1,zeroCLn,1:DMnum,'y');
+  Exp(1).hzeroCLn(expLdCnt)=plot(DNLaxes1,zeroCLn,1:DMnum,'y');
 end
 
 if expN==2  %Adapted to accomodate AppDesigner 230821
@@ -283,7 +283,7 @@ if expN==2  %Adapted to accomodate AppDesigner 230821
    set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtGnLst)
   end
   DNLaxes2= handles.DNLaxes2;
-  Exp(2).hzeroCLn(expLdCnt) = plot(DNLaxes2,zeroCLn,1:DMnum,'y');
+  Exp(2).hzeroCLn(expLdCnt)=plot(DNLaxes2,zeroCLn,1:DMnum,'y');
   
 end
 
@@ -301,7 +301,7 @@ if expN==3  %Adapted to accomodate AppDesigner 230821
    set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtGnLst)
   end
   DNLaxes3= handles.DNLaxes3;
-  Exp(3).hzeroCLn(expLdCnt) = plot(DNLaxes3,zeroCLn,1:DMnum,'y');
+  Exp(3).hzeroCLn(expLdCnt)=plot(DNLaxes3,zeroCLn,1:DMnum,'y');
 end
 
 if Exp(4).interacPBsel==0  %if interaction "raw" don't show a center line

workflow/apps/matlab/ezview/EZmultiGeneRFsLst.m

@@ -301,7 +301,7 @@ else
   Exp(expN).Dexp(n).RFmd1indx(d+1)=firstZero; 
   Exp(expN).Dexp(n).RFmd1pltN= RF1mp; 
     
-   try medValList1{d+1}= Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt; catch, catcherror = 'Ln356', end
+   try medValList1{d+1}= Exp(expN).Dexp(n).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt; catch, catcherror='Ln356', end
      
 end  %~isempty(nonZeroIndx) && length(medianIndx) > (.15*384)
 catch   %try ~ln375
@@ -595,8 +595,8 @@ uu= horzcat(uu,vv);
 for d=1:DMnum
     medianIndxG=[];
     NZrfIndxG=[];
-    minG = min(nonzeros(vv(:,d)));
+    minG=min(nonzeros(vv(:,d)));
-    maxG = max(nonzeros(vv(:,d)));
+    maxG=max(nonzeros(vv(:,d)));
     RFmeanG= mean(nonzeros(vv(:,d)));
     RFstdG= std(nonzeros(vv(:,d)));
     NZrfIndxG= find(vv(:,d));   %find(nonzeros(vv(:,d)));

workflow/apps/matlab/ezview/EZplotUcmp.m

@@ -1,221 +1,182 @@
-%EZplotUcmp.m
+% EZplotUcmp.m
+% User find and build composite of Selected Gene Composite and
+% Plot it on OLay Plot and Trend plot DNLaxles
+% For Single and Multi experiment Studies 
+% Called when Composite_ toggle button is clicked.
+% Data stored for printable Trend Plot production (click [L] in DNLaxes )
 
-%***********User find and build composite of Selected Gene Composite and
-%*************Plot it on OLay Plot and Trend plot DNLaxles
-%***************For Single and Multi experiment Studies 
-%Called when Composite_ toggle button is clicked.
-%Data stored for printable Trend Plot production (click [L] in DNLaxes )
-%*********************
 global ghandles
 global Exp
 global exDlst
-global exFolder
-
 
 traceN=Exp(expN).traceN;
-DexpN= Exp(expN).DexpN;
+DexpN=Exp(expN).DexpN;
 dmSel=Exp(zoneSel).Dexp(DexpN).pertSel;
-%dmSel= str2num(get(ghandles.DMed3,'string'))
+% dmSel=str2num(get(ghandles.DMed3,'string'))
+patrnN=strfind(selGnOrf{1},':'); % extract Gene-Orf Name
+patrndash=strfind(selGnOrf{1},'-');
+selStrNm=char(selGnOrf);
+usrGene=selStrNm(1:(patrnN(1)-1));
 
-
-patrnN=strfind(selGnOrf{1},':');  %Extract Gene-Orf Name
-patrndash= strfind(selGnOrf{1},'-');
-selStrNm= char(selGnOrf)
-usrGene= selStrNm(1:(patrnN(1)-1));
 if strcmpi(selStrNm(1:3),'RF-')
-    usrGeneSearch= selStrNm(4:(patrndash(2)-1));    
+  usrGeneSearch=selStrNm(4:(patrndash(2)-1));    
 elseif strcmp(selStrNm(1:3),'RF1')
-    usrGeneSearch= selStrNm(1:3);
+  usrGeneSearch=selStrNm(1:3);
 else
-    usrGeneSearch= selStrNm(1:(patrnN(1)-1));
+  usrGeneSearch=selStrNm(1:(patrnN(1)-1));
 end
 
+prompt={'Enter Specifics Term if used to futher specify selection '};       
+dlg_title='User Specifics Term for Refinement Composite';
+num_lines=1;
+def={'None'};
+answer=inputdlg(prompt,dlg_title,num_lines,def);
+usrSpec=cell2mat(answer(1));
 
+if strcmpi(usrSpec,'None'), usrGnSp={strcat(usrGene,'-')}; 
+elseif length(usrSpec)> 8, 
+  trimUspec=usrSpec(1:8); 
+  usrGnSp=strcat(usrGene,',',{trimUspec});   
+else
+  trimUspec=usrSpec;
+  usrGnSp=strcat(usrGene,',',{trimUspec}); 
+end
          
-   prompt = {'Enter Specifics Term if used to futher specify selection '};       
+% For n=DexpN:DexpN  %n=1:Exp(expN).DexpLength   %LOOP Thru DayExps
-    dlg_title = 'User Specifics Term for Refinement Composite';
+n=DexpN;
-    num_lines = 1;
-    def = {'None'};
-    answer = inputdlg(prompt,dlg_title,num_lines,def);
-    usrSpec= cell2mat(answer(1)); 
-    if strcmpi(usrSpec,'None'), usrGnSp= {strcat(usrGene,'-')}; 
-    elseif length(usrSpec)> 8, 
-        trimUspec= usrSpec(1:8); 
-        usrGnSp= strcat(usrGene,',',{trimUspec});   
-    else
-        trimUspec= usrSpec;
-        usrGnSp= strcat(usrGene,',',{trimUspec}); 
-    end
-         
-%for n= DexpN:DexpN  %n= 1:Exp(expN).DexpLength   %LOOP Thru DayExps
-n= DexpN;
 MPnum=length(Exp(expN).Dexp(DexpN).MP);
-DMnum= length(Exp(expN).Dexp(DexpN).DM.drug);
+DMnum=length(Exp(expN).Dexp(DexpN).DM.drug);
-
+% Extract expDay from ExpName string
-%Extract expDay from ExpName string
+dayNpos=max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '_D'));
-dayNpos= max(strfind(Exp(expN).Dexp(DexpN).ExpFoldr, '_D'));
+dayLbl=Exp(expN).Dexp(DexpN).ExpFoldr(dayNpos+1:end);
-dayLbl= Exp(expN).Dexp(DexpN).ExpFoldr(dayNpos+1:end);
-
-
-%*********************************
-
 dRF1indx=0;
+usrSp=usrSpec;  % user entry of Specifics for Ref selection
 
-usrSp= usrSpec;  %user entry of Specifics for Ref selection
-
-%*******************************************************
 for mp=1:length(Exp(expN).Dexp(DexpN).MP) 
-   
   for ind384=1:384   
-     try  %         
+    try      
-         %Insert test for numeric in genename and orf if isnumeric
+      % Insert test for numeric in genename and orf if isnumeric
-         %Correct common EXCEL problem of converting OCT1 into a date numeric
+      % Correct common EXCEL problem of converting OCT1 into a date numeric
       if cell2mat(Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384))==38991,
           Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)={'OCT1_'}; 
       elseif isnumeric(cell2mat(Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)))
           Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)={' '}; 
       end
-         %*****************************************************************
               
-    %DISPersed REFerence capture and find Medians                
+      % DISPersed REFerence capture and find Medians                
       if ( ((strcmpi((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)),usrGeneSearch) && ...
-                strcmpi((Exp(expN).Dexp(DexpN).MP(mp).specifics{1}(ind384)),usrSp)))...
+      strcmpi((Exp(expN).Dexp(DexpN).MP(mp).specifics{1}(ind384)),usrSp))) || ...
-           || ((strcmpi((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)),usrGeneSearch) && ...
+      ((strcmpi((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)),usrGeneSearch) && ...
       strcmpi(usrSp,'None'))) ),
-           
         dRF1indx=dRF1indx+1;
         Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384)),':',' ');
-            drf(dRF1indx,1)= (Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384));
+        drf(dRF1indx,1)=(Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384));
-            drf(dRF1indx,2)={mp}; drfMP(dRF1indx,mp)= mp;
+        drf(dRF1indx,2)={mp}; drfMP(dRF1indx,mp)=mp;
-            drf(dRF1indx,3)={ind384}; drfPindx(dRF1indx,mp)= ind384;
+        drf(dRF1indx,3)={ind384}; drfPindx(dRF1indx,mp)=ind384;
-            %drf(dRF1indx,7)= (Exp(expN).Dexp(DexpN).MP(mp).specifics{1}(ind384));
+        %drf(dRF1indx,7)=(Exp(expN).Dexp(DexpN).MP(mp).specifics{1}(ind384));  
-          
+      end      
-    end   %if isempty(regexpi(char((Exp(expN).Dexp(DexpN).MP(mp).genename{1}(ind384))),'blank'))...  
+    catch
-    %*******************************************************************************       
+      msgBadGeneName=strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
-     catch
+    end   
-      msgBadGeneName= strcat('check genename at mp=',num2str(mp),' indx=',num2str(ind384))
   end
-         
-  end  %end associated with for ind384=1:384  
   mp 
-end   %end associated with for mp=1:length(Exp(expN).Dexp(DexpN).MP)
+end
-%*****************************************************
-%************************************************************************************************
 
-vvL=[];  %Initialize to cover case where all spot are Zero NoGrowth See NIGrowthflg==0
+vvL=[];  % initialize to cover case where all spot are Zero NoGrowth See NIGrowthflg==0
 if exist('drf','var')
-%Det. index of change from one MP to the next    
+  % Det. index of change from one MP to the next    
   i=2;
   clear chgIndx
   chgIndx(1)=1;
-for j=1:length(drf(:,3))
+  for j=1:length(drf(:,3))
     if j>1
-        if cell2mat(drf(j,2))~= cell2mat(drf((j-1),2)), chgIndx(i)=j; i=i+1; end
+      if cell2mat(drf(j,2))~=cell2mat(drf((j-1),2)), chgIndx(i)=j; i=i+1; end
     end
-end
+  end
-chgIndx(length(chgIndx)+1)= size(drf,1) +1;  %length(drf)+1;  
+  chgIndx(length(chgIndx)+1)=size(drf,1) +1; % length(drf)+1;  
-
+  vvL=zeros(size(drf,1),1 ); % length(drf)+1;
-vvL= zeros(size(drf,1),1 );  %length(drf)+1;
+  dMPs=unique(cell2mat(drf(:,2))); 
-%************************************
+  for d=1:length(Exp(expN).Dexp(DexpN).DM.drug)
- dMPs= unique(cell2mat(drf(:,2))); 
- %*****************************************
- for d= 1:length(Exp(expN).Dexp(DexpN).DM.drug)
     for mm=1:length(dMPs) % length(chgIndx)
       usrScNdisp=((dMPs(mm)-1)*DMnum)+(d); 
-    NZusrIndx= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm));    medianIndxDisp= NZusrIndx;
+      NZusrIndx=drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm)); 
+      medianIndxDisp=NZusrIndx;
       vvL(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(DexpN).scan(usrScNdisp).plate(1).CFout(NZusrIndx,5);
-    %For Global Ref Composite 17_1009 %**************************************************************************
       vvK(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(DexpN).scan(usrScNdisp).plate(1).CFout(NZusrIndx,3);
       vvr(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(DexpN).scan(usrScNdisp).plate(1).CFout(NZusrIndx,4);
-    %*****************************************************************************************************
+    end
-   end    %for mm=1:length(dMPs)
 
-%****************CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES******************************************************************
+    % CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES
-    %for d= 1:length(Exp(expN).Dexp(DexpN).DM.drug)
+    % for d=1:length(Exp(expN).Dexp(DexpN).DM.drug)
     NZusrIndxG=[];
-    NZusrIndxG= find(vvL);   
+    NZusrIndxG=find(vvL);   
  
-  if isempty(nonzeros(vvL)), nonZeroCntD=0;  
+    if isempty(nonzeros(vvL))
-     else nonZeroCntD= length(nonzeros(vvL)); 
+      nonZeroCntD=0;  
+    else 
+      nonZeroCntD=length(nonzeros(vvL)); 
     end
     %Calc. of median value for composite doesn't require and odd number of Indx items
-  NZusrIndxG= NZusrIndxG(:);
+    NZusrIndxG=NZusrIndxG(:);
     if ~isempty(NZusrIndxG) && length(NZusrIndxG) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero 
-
+      UsrLvals{d}=vvL(NZusrIndxG);
-UsrLvals{d}= vvL(NZusrIndxG);
+      UsrKvals{d}=vvK(NZusrIndxG);
-UsrKvals{d}= vvK(NZusrIndxG);
+      Usrrvals{d}=vvr(NZusrIndxG);
-Usrrvals{d}= vvr(NZusrIndxG);
+    end
   end 
 end
 
-
+if ~exist('drf','var')
-end  % if exist('drf','var')
-
-%END OF DISPERSE   
-%*********************************************************************
-%####################################################################
-%end  %for n=1:Exp(expN).DexpLength   %Loop thru Dayexps
-
-
-if ~exist('drf','var'),
   errordlg('Gene-Specifics combination not found. Check spelling of Specifics entry.','Entry Warning');
   break; 
 end
 
 NoGrowthflg=0;
-if  isempty(vvL), 
+if isempty(vvL)
   warndlg('No Growth condition found for Gene-Specifics combination. . ','No Growth warning');
   NoGrowthflg=1;
 end
 
-
+% Plot Values Selected Gene-Specifics Composite
-%#######################################################################
-
-
-%***********PLOT Values Selected Gene-Specifics Composite  ******************************************try
 if NoGrowthflg==0
-smpSz= size(NZusrIndxG,1);
+  smpSz=size(NZusrIndxG,1);
-K= median(cell2mat((UsrKvals(dmSel)))); Ks= num2str(K);  Kstd= std(cell2mat((UsrKvals(dmSel)))); KstdStr= num2str(Kstd);
+  K=median(cell2mat((UsrKvals(dmSel)))); Ks=num2str(K);  Kstd=std(cell2mat((UsrKvals(dmSel)))); KstdStr=num2str(Kstd);
-r= median(cell2mat((Usrrvals(dmSel)))); rs= num2str(r);  rstd= std(cell2mat((Usrrvals(dmSel)))); rstdStr= num2str(rstd);
+  r=median(cell2mat((Usrrvals(dmSel)))); rs=num2str(r);  rstd=std(cell2mat((Usrrvals(dmSel)))); rstdStr=num2str(rstd);
-l= median(cell2mat((UsrLvals(dmSel)))); Ls= num2str(l);  Lstd= std(cell2mat((UsrLvals(dmSel))));  LstdStr= num2str(Lstd);
+  l=median(cell2mat((UsrLvals(dmSel)))); Ls=num2str(l);  Lstd=std(cell2mat((UsrLvals(dmSel))));  LstdStr=num2str(Lstd);
-Kl= K - Kstd;  %std(UsrKvals(dmSel));  
+  Kl=K - Kstd;  %std(UsrKvals(dmSel));  
-Ku= K + Kstd;  %std(UsrKvals(dmSel));  
+  Ku=K + Kstd;  %std(UsrKvals(dmSel));  
-rl= r - rstd;  %std(Usrrvals(dmSel));  
+  rl=r - rstd;  %std(Usrrvals(dmSel));  
-ru= r + rstd;  %std(UsrKvals(dmSel));  
+  ru=r + rstd;  %std(UsrKvals(dmSel));  
-lfast= l - Lstd;
+  lfast=l - Lstd;
-lslow= l + Lstd;
+  lslow=l + Lstd;
-elseif NoGrowth==1   %if all data is zero (NoGrowth)
+elseif NoGrowth==1 % if all data is zero (NoGrowth)
-   smpSz= size(NZusrIndxG,1);
+  smpSz=size(NZusrIndxG,1);
-K= 0; Ks= num2str(K);  Kstd= 0; KstdStr= num2str(0);
+  K=0; Ks=num2str(K); Kstd=0; KstdStr=num2str(0);
-r= 0; rs= num2str(r);  rstd= 0; rstdStr= num2str(0);
+  r=0; rs=num2str(r); rstd=0; rstdStr=num2str(0);
-l= 0; Ls= num2str(l);  Lstd= 0;  LstdStr= num2str(0);
+  l=0; Ls=num2str(l); Lstd=0; LstdStr=num2str(0);
-Kl= K - Kstd;  
+  Kl=K - Kstd;  
-Ku= K + Kstd;  
+  Ku=K + Kstd;  
-rl= r - rstd;  
+  rl=r - rstd;  
-ru= r + rstd;  
+  ru=r + rstd;  
-lfast= l - Lstd;
+  lfast=l - Lstd;
-lslow= l + Lstd;
+  lslow=l + Lstd;
 end
     
-try Kstr=Ks(1:5); catch, Kstr = Ks(1:length(Ks)); end
+try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
-try rstr=rs(1:5); catch, rstr = rs(1:length(rs)); end
+try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
-try Lstr=Ls(1:5); catch, Lstr = Ls(1:length(Ls)); end
+try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
         
-            
+plateNum=(LBmp-1)*destPerMP + dmSel;
-            plateNum=(LBmp-1)*destPerMP + dmSel;
+MP=Exp(zoneSel).Dexp(DexpN).MP;
-            MP=Exp(zoneSel).Dexp(DexpN).MP;
            
 try
-
+  t=1:200;
-t=1:200;
+  clear g;
-clear g;
+  try
-
+    g=K ./ (1 +  exp(-r.* (t - l )));
-try
+    gSlow=Kl ./ (1 +  exp(-rl.* (t - lslow )));
-g =  K ./ (1 +  exp(-r.* (t - l )));
+    gFast=Ku ./ (1 +  exp(-ru.* (t - lfast )));
-gSlow= Kl ./ (1 +  exp(-rl.* (t - lslow )));
+    if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
-gFast= Ku ./ (1 +  exp(-ru.* (t - lfast )));
-if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
-
     if zoneSel==1, plotAxes=ghandles.Paxes1; OLaxes=ghandles.OLaxes1;
       Dlaxes=ghandles.Dlaxes1;Dkaxes=ghandles.Dkaxes1;Draxes=ghandles.Draxes1;
       Exp(1).traceN=Exp(1).traceN+1;
@@ -231,69 +192,65 @@ if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
       Exp(3).traceN=Exp(3).traceN+1;
       traceN=Exp(3).traceN;
     end
-plot(plotAxes,t,g);hold (plotAxes,'on');
+    plot(plotAxes,t,g);hold (plotAxes,'on');
-plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
+    plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
+    Exp(expN).Trace(traceN).UsrGLB=usrGnSp;
+    Exp(expN).Trace(traceN).dmSel=dmSel;
+    Exp(expN).Trace(traceN).DexpN=DexpN;
+    for d=1:length(Exp(expN).Dexp(DexpN).DM.drug)  %LOOP Thru DrugMedias 
+      Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).UsrLvals=UsrLvals(d);
+      Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).UsrKvals=UsrKvals(d);
+      Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).Usrrvals=Usrrvals(d);
+    end
 
-Exp(expN).Trace(traceN).UsrGLB= usrGnSp;
+    % Store L R and K valves for manual selected Composite [C] plots
-Exp(expN).Trace(traceN).dmSel= dmSel;
+    Exp(expN).ll(traceN)=l; Exp(expN).rr(traceN)=r; Exp(expN).kk(traceN)=K;
-Exp(expN).Trace(traceN).DexpN= DexpN;
+    Exp(expN).lslow(traceN)=lslow; Exp(expN).lfast(traceN)=lfast;                       
-for d= 1:length(Exp(expN).Dexp(DexpN).DM.drug)  %LOOP Thru DrugMedias 
-Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).UsrLvals= UsrLvals(d);
-Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).UsrKvals= UsrKvals(d);
-Exp(expN).Trace(traceN).Dexp(DexpN).DM(d).Usrrvals= Usrrvals(d);
-end
-%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
-%Store L R and K valves for manual selected Composite [C] plots
-Exp(expN).ll(traceN)= l; Exp(expN).rr(traceN)= r; Exp(expN).kk(traceN)= K;
-Exp(expN).lslow(traceN)= lslow; Exp(expN).lfast(traceN)= lfast;                       
-%************************************************************************
-try for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end,  catch; end                    
-Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
-set(Exp(zoneSel).hOL(traceN),'color',[1 0 0]) 
 
-catch  
+    try 
+      for i=1:length(Exp(zoneSel).hOL(:)),set(Exp(zoneSel).hOL(i),'color',[0 0 1]); end
+    catch
+    end
+
+    Exp(zoneSel).hOL(traceN)=plot(OLaxes,t,g);hold on;
+    set(Exp(zoneSel).hOL(traceN),'color',[1 0 0]) 
+  catch  
     catchissue='Ln100 EZlstBoxExt'
-end  %trycatch
+  end
 
-%Get the DM agar description
+  % Get the DM agar description
-if expN==1,DMstr=char(get(handles.DM1,'string'));end
+  if expN==1,DMstr=char(get(handles.DM1,'string'));end
-if expN==2,DMstr=char(get(handles.DM2,'string'));end
+  if expN==2,DMstr=char(get(handles.DM2,'string'));end
-if expN==3,DMstr=char(get(handles.DM3,'string'));end
+  if expN==3,DMstr=char(get(handles.DM3,'string'));end
+  gene=usrGnSp; orf=''   %MP(1,LBmp).orf{1,1}(indx);
+  geneOrfstr=strcat(gene,'_',orf,'_');
+  grfgenestr=strcat(gene,'_',orf,'_');
+  graphStr=strcat(usrGnSp,'_','L=',Lstr,'_','Ls=',LstdStr,'_','r=',rstr,'_','rs=',rstdStr,'_','K=',Kstr,'Ks=',KstdStr);
+  spotDescrip=strcat(graphStr,'->',DMstr);
 
-
+  xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
-
+  if ispc,
-  gene= usrGnSp; orf= ''   %MP(1,LBmp).orf{1,1}(indx);
-  geneOrfstr= strcat(gene,'_',orf,'_');
-  grfgenestr= strcat(gene,'_',orf,'_');
-
-graphStr= strcat(usrGnSp,'_','L=',Lstr,'_','Ls=',LstdStr,'_','r=',rstr,'_','rs=',rstdStr,'_','K=',Kstr,'Ks=',KstdStr);
-spotDescrip=strcat(graphStr,'->',DMstr);
-
-xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
-if ispc,
     slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'\');
-else
+  else
     slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'/');
-end
+  end
     
-startPos=slashPos(length(slashPos)-1) +1;
+  startPos=slashPos(length(slashPos)-1) +1;
-endPos=slashPos(length(slashPos)) -1
+  endPos=slashPos(length(slashPos)) -1
-expStr= {xp(startPos:endPos)}
+  expStr={xp(startPos:endPos)}
 
-Exp(zoneSel).hOLname(traceN)= spotDescrip;  
+  Exp(zoneSel).hOLname(traceN)=spotDescrip;  
-Exp(zoneSel).hOLexpNm(traceN)= expStr;  
+  Exp(zoneSel).hOLexpNm(traceN)=expStr;  
-Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
+  Exp(zoneSel).hOLresDir(traceN)={Exp(zoneSel).Dexp(DexpN).resDir};
-Exp(zoneSel).hOLplateNum(traceN)= plateNum; 
+  Exp(zoneSel).hOLplateNum(traceN)=plateNum; 
 
-
+  if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end  % Displays the value.
-
+  if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
-if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end  % Displays the value.
+  if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
-if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
+  if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end  %graphStr);end % Displays the value.
-if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
+  if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end  %graphStr);end    
-if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end  %graphStr);end % Displays the value.
+  if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end  %graphStr);end
-if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end  %graphStr);end    
-if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end  %graphStr);end
 catch
   catchissue='Ln141 EZlstBoxExt'
   msg='Error'
-end % trycatch zoneSel<4  datatip selection from Image (not from an OverLay Plot)
+end

workflow/apps/matlab/ezview/EZsingleExUserRF.m

@@ -3,12 +3,12 @@ global exp
 
 
    usrRefFg=0;
-   prompt = {'Enter GeneName to use as Reference:',...
+   prompt={'Enter GeneName to use as Reference:',...
        'Enter Specifics Term if used to futher specify Reference '}       
-    dlg_title = 'User Reference Input';
+    dlg_title='User Reference Input';
-    num_lines = 1;
+    num_lines=1;
-    def = {'RF1','None'};
+    def={'RF1','None'};
-    answer = inputdlg(prompt,dlg_title,num_lines,def);
+    answer=inputdlg(prompt,dlg_title,num_lines,def);
     rfGene= cell2mat(answer(1));
     if ~strcmpi(rfGene,'RF1')|| ~strcmpi(rfGene,'RF2'), usrRefFg=1; end
     rfSpec= answer(2); %if strcmpi(answer(2),'None'), rfSpec= ''; end
@@ -81,7 +81,7 @@ if expN==1
    set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
   end
   DNLaxes1= handles.DNLaxes1;
-  Exp(1).hzeroCLn(expLdCnt) = plot(DNLaxes1,zeroCLn,1:DMnum,'y');
+  Exp(1).hzeroCLn(expLdCnt)=plot(DNLaxes1,zeroCLn,1:DMnum,'y');
 end
 
 if expN==2
@@ -95,7 +95,7 @@ if expN==2
    set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtGnLst)
   end
   DNLaxes2= handles.DNLaxes2;
-  Exp(2).hzeroCLn(expLdCnt) = plot(DNLaxes2,zeroCLn,1:DMnum,'y');
+  Exp(2).hzeroCLn(expLdCnt)=plot(DNLaxes2,zeroCLn,1:DMnum,'y');
   
 end
 
@@ -110,7 +110,7 @@ if expN==3
    set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtGnLst)
   end
   DNLaxes3= handles.DNLaxes3;
-  Exp(3).hzeroCLn(expLdCnt) = plot(DNLaxes3,zeroCLn,1:DMnum,'y');
+  Exp(3).hzeroCLn(expLdCnt)=plot(DNLaxes3,zeroCLn,1:DMnum,'y');
 end
 
 if Exp(4).interacPBsel==0  %if interaction "raw" don't show a center line

workflow/apps/matlab/ezview/EZspotview.m

@@ -19,7 +19,7 @@ if NoOLay==0
         prevExp=1;
     end
     if prevExp==0
-      expDir = Exp(expN).Dexp(DexpN).ExpFoldr;  
+      expDir=Exp(expN).Dexp(DexpN).ExpFoldr;  
     else
         
        cd(fullfile(char(OLresDir)))
@@ -30,7 +30,7 @@ if NoOLay==0
         %expDir=fullfile(char(OLresDir),'..');
     end
 else
-  expDir = Exp(expN).Dexp(DexpN).ExpFoldr  
+  expDir=Exp(expN).Dexp(DexpN).ExpFoldr  
 end
 
 %ExpHmDir= char(Exp(expN).Dexp(DexpN).resDir);
@@ -94,7 +94,7 @@ cd(w)
 
 %tPtsSize=size(Exp(expN).Dexp(DexpN).FexpScanBMtp{1,1},(3));
 tPtsSize=size(FexpScanBMtp{1,plateNum},(3));  %tPtsSize=size(FexpScanBMtp{1,1},(3)); 20160110
-%bmpFileLst = dirfullfile(char(OLresDir),num2str(plateNum),'*.bmp'));     %(fullfile(expDir, char(ScLst(ScLstCnt)), '*.bmp'));
+%bmpFileLst=dirfullfile(char(OLresDir),num2str(plateNum),'*.bmp'));     %(fullfile(expDir, char(ScLst(ScLstCnt)), '*.bmp'));
 hsafety=figure;
 dc= get(datacursormode)
 imInterval=1;

workflow/apps/matlab/ezview/EZtableRFdiag.m

@@ -1,11 +1,11 @@
-%Create and display Reference data in a table
+% Create and display Reference data in a table
 global Exp
-DexpN= Exp(expN).DexpN;
+DexpN=Exp(expN).DexpN;
 rnames=Exp(expN).Dexp(DexpN).RFrnames;
-data= Exp(expN).Dexp(DexpN).RFdata;
+data=Exp(expN).Dexp(DexpN).RFdata;
-cnames= [{'Median'},{'Mean'},{'STD'},{'Minimum'},{'Maximum'}];
+cnames=[{'Median'},{'Mean'},{'STD'},{'Minimum'},{'Maximum'}];
-f = figure('Menubar','none','Position',[1000 100 640 750],'Name',Exp(expN).Dexp(DexpN).ExpFoldr );
+f=figure('Menubar','none','Position',[1000 100 640 750],...
-
+  'Name',Exp(expN).Dexp(DexpN).ExpFoldr );
-t = uitable('Parent',f,'Data',data,'ColumnName',cnames,... 
+t=uitable('Parent',f,'Data',data,'ColumnName',cnames,... 
   'RowName',rnames,'Position',[20 20 620 730]);
         

workflow/apps/matlab/ezview/EZusrSelRefx.m

@@ -4,7 +4,7 @@
 try
 if n==1 && ~exist('RF1scanN','var') && ~exist('RF2scanN','var')  %change || &&
    %{
-   prompt = {'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
+   prompt={'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
               'Enter GeneName of Your Reference:'};
     rfMPstr= cell2mat(answer(1));
     rfMPcomas=strfind((cell2mat(answer(1))),','); 
@@ -23,12 +23,12 @@ if n==1 && ~exist('RF1scanN','var') && ~exist('RF2scanN','var')  %change || &&
     usrMPs= answer(1); 
     refGene= answer(2);
           %}
-   prompt = {'Enter GeneName to use as Reference:',...
+   prompt={'Enter GeneName to use as Reference:',...
        'Enter Specifics Term if used to futher specify Reference '}       
-    dlg_title = 'User Reference Input';
+    dlg_title='User Reference Input';
-    num_lines = 1;
+    num_lines=1;
-    def = {'None','Specifics Term'};
+    def={'None','Specifics Term'};
-    answer = inputdlg(prompt,dlg_title,num_lines,def);
+    answer=inputdlg(prompt,dlg_title,num_lines,def);
     rfGenestr= cell2mat(answer(1));
     rfSpec= cell2mat(answer(2));
 
@@ -172,8 +172,8 @@ uu= horzcat(uu,vv);
 for d=1:DMnum
     medianIndxG=[];
     NZrfIndxG=[];
-    minG = min(nonzeros(vv(:,d)));
+    minG=min(nonzeros(vv(:,d)));
-    maxG = max(nonzeros(vv(:,d)));
+    maxG=max(nonzeros(vv(:,d)));
     RFmeanG= mean(nonzeros(vv(:,d)));
     RFstdG= std(nonzeros(vv(:,d)));
     NZrfIndxG= find(nonzeros(vv(:,d)));

workflow/apps/matlab/ezview/EZvDatatip.m

@@ -79,9 +79,9 @@ try
 K=scan(1,plateNum).plate(1).CFout(indx,3); Ks= num2str(K);
 r=scan(1,plateNum).plate(1).CFout(indx,4); rs= num2str(r);
 l=scan(1,plateNum).plate(1).CFout(indx,5); Ls= num2str(l);
-try Kstr=Ks(1:5); catch, Kstr = Ks(1:length(Ks)); end
+try Kstr=Ks(1:5); catch, Kstr=Ks(1:length(Ks)); end
-try rstr=rs(1:5); catch, rstr = rs(1:length(rs)); end
+try rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
-try Lstr=Ls(1:5); catch, Lstr = Ls(1:length(Ls)); end
+try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end
 
 Kl=scan(1,plateNum).plate(1).CFout(indx,7);
 Ku=scan(1,plateNum).plate(1).CFout(indx,8);
@@ -93,7 +93,7 @@ t=1:200;
 clear g;
 
 try
-g =  K ./ (1 +  exp(-r.* (t - l )));
+g= K ./ (1 +  exp(-r.* (t - l )));
 gSlow= Kl ./ (1 +  exp(-rl.* (t - lslow )));
 gFast= Ku ./ (1 +  exp(-ru.* (t - lfast )));
 if K==0||r==0||l==0, g(1:200)=1;gSlow(1:200)=1;gFast(1:200)=1;end
@@ -140,7 +140,7 @@ end
 
 catch
     %{
-    g =  K ./ (1 +  exp(-r.* (t - l )));
+    g= K ./ (1 +  exp(-r.* (t - l )));
     if K==0||r==0||l==0, g(1:200)=1;end
     tser=(scan(1,plateNum).plate(1).t0Series(:));
     rawData= scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);

workflow/apps/matlab/ezview/EZvInitLoad.m

@@ -136,7 +136,7 @@ Exp(numExps+1).interacPBsel=0;
 % directory in the uigetfile to load the experiment .mat file.
 
 try 
-  [openExpfile,scansDir] = uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off')
+  [openExpfile,scansDir]=uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off')
 
 
   load (fullfile(Exp(1).Dexp(1).ExpFoldr,'MasterPlateFiles','MPDMmat.mat'))
@@ -180,7 +180,7 @@ try
   Exp(1).traceN=0; Exp(2).traceN=0; Exp(3).traceN=0;  %ZoneRelated
 
   Exp(1).hOL =[]; Exp(1).hOLb=[];
-  Exp(1).hOLname = {}; Exp(1).hOLexpNm={}; Exp(1).hOLresDir={}
+  Exp(1).hOLname={}; Exp(1).hOLexpNm={}; Exp(1).hOLresDir={}
   Exp(1).hOLplateNum=[];
   Exp(1).hOLresDir= {};
   Exp(1).RFmd1indx=[];
@@ -189,7 +189,7 @@ try
   Exp(1).RFmd2pltN=[];
 
   Exp(2).hOL =[]; Exp(2).hOLb=[];
-  Exp(2).hOLname = {}; Exp(2).hOLexpNm={}; Exp(2).hOLresDir={};
+  Exp(2).hOLname={}; Exp(2).hOLexpNm={}; Exp(2).hOLresDir={};
   Exp(2).hOLplateNum=[];
   Exp(2).hOLresDir= {};
   Exp(2).RFmd1indx=[];
@@ -198,7 +198,7 @@ try
   Exp(2).RFmd2pltN=[];
 
   Exp(3).hOL =[]; Exp(3).hOLb=[];
-  Exp(3).hOLname = {}; Exp(3).hOLexpNm={}; Exp(3).hOLresDir={};
+  Exp(3).hOLname={}; Exp(3).hOLexpNm={}; Exp(3).hOLresDir={};
   Exp(3).hOLplateNum=[];
   Exp(3).hOLresDir= {};
   Exp(3).RFmd1indx=[];
@@ -274,9 +274,9 @@ try
       DNLaxes1= handles.DNLaxes1; DNLaxes2= handles.DNLaxes2; DNLaxes3= handles.DNLaxes3;
       zeroCLn= zeros(1,DMnum);
       %Exp(expN).expLoadCnt(1)=1;  %ZoneRelated
-      Exp(1).hzeroCLn(1) = plot(DNLaxes1,zeroCLn,1:DMnum,'y'); try set(Exp(1).hzeroCLn,'visible','off'); catch ME, end
+      Exp(1).hzeroCLn(1)=plot(DNLaxes1,zeroCLn,1:DMnum,'y'); try set(Exp(1).hzeroCLn,'visible','off'); catch ME, end
-      Exp(2).hzeroCLn(1) = plot(DNLaxes2,zeroCLn,1:DMnum,'y'); try set(Exp(2).hzeroCLn,'visible','off'); catch ME, end
+      Exp(2).hzeroCLn(1)=plot(DNLaxes2,zeroCLn,1:DMnum,'y'); try set(Exp(2).hzeroCLn,'visible','off'); catch ME, end
-      Exp(3).hzeroCLn(1) = plot(DNLaxes3,zeroCLn,1:DMnum,'y'); try set(Exp(3).hzeroCLn,'visible','off'); catch ME, end
+      Exp(3).hzeroCLn(1)=plot(DNLaxes3,zeroCLn,1:DMnum,'y'); try set(Exp(3).hzeroCLn,'visible','off'); catch ME, end
       Exp(1).expLoadCnt=1;
       Exp(2).expLoadCnt=1;
       Exp(3).expLoadCnt=1;
@@ -438,7 +438,7 @@ try
         rf1scN=RF1scanN+d;
 
   try  %if RF1scanN doesn't exist this addition to list will be skipped
-      nonZeroIndx = find(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5));
+      nonZeroIndx=find(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5));
       
       if isempty(nonZeroIndx), nonZeroCnt=0; medianIndx= nonZeroIndx; 
       else nonZeroCnt=length(nonZeroIndx); 
@@ -793,8 +793,8 @@ try
   for d=1:DMnum
       medianIndxD=[];
       NZrfIndxG=[];
-      minG = min(nonzeros(vv(:,d)));
+      minG=min(nonzeros(vv(:,d)));
-      maxG = max(nonzeros(vv(:,d)));
+      maxG=max(nonzeros(vv(:,d)));
       RFmeanG=mean(nonzeros(vv(:,d)));
       RFstdG= std(nonzeros(vv(:,d)));
       NZrfIndxG= find(vv(:,d));  %find(nonzeros(vv(:,d)));  WWRONG FOR A WHILE! find(nonzeros(vv(:,d)));

workflow/apps/matlab/ezview/EZvNIcircle.m

@@ -26,8 +26,8 @@ diaExt=2*(radius+1);
 circBoxA=zeros(diaExt,diaExt);
 center= [radius+2, radius+2];
 [m n ]=size(circBoxA);
-X = bsxfun(@plus,(1:m)', zeros(1,n));
+X=bsxfun(@plus,(1:m)', zeros(1,n));
-Y = bsxfun(@plus,(1:n), zeros(m,1));
+Y=bsxfun(@plus,(1:n), zeros(m,1));
 cirMask= sqrt(sum(bsxfun(@minus,cat(3,X,Y),reshape(center,1,1,[])) .^2,3))<=radius;
 area=pi*radius^2;
 
@@ -43,8 +43,8 @@ FdiaExt=2*(radExpan);
 circBoxA=zeros(FdiaExt,FdiaExt);
 center= [radExpan+1, radExpan+1];
 [m n ]=size(circBoxA);
-X = bsxfun(@plus,(1:m)', zeros(1,n));
+X=bsxfun(@plus,(1:m)', zeros(1,n));
-Y = bsxfun(@plus,(1:n), zeros(m,1));
+Y=bsxfun(@plus,(1:n), zeros(m,1));
 FcirMask= sqrt(sum(bsxfun(@minus,cat(3,X,Y),reshape(center,1,1,[])) .^2,3))<=radExpan;
 
 %FcirPixA= nnz(cirMask);

workflow/apps/matlab/ezview/EZvapendLabel.m

@@ -2,25 +2,25 @@
 
 hFstrip=figure;
 %figure(hFstrip,'Visible','off')
-t = text(.05,.05,tmPtTx,'FontSize',8, 'FontWeight','bold');  %, 'FontWeight','demi')
+t=text(.05,.05,tmPtTx,'FontSize',8, 'FontWeight','bold');  %, 'FontWeight','demi')
 %Bspace= zeros(20,size(Fcutsc,2))+255;
 
 F=[];
 % Capture the text from the screen:
-F = getframe(gca,[10 10 200 200]);
+F=getframe(gca,[10 10 200 200]);
 % Close the figure:
 close
 cc=[];
 c=[];
 % Select any plane of the resulting image:
-cc = F.cdata(:,:,1);
+cc=F.cdata(:,:,1);
 c= cc(182:195,18:60);
 %
 i=[];
 j=[];
 % Determine where the text was (black is 0):
-%[i,j] = find(cc == 0);
+%[i,j]=find(cc == 0);
-[i,j] = find(c < 255);
+[i,j]=find(c < 255);
 
 % Read in or load the image that is to contain the text:
 
@@ -29,10 +29,10 @@ j=[];
 %Bspace= zeros(20,size(Fcutsc,2))+255;
 Bspace= zeros((210-size(Fcutsc,1)),size(Fcutsc,2))+255;
 ind=[];
-ind = sub2ind(size(Bspace),i,j);
+ind=sub2ind(size(Bspace),i,j);
 
 % Index into new image, replacing pixels with white:
-Bspace(ind) = uint8(0);
+Bspace(ind)=uint8(0);
 %figure
 % Display and color the new image:
 %imagesc(Bspace)

workflow/apps/matlab/ezview/EZviewGui.m

@@ -3,7 +3,7 @@ function varargout = EZviewGui(varargin)
 %      EZVIEWGUI, by itself, creates a new EZVIEWGUI or raises the existing
 %      singleton*.
 %
-%      H = EZVIEWGUI returns the handle to a new EZVIEWGUI or the handle to
+%      H=EZVIEWGUI returns the handle to a new EZVIEWGUI or the handle to
 %      the existing singleton*.
 %
 %      EZVIEWGUI('CALLBACK',hObject,eventData,handles,...) calls the local
@@ -20,8 +20,8 @@ function varargout = EZviewGui(varargin)
 %
 % See also: GUIDE, GUIDATA, GUIHANDLES
 
-  gui_Singleton = 0;
+  gui_Singleton=0;
-  gui_State = struct( ...
+  gui_State=struct( ...
     'gui_Name',       mfilename, ...
     'gui_Singleton',  gui_Singleton, ...
     'gui_OpeningFcn', @EZviewGui_OpeningFcn, ...
@@ -30,11 +30,11 @@ function varargout = EZviewGui(varargin)
     'gui_Callback',   []);
 
   if nargin && ischar(varargin{1})
-    gui_State.gui_Callback = str2func(varargin{1});
+    gui_State.gui_Callback=str2func(varargin{1});
   end
 
   if nargout
-    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
+    [varargout{1:nargout}]=gui_mainfcn(gui_State, varargin{:});
   else
     try
       gui_mainfcn(gui_State, varargin{:});
@@ -52,7 +52,7 @@ function EZviewGui_OpeningFcn(hObject, eventdata, handles, varargin)
 % varargin   command line arguments to EZviewGui (see VARARGIN)
 
   % Choose default command line output for EZviewGui
-  handles.output = hObject;
+  handles.output=hObject;
 
   % Update handles structure
   guidata(hObject, handles);
@@ -94,13 +94,13 @@ function EZviewGui_OpeningFcn(hObject, eventdata, handles, varargin)
 end
 
 % Outputs from this function are returned to the command line.
-function varargout = EZviewGui_OutputFcn(hObject, eventdata, handles)
+function varargout=EZviewGui_OutputFcn(hObject, eventdata, handles)
 % varargout  cell array for returning output args (see VARARGOUT);
 % hObject    handle to figure
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
 % Get default command line output from handles structure
-  varargout{1} = handles.output;
+  varargout{1}=handles.output;
 end
 
 % Menu bar
@@ -368,7 +368,7 @@ function clrOlay1_Callback(hObject, eventdata, handles)
   Exp(1).traceN= 0;
   %Exp(1).cTraceN= 0; 
   Exp(1).hOL =[]; Exp(1).hOLb=[];
-  Exp(1).hOLname = {}; Exp(1).hOLexpNm={}; Exp(1).hOLresDir={};
+  Exp(1).hOLname={}; Exp(1).hOLexpNm={}; Exp(1).hOLresDir={};
   Exp(1).hOLplateNum=[];
   Exp(1).hOLresDir= {};
   cla(ghandles.Dlaxes1); cla(ghandles.Dkaxes1); cla(ghandles.Draxes1);
@@ -587,7 +587,7 @@ function clrOlay2_Callback(hObject, eventdata, handles)
   %Exp(2).cTraceN= 0;
 
   Exp(2).hOL =[]; Exp(2).hOLb=[];
-  Exp(2).hOLname = {}; Exp(2).hOLexpNm={}; Exp(2).hOLresDir={}
+  Exp(2).hOLname={}; Exp(2).hOLexpNm={}; Exp(2).hOLresDir={}
   Exp(2).hOLplateNum=[];
   Exp(2).hOLresDir= {};
 
@@ -801,7 +801,7 @@ function clrOlay3_Callback(hObject, eventdata, handles)
   %Exp(3).cTraceN= 0;
 
   Exp(3).hOL =[]; Exp(3).hOLb=[];
-  Exp(3).hOLname = {}; Exp(3).hOLexpNm={}; Exp(3).hOLresDir={}
+  Exp(3).hOLname={}; Exp(3).hOLexpNm={}; Exp(3).hOLresDir={}
   Exp(3).hOLplateNum=[];
   Exp(3).hOLresDir= {};
 
@@ -1534,7 +1534,7 @@ set(ghandles.OLexp1,'string',{''})
 cla(ghandles.OLaxes1)
 Exp(1).traceN=0;
 Exp(1).hOL =[]; Exp(1).hOLb=[];
-Exp(1).hOLname = {}; Exp(1).hOLexpNm={}; Exp(1).hOLresDir={}
+Exp(1).hOLname={}; Exp(1).hOLexpNm={}; Exp(1).hOLresDir={}
 Exp(1).hOLplateNum=[];
 Exp(1).hOLresDir= {};
 
@@ -1543,7 +1543,7 @@ set(ghandles.OLexp2,'string',{''})
 cla(ghandles.OLaxes2)
 Exp(2).traceN=0;
 Exp(2).hOL =[]; Exp(2).hOLb=[];
-Exp(2).hOLname = {}; Exp(2).hOLexpNm={}; Exp(2).hOLresDir={}
+Exp(2).hOLname={}; Exp(2).hOLexpNm={}; Exp(2).hOLresDir={}
 Exp(2).hOLplateNum=[];
 Exp(2).hOLresDir= {};
 
@@ -1552,7 +1552,7 @@ set(ghandles.OLexp3,'string',{''})
 cla(ghandles.OLaxes3);
 Exp(3).traceN=0; 
 Exp(3).hOL =[]; Exp(3).hOLb=[];
-Exp(3).hOLname = {}; Exp(3).hOLexpNm={}; Exp(3).hOLresDir={}
+Exp(3).hOLname={}; Exp(3).hOLexpNm={}; Exp(3).hOLresDir={}
 Exp(3).hOLplateNum=[];
 Exp(3).hOLresDir= {};
 %}
@@ -1946,7 +1946,7 @@ function zonePB2_Callback(hObject, eventdata, handles)
   global ghandles
   global zonePB
 
-  zonePB = 2
+  zonePB=2
   %if get(handles.zonePB2,'value')==0, set(handles.zonePB2,'value',1); end
   set(handles.zonePB2,'value',1);
   DexpN= get(handles.DN2,'value')

workflow/apps/matlab/ezview/datatipp.m

@@ -3,14 +3,11 @@ function output_txt = myfunction(obj,event_obj)
 % obj          Currently not used (empty)
 % event_obj    Handle to event object
 % output_txt   Data cursor text string (string or cell array of strings).
-
+  pos=get(event_obj,'Position');
-
+  output_txt={['X: ',num2str(pos(1),4)], ['Y: ',num2str(pos(2),4)]};
-pos = get(event_obj,'Position');
+  % If there is a Z-coordinate in the position, display it as well
-output_txt = {['X: ',num2str(pos(1),4)],...
+  if length(pos) > 2
-    ['Y: ',num2str(pos(2),4)]};
+    output_txt{end+1}=['Z: ',num2str(pos(3),4)];
-
+  end
-% If there is a Z-coordinate in the position, display it as well
+  %waitforbuttonpress
-if length(pos) > 2
-    output_txt{end+1} = ['Z: ',num2str(pos(3),4)];
 end
-%waitforbuttonpress

workflow/apps/matlab/ezview/questdlgJWR.m

@@ -1,12 +1,12 @@
 function ButtonName=questdlg(Question,Title,Btn1,Btn2,Btn3,Default)
 %QUESTDLG Question dialog box.
-%  ButtonName = QUESTDLG(Question) creates a modal dialog box that
+%  ButtonName=QUESTDLG(Question) creates a modal dialog box that
 %  automatically wraps the cell array or string (vector or matrix)
 %  Question to fit an appropriately sized window.  The name of the
 %  button that is pressed is returned in ButtonName.  The Title of
 %  the figure may be specified by adding a second string argument:
 %
-%    ButtonName = questdlg(Question, Title)
+%    ButtonName=questdlg(Question, Title)
 %
 %  Question will be interpreted as a normal string.
 %
@@ -17,7 +17,7 @@ function ButtonName=questdlg(Question,Title,Btn1,Btn2,Btn3,Default)
 %  This can be changed by adding a third argument which specifies the
 %  default Button:
 %
-%    ButtonName = questdlg(Question, Title, 'No')
+%    ButtonName=questdlg(Question, Title, 'No')
 %
 %  Up to 3 custom button names may be specified by entering
 %  the button string name(s) as additional arguments to the function
@@ -26,7 +26,7 @@ function ButtonName=questdlg(Question,Title,Btn1,Btn2,Btn3,Default)
 %  setting DEFAULT to the same string name as the button you want
 %  to use as the default button:
 %
-%    ButtonName = questdlg(Question, Title, Btn1, Btn2, DEFAULT);
+%    ButtonName=questdlg(Question, Title, Btn1, Btn2, DEFAULT);
 %
 %  where DEFAULT is set to Btn1.  This makes Btn1 the default answer.
 %  If the DEFAULT string does not match any of the button string names,
@@ -35,7 +35,7 @@ function ButtonName=questdlg(Question,Title,Btn1,Btn2,Btn3,Default)
 %  To use TeX interpretation for the Question string, a data
 %  structure must be used for the last argument, i.e.
 %
-%    ButtonName = questdlg(Question, Title, Btn1, Btn2, OPTIONS);
+%    ButtonName=questdlg(Question, Title, Btn1, Btn2, OPTIONS);
 %
 %  The OPTIONS structure must include the fields Default and Interpreter.
 %  Interpreter may be 'none' or 'tex' and Default is the default button
@@ -46,7 +46,7 @@ function ButtonName=questdlg(Question,Title,Btn1,Btn2,Btn3,Default)
 %
 %  Example:
 %
-%  ButtonName = questdlg('What is your favorite color?', ...
+%  ButtonName=questdlg('What is your favorite color?', ...
 %                        'Color Question', ...
 %                        'Red', 'Green', 'Blue', 'Green');
 %  switch ButtonName,
@@ -72,7 +72,7 @@ if nargin<1
 end
 
 Interpreter='none';
-Question = dialogCellstrHelper(Question);
+Question=dialogCellstrHelper(Question);
 
 %%%%%%%%%%%%%%%%%%%%%
 %%% General Info. %%%
@@ -109,10 +109,10 @@ end
 %%%%%%%%%%%%%%%%%%%%%%%
 %%% Create QuestFig %%%
 %%%%%%%%%%%%%%%%%%%%%%%
-FigPos    = get(0,'DefaultFigurePosition');
+FigPos   =get(0,'DefaultFigurePosition');
-FigPos(3) = 267;
+FigPos(3)=267;
-FigPos(4) =  70;
+FigPos(4)= 70;
-FigPos    = getnicedialoglocation(FigPos, get(0,'DefaultFigureUnits'));
+FigPos   =getnicedialoglocation(FigPos, get(0,'DefaultFigureUnits'));
 
 QuestFig=dialog(                                    ...
   'Visible'         ,'off'                      , ...
@@ -164,7 +164,7 @@ if NumButtons > 1
     BtnWidth=max(BtnWidth,BtnExtent(3)*btnMargin);
   end
 end
-BtnHeight = max(BtnHeight,BtnExtent(4)*btnMargin);
+BtnHeight=max(BtnHeight,BtnExtent(4)*btnMargin);
 
 delete(ExtControl);
 
@@ -198,36 +198,36 @@ MsgTxtForeClr=Black;
 MsgTxtBackClr=get(QuestFig,'Color');
 
 CBString='uiresume(gcbf)';
-DefaultValid = false;
+DefaultValid=false;
-DefaultWasPressed = false;
+DefaultWasPressed=false;
-BtnHandle = cell(NumButtons, 1);
+BtnHandle=cell(NumButtons, 1);
-DefaultButton = 0;
+DefaultButton=0;
 
 % Check to see if the Default string passed does match one of the
 % strings on the buttons in the dialog. If not, throw a warning.
-for i = 1:NumButtons
+for i=1:NumButtons
   switch i
     case 1
       ButtonString=Btn1;
       ButtonTag='Btn1';
       if strcmp(ButtonString, Default)
-        DefaultValid = true;
+        DefaultValid=true;
-        DefaultButton = 1;
+        DefaultButton=1;
       end
 
     case 2
       ButtonString=Btn2;
       ButtonTag='Btn2';
       if strcmp(ButtonString, Default)
-        DefaultValid = true;
+        DefaultValid=true;
-        DefaultButton = 2;
+        DefaultButton=2;
       end
     case 3
       ButtonString=Btn3;
       ButtonTag='Btn3';
       if strcmp(ButtonString, Default)
-        DefaultValid = true;
+        DefaultValid=true;
-        DefaultButton = 3;
+        DefaultButton=3;
       end
   end
 
@@ -243,7 +243,7 @@ for i = 1:NumButtons
 end
 
 if ~DefaultValid
-  warnstate = warning('backtrace','off');
+  warnstate=warning('backtrace','off');
   warning('MATLAB:QUESTDLG:stringMismatch','Default string does not match any button string name.');
   warning(warnstate);
 end
@@ -278,7 +278,7 @@ texthandle=text( ...
     'Tag'                 ,'Question'                        ...
     );
 
-textExtent = get(texthandle, 'Extent');
+textExtent=get(texthandle, 'Extent');
 
 % (g357851)textExtent and extent from uicontrol are not the same. For window, extent from uicontrol is larger
 %than textExtent. But on Mac, it is reverse. Pick the max value.
@@ -395,7 +395,7 @@ end
     switch(evd.Key)
       case {'return','space'}
         if DefaultValid
-          DefaultWasPressed = true;
+          DefaultWasPressed=true;
           uiresume(gcbf);
         end
       case 'escape'
@@ -407,7 +407,7 @@ end
     switch(evd.Key)
       case {'return'}
         if DefaultValid
-          DefaultWasPressed = true;
+          DefaultWasPressed=true;
           uiresume(gcbf);
         end
       case 'escape'

workflow/qhtcp-workflow

@@ -598,7 +598,7 @@ easy() {
     # Make EASY dirs
     debug "mkdir -p $EASY_RESULTS_DIR"
     mkdir -p "$EASY_RESULTS_DIR"
-    dirs=('PrintResults' 'CFfigs' 'Fotos' 'Fotos/BkUp' 'matResults')
+    dirs=('PrintResults' 'CFfigs' 'Fotos')
     for d in "${dirs[@]}"; do
       debug "mkdir $EASY_RESULTS_DIR/$d" 
       mkdir "$EASY_RESULTS_DIR/$d"

workflow/templates/exp/.Rhistory

@@ -1,15 +0,0 @@
-is.numeric(NA)
-is.numeric(as.numeric(NA)
-)
-inp= a
-inp= "a"
-inp <- inp[!is.na(inp)]
-inp
-!is.na(inp)
-is.na(inp)
-inp
-gsub(pattern = (/D)), replacement= 3)
-gsub(pattern = ("[/D)"), replacement= 3)
-gsub(pattern = inp("[/D)"), replacement= 3)
-list.files
-list.files()

workflow/templates/exp/ExpFrontend.m

@@ -1,212 +0,0 @@
-% FrontEnd utility to copy source result sheet into Exp_ folders of
-% StudiesQHTCP/StudyName/Exp1(2,3,4). This allow the automation of path
-% capture to the StudiesDataArchieve.txt study log.
-% Select, copy and Capture Study Exp_ details to study log
-
-%Exp meta data collection 
-
-% Set path variables
-wCodeDir=pwd;
-Wstudy=fullfile('../', wCodeDir);
-studyDate=datetime('now');
-
-%Load results file meta data  into workspace
-try 
-    ExpLabel= strcat('Exp',wCodeDir(end))
-    questdlg('\fontsize{20} Select the !!Results File','File Selection','OK', struct('Default','OK','Interpreter','tex'));
-    [resFile,resPath]= uigetfile('*.txt')
-    copyfile((fullfile(resPath,resFile)),fullfile(wCodeDir))
-    resDate= char(regexp(resFile, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)','match'))
-    cd ..
-
-    if ispc
-        lastSep=max(strfind(Wstudy,'\'))
-        studyName=Wstudy((lastSep+1):end)
-    else
-        lastSep=max(strfind(Wstudy,'/'))
-        studyName=Wstudy((lastSep+1):end)
-    end
-
-    % Build the study info array
-    S.sDate(1)= {studyDate};
-    S.sName(1)= {studyName}
-    S.sPath(1)= {Wstudy}
-    S.ELabel(1)= {ExpLabel}
-    S.EresDate(1)= {resDate}
-    S.EresFile(1)= {resFile}
-    S.EresPath(1)= {resPath}
-    
-    cd ..
-
-    fid = fopen('StudiesDataArchive.txt','a');  
-    fprintf(fid,'StudyDate\tStudyName\tStudyPath\tExpNum\tExpDate\tExpPath\tResultFile\n');
-    fprintf(fid, '%s\t %s\t %s\t %s\t %s\t %s\t %s \n',S.sDate{1},S.sName{1},S.sPath{1},S.ELabel{1},S.EresDate{1},S.EresPath{1},S.EresFile{1});
-    fclose(fid);
-    fclose('all');
-
-catch
-    cd(wCodeDir)
-    disp('Error: Unable to Execute ExpFrontend.m')
-end
-
-cd(wCodeDir)
-
-%*************************************************************************************
-%*************************************************************************************
-%#####################################################################################
-%Improved storage ammenable for database use
-%FrontEnd utility to copy source result sheet into Exp_ folders of
-%StudiesQHTCP/StudyName/Exp1(2,3,4). This allow the automation of path
-%capture to the StudiesDataArchieve.txt study log.
-%Select, copy and Capture Study Exp_ details to study log
-studyDateNow= studyDate  %preserve the 'Now' date 
-nowNumFNm= strcat((int2str(now)),'.mat') % from previous section incase the /StudyName doesn't have a standard date 
-%capture the /StudiesQHTCP directory for storing log data
-cd ../..
-logPath= pwd  %is /.../Exp_
-cd(wCodeDir)
-%Try to load an existing data set from previous Frontend calls
-try  %end ~ln121
-  load(fullfile(logPath,'.studyLog.mat')) %load(fullfile('../../','studyLog.mat'))
-catch  %If no studyLog.mat found [Initial First Entry]
-    ExpLabel= strcat('Exp',wCodeDir(end))
-    resDate= char(regexp(resFile, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)','match'))
-    cd .. %move up to current study folder from ../Exp_ folder; 
-    %Study meta data collection
-    Wstudy= pwd %Capture the specific current Study directory
-    try %try to extract study date from folder name
-     studyDate= char(regexp(Wstudy, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)| \d\d\d\d\d\d)','match'))
-     S.sDate(1)= {studyDate};
-    catch %if unsuccessful, accept the current date and convert to a 6 char string
-     studyDate= yyyymmdd(studyDateNow);
-     studyDate= (int2str(studyDate))
-     studyDate= studyDate(3:8)
-    end
-   %Capture StudyName
-   if ispc
-    lastSep=max(strfind(Wstudy,'\'))
-    studyName= Wstudy((lastSep+1):end)
-   else
-    lastSep=max(strfind(Wstudy,'/'))
-    studyName= Wstudy((lastSep+1):end)
-    
-   end
-  %Put current First data entry into Structure of Save to StudyLog.mat file
-   S.sDate(1)= {studyDate};
-   S.sName(1)= {studyName}
-   S.sPath(1)= {Wstudy}
-   S.ELabel(1)= {ExpLabel}
-   S.EresDate(1)= {resDate}
-   S.EresFile(1)= {resFile}
-   S.EresPath(1)= {resPath}
-   
- cd(wCodeDir)
-
-logFiletxt= fullfile(logPath,'StudiesDataArchive4DB.txt') %relative .txt path 
-%Initialize the StudiesDataArchive.txt file with the First row of meta data
-
-%Print to a .txt spreadsheet the first set of data in the logFiletxt file
-fid = fopen(logFiletxt,'w');
-fprintf(fid,'StudyDate\tStudyName\tStudyPath\tExpNum\tExpDate\tExpPath\tResultFile\n');
-fprintf(fid, '%s\t %s\t %s\t %s\t %s\t %s\t %s \n',studyDate,studyName,Wstudy,ExpLabel,resDate,resPath,resFile);
-fclose(fid);
-%Save the first entry meta data into a permanent .mat files for future recall
-save(fullfile(logPath,'studyLog4DB.mat'), 'S')
-save(fullfile(logPath,'.studyLog.mat'), 'S')
-save(fullfile(logPath,'.nowNumFNm.mat'), 'S')
-
-
-
-end  %end for try  for the First entry only
-%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-%++++++++END of FIRST ENTRY startup section++++++++++++++++++++++++++++++++
-%++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-
-
-
-%Begin routine for all Entries After the Initial data entry**************** 
-ExpLabel= strcat('Exp',wCodeDir(end))
-resDate= char(regexp(resFile, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)','match')) %Capture date from !!Results file
-
-cd .. %Move to the current study folder
-
-%Capture study meta dat
-Wstudy= pwd % Capture the path to the current study
-
-  %Attempt to extract study date from folder name and convert to a
-  %searchable numeric date
-   studyDate= char(regexp(Wstudy, '(\d\d\_\d\d\d\d)|( \d\d\_\d\d\d\d|\d\d\d\d\d\d)| \d\d\d\d\d\d)','match'))
-      if ~isempty(studyDate)  %If no date in folder name use current date and convert to 6char string
-       S.sDate(1)= {studyDate};
-       if isequal((str2num(studyDate(3))),'_') %Remove '_' so that date is a number for easy DB search
-           studyDate= strcat(studyDate(1:2),studyDate(4:6))
-       end
-      else
-       studyDate= yyyymmdd(studyDateNow);
-       studyDate= (int2str(studyDate)) 
-       studyDate= studyDate(3:8) 
-     end
-    
-if ispc
-    lastSep=max(strfind(Wstudy,'\'))
-    studyName= Wstudy((lastSep+1):end)
-else
-    lastSep=max(strfind(Wstudy,'/'))
-    studyName= Wstudy((lastSep+1):end)
-end
-
-%Put meta data into a structure for storage (studyLog.mat) and future
-%compare operations
-lastRow= length(S.sPath)
-
-%Compare these just obtained paths with those stored in the studyLog.mat
-%file and add a new row if the study or results sheet meta data is new or different
-cd ..  %Move the the /QHTPCstudies folder
-logtxt= 'StudiesDataArchive4DB.txt'
-logFiletxt= fullfile(logPath,logtxt) %
-try
-  matched=0;
- for n= 1:(lastRow)
-    if strcmp(Wstudy,S.sPath(n)) && strcmp(resPath, S.EresPath(n)) && strcmp(ExpLabel, S.ELabel(n))
-        matched= 1;
-        break
-    end
- end
-      
-    
-%Update the StudiesDataArchive.txt file with a new row of meta data
-if matched== 0 %if no match for this entry then add a line to the text archive file
-     fid = fopen(logFiletxt,'w');  
-      S.sDate(lastRow+1)= {studyDate};
-      S.sName(lastRow+1)= {studyName};
-      S.sPath(lastRow+1)= {Wstudy};
-      S.ELabel(lastRow+1)= {ExpLabel};
-      S.EresDate(lastRow+1)= {resDate};
-      S.EresFile(lastRow+1)= {resFile};
-      S.EresPath(lastRow+1)= {resPath};
-  for n= 1:(lastRow +1)
-   %Print to a .txt spreadsheet and Save update to .mat files
-    if n==1
-     fprintf(fid,'StudyDate\tStudyName\tStudyPath\tExpNum\tExpDate\tExpPath\tResultFile\n');
-    end
-    fprintf(fid, '%s\t %s\t %s\t %s\t %s\t %s\t %s \n',S.sDate{n},S.sName{n},S.sPath{n},S.ELabel{n},S.EresDate{n},S.EresPath{n},S.EresFile{n});
-  end
-
-  fclose(fid); %close DBase amenable study log file after data update
- 
- save((fullfile(logPath,'studyLog4DB.mat')), 'S') % path for  studyLog.mat
- save((fullfile(logPath,'.studyLog.mat')), 'S')  %path backup studyLogBU.mat
- save((fullfile(logPath,strcat('.',nowNumFNm))), 'S') 
-end 
-fclose('all');
-
-catch
-    cd(wCodeDir) %Return to the location of the frontend.m code (/studyName/Exp_)
-    fclose('all');
-    clear S %clear data structure variable 'S.'
-end
-
-cd(wCodeDir) %Return to the location of the frontend.m code (/studyName/Exp_)
-clear all %clear workspace variables
-
-