%***********User find and build composite of Selected Gene Composite and
%*************Plot it on OLay Plot and Trend plot DNLaxles
%***************For Chonological Studies (multi Day 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


tracN=Exp(expN).traceN;
n= Exp(expN).DexpN;  %Temp input for development
%UmDayaa= cell(3,n);   UmDaybb= cell(3,n);
patrnN=strfind(selGnOrf{1},':');  %Extract Gene-Orf Name
selStrNm= char(selGnOrf)
usrGene= selStrNm(1:(patrnN(1)-1))


   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);
    %usrGene= cell2mat(answer(1));
    usrSpec= answer(1); 
    usrGnSp= strcat(usrGene,usrSpec);
    if strcmpi(usrSpec,'None'), usrGnSp= {strcat(usrGene,'-')}; end
    
%if strfind(Exp(expN).UgeneSpLst,usrGnSp), break; end  

Exp(expN).Dexp(n).UsrmdPLB= {[]};

Exp(expN).Dexp(n).UsrMedianG= [];
Exp(expN).Dexp(n).UsrminG= [];
Exp(expN).Dexp(n).UsrmaxG= [];
Exp(expN).Dexp(n).UsrstdG= [];
Exp(expN).Dexp(n).UsrmeanG= [];
Exp(expN).Dexp(n).UsrCmpGL= []; %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGK= []; %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGr= []; %For Ref Composite 17_1026 

    
Exp(expN).Dexp(n).UsrGLB= {};
    
for n=1:Exp(expN).DexpLength   %LOOP Thru DayExps

MPnum=length(Exp(expN).Dexp(n).MP);
DMnum= length(Exp(expN).Dexp(n).DM.drug);
tPtsSize= size(Exp(expN).Dexp(n).FexpScanBMtp{1,1},(3)); 
%*********************************

%lstindx= size(aa,1);
%lstindxOrf= size(bb,1);
spN=0;
rfcnt=0;
dRF1indx=0;

%usrGene= cell2mat(usrGene);  %user entry of Specifics for Ref selection
usrSp= cell2mat(usrSpec);  %user entry of Specifics for Ref selection

%*******************************************************
for mp=1:length(Exp(expN).Dexp(n).MP) 
   %RF1fullPlate=0;
  for ind384=1:384   
      spN=spN+1;
    
     try  %
          r= ceil(ind384/24); 
          if rem(ind384,24)==0, c=24; else c=rem(ind384,24); end
          
         %Insert test for numeric in genename and orf if isnumeric
         %Correct common EXCEL problem of converting OCT1 into a date numeric
             if cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))==38991,
                 Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={'OCT1_'}; 
             elseif isnumeric(cell2mat(Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)))
                 Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)={' '}; 
             end
         %*****************************************************************
               
    %DISPersed REFerence capture and find Medians                
    if ( ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) && ...
                strcmpi((Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384)),usrSp)))...
           || ((strcmpi((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),usrGene) && ...
                strcmpi(usrSp,'None'))) ),
           
               dRF1indx=dRF1indx+1;
           Exp(expN).Dexp(n).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384)),':',' ');
            drf(dRF1indx,1)= (Exp(expN).Dexp(n).MP(mp).genename{1}(ind384));
            drf(dRF1indx,2)= {strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};  
            drf(dRF1indx,3)={mp}; drfMP(dRF1indx,mp)= mp;
            drf(dRF1indx,4)={r};  drfr(dRF1indx,mp)= r;
            drf(dRF1indx,5)={c};  drfc(dRF1indx,mp)= c;
            drf(dRF1indx,6)={ind384}; drfPindx(dRF1indx,mp)= ind384;
            %drf(dRF1indx,7)= (Exp(expN).Dexp(n).MP(mp).specifics{1}(ind384));
          
    end   %if isempty(regexpi(char((Exp(expN).Dexp(n).MP(mp).genename{1}(ind384))),'blank'))...  
    %*******************************************************************************       
      catch
      error='EZexpSel lineAfter 24 EZmultiGeneLst.m'   
      mp     %Disable in future to prevent a bomb out OR put into a nested TryCatch
      ind384 %Disable in future to prevent a bomb out OR put into a nested TryCatch
      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(n).MP)
%*****************************************************
%************************************************************************************************





%Exp(expN).Dexp(n).UsrmdPindx=[];
%Exp(expN).Dexp(n).UsrmdPpltN=[];
if exist('drf','var')
%Det. index of change from one MP to the next    

  i=2;
  clear chgIndx
  chgIndx(1)=1;
for j=1:length(drf(:,3))
    
      if j>1
        if cell2mat(drf(j,3))~= cell2mat(drf((j-1),3)), chgIndx(i)=j; i=i+1; end
      end
end
chgIndx(length(chgIndx)+1)= length(drf)+1;
uu=zeros(size(drf,1),4);
uu(:,1:4)= cell2mat(drf(:,3:6));
vv= zeros(length(drf),1 );  %DMnum);
%************************************
 dMPs= unique(cell2mat(drf(:,3))); 
 %*****************************************
 
 for mm=1:length(dMPs)    % length(chgIndx)
    usrScNdisp=((dMPs(mm)-1)*DMnum)+(dmSel); 
    NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm));    medianIndxDisp= NZrefIndxP;
    vv(chgIndx(mm):(chgIndx(mm+1)-1),dmSel)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5);
    %For Global Ref Composite 17_1009 %**************************************************************************
    vvK(chgIndx(mm):(chgIndx(mm+1)-1),dmSel)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3);
    vvr(chgIndx(mm):(chgIndx(mm+1)-1),dmSel)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4);
    %*****************************************************************************************************
  end    %for mm=1:length(dMPs)
%****************CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES******************************************************************
uu= horzcat(uu,vv);
for d=dmSel:dmSel
    medianIndxG=[];
    NZusrIndxG=[];
    minG=min(nonzeros(vv(:,d)));
    maxG=max(nonzeros(vv(:,d)));
    usrmeanG= mean(nonzeros(vv(:,d)));
    usrStdG= std(nonzeros(vv(:,d)));
    NZusrIndxG= find(vv(:,d));   
 
  if isempty(usrmeanG), nonZeroCntD=0,    %medianIndxDisp= RFmeanG(d); 
     else nonZeroCntD= length(nonzeros(vv(:,d))); 
  end
  %Calc. of median value for composite doesn't require and odd number of Indx items
  medianIndxG= NZusrIndxG(:);
    if ~isempty(NZusrIndxG) && length(medianIndxG) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero 

Exp(expN).Dexp(n).UsrGLB(d)= usrGnSp;   %strcat(aa(lstindx,1),aa(lstindx,2));   
Exp(expN).Dexp(n).UsrLvals= vv(medianIndxG);
Exp(expN).Dexp(n).UsrKvals= vvK(medianIndxG);
Exp(expN).Dexp(n).Usrrvals= vvr(medianIndxG);
     end
end  

end  % if exist('drf','var')
%END OF DISPERSE REFERENCE PLATAES CALCULATIONS AND LIST ADDITIONS   
%*********************************************************************
%####################################################################
end  %for n=1:Exp(expN).DexpLength   %Loop thru Dayexps
Exp(expN).UgeneCnt= Exp(expN).UgeneCnt +1;
Exp(expN).UgeneSpLst(Exp(expN).UgeneCnt)= usrGnSp;
%#######################################################################


%***********PLOT Values Selected Gene-Specifics Composite  ******************************************try
smpSz= size(medianIndxG,1);
K= median(vvK(medianIndxG,dmSel)); Ks= num2str(K);  Kstd= std(vvK(medianIndxG,dmSel)); KstdStr= num2str(Kstd);
r= median(vvr(medianIndxG,dmSel)); rs= num2str(r);  rstd= std(vvr(medianIndxG,dmSel)); rstdStr= num2str(rstd);
l= median(vv(medianIndxG,dmSel)); Ls= num2str(l);   Lstd= std(vv(medianIndxG,dmSel));  LstdStr= num2str(Lstd);
Kl= K - std(vvK(medianIndxG,dmSel));   %K - Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Ku= K + std(vvK(medianIndxG,dmSel));   %K + Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
rl= r - std(vvr(medianIndxG,dmSel));   %r - Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
ru= r + std(vvr(medianIndxG,dmSel));   %r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
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 rstr=rs(1:5); catch, rstr=rs(1:length(rs)); end
try Lstr=Ls(1:5); catch, Lstr=Ls(1:length(Ls)); end

            
            pertSel=Exp(zoneSel).Dexp(DexpN).pertSel;  %floor(get(handles.DMsldr1,'value'));
            plateNum=(LBmp-1)*destPerMP + pertSel;
            indx=((LBr-1)*24) +LBc
            MP=Exp(zoneSel).Dexp(DexpN).MP;
           
try                

t=1:200;
clear g;

try
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

            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;
            traceN=Exp(1).traceN;
            end
            if zoneSel==2, plotAxes=ghandles.Paxes2; OLaxes=ghandles.OLaxes2;Daxes=ghandles.Daxes2;
                Dlaxes=ghandles.Dlaxes2;Dkaxes=ghandles.Dkaxes2;Draxes=ghandles.Draxes2;
            Exp(2).traceN=Exp(2).traceN+1;
            traceN=Exp(2).traceN;
            end
            if zoneSel==3, plotAxes=ghandles.Paxes3; OLaxes=ghandles.OLaxes3;Daxes=ghandles.Daxes3;
                Dlaxes=ghandles.Dlaxes3;Dkaxes=ghandles.Dkaxes3;Draxes=ghandles.Draxes3;
            Exp(3).traceN=Exp(3).traceN+1;
            traceN=Exp(3).traceN;
            end
plot(plotAxes,t,g);hold (plotAxes,'on');
plot(plotAxes,t,gSlow,'y');plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
%Store L R and K valves for 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  
    catchissue='Ln100 EZlstBoxExt'
end  %trycatch

%Get the DM agar description
if expN==1,DMstr=char(get(handles.DM1,'string'));end
if expN==2,DMstr=char(get(handles.DM2,'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,'_');

%spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
%tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
%graphStr=strcat(grfgenestr,'_','L=',Lstr,'_','r=',rstr,'_','K=',Kstr);
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
    slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'/');
end
    
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1
expStr= {xp(startPos:endPos)}

Exp(zoneSel).hOLname(traceN)= spotDescrip;  %graphStr;  %ghandles.Exp(zoneSel).hOLname(traceN)= graphStr;
Exp(zoneSel).hOLexpNm(traceN)= expStr;  %ghandles.Exp(expN).hOLexpNm(traceN)= expStr;
Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
Exp(zoneSel).hOLplateNum(traceN)= plateNum; 

%traceData= vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));  

if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end  % Displays the value.
if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end  %graphStr);end % Displays the value.
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)
















































%{
% If a specific spot median is ever needed
   %Calc. of EXACT median specific culture requires an odd number of indx items 
     if ~isempty(NZusrIndxG) && mod(nonZeroCntD,2)==0, medianIndxOdd=  NZusrIndxG(1:(size(NZusrIndxG,1)-1)); end
     if ~isempty(NZusrIndxG) && mod(nonZeroCntD,2)~=0, medianIndxOdd= NZusrIndxG(:); end 
      mvalsDG= median(vv(medianIndxOdd,d));                  %(nonzeros(vv(:,d))); 
      nzPosIndxDG=find(mvalsDG==vv(:,d));    
Exp(expN).Dexp(n).UsrMedianG(d)= mvalsDG;
Exp(expN).Dexp(n).UsrminG(d)= minG;
Exp(expN).Dexp(n).UsrmaxG(d)= maxG;
Exp(expN).Dexp(n).UsrstdG(d)= usrStdG;
Exp(expN).Dexp(n).UsrmeanG(d)= usrmeanG; 
%}
%{
Exp(expN).Dexp(n).UsrCmpGL.dm(d).med= median(vv(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGL.dm(d).mean= mean(vv(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGL.dm(d).std= std(vv(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGL.dm(d).min= min(vv(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGL.dm(d).max= max(vv(medianIndxP,d)); %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpGK.dm(d).med= median(vvK(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGK.dm(d).mean= mean(vvK(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGK.dm(d).std= std(vvK(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGK.dm(d).min= min(vvK(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGK.dm(d).max= max(vvK(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGr.dm(d).med= median(vvr(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGr.dm(d).mean= mean(vvr(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGr.dm(d).std= std(vvr(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGr.dm(d).min= min(vvr(medianIndxP,d)); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpGr.dm(d).max= max(vvr(medianIndxP,d)); %For Ref Composite 17_1026 
%}


 %{   
  for mm=1:length(dMPs)    % length(chgIndx)
      
    for d= selDM:selDM  %1:(DMnum)
      medianIndxDisp=[];
      NZrefIndxP=[];
      nonZeroValsP=[];
      medValLstDisp=[];
     usrScNdisp=((dMPs(mm)-1)*DMnum)+(d);

try  % Determine the dispersed User Gene median mean and std if such exist
    NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm));    medianIndxDisp= NZrefIndxP
    vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5);
    %For Global Ref Composite 17_1009 %**************************************************************************
    vvK(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3);
    vvr(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4);
    %*****************************************************************************************************
    %{
    nonZeroValsP= nonzeros(Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5));
    std1Disp= std(nonZeroValsP);
    mean1Disp= mean(nonZeroValsP);
    minDisp= min(nonZeroValsP);
    maxDisp= max(nonZeroValsP);
    drfVals=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5);
    
    %nzValsAcc(mm).DM(d,:)= nonZeroValsP;
    
    %MEDIAN Determination for PLATES with Dispersed RFs
    %NZrefIndxP= NZrefIndxP %find(Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5));
     if isempty(NZrefIndxP), nonZeroCntDisp=0, medianIndxDisp= NZrefIndxP; 
     else nonZeroCntDisp=length(NZrefIndxP); 
     end                            
     if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)==0, medianIndxDisp=  NZrefIndxP(1:nonZeroCntDisp-1); end
     if ~isempty(NZrefIndxP) && mod(nonZeroCntDisp,2)~=0, medianIndxDisp= NZrefIndxP; end 
      %}
if ~isempty(NZrefIndxP) && length(medianIndxDisp) > 0 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
    medValLstDisp= Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(medianIndxDisp,5);
    mval1Disp=median(medValLstDisp);  
    nzMedPosIndx=find(mval1Disp==nonZeroValsP);   
medianIndxP= NZrefIndxP(nzMedPosIndx);  
%UsrmdlocP(1)= ceil(medianIndxP/24); %calc r value
%UsrmdlocP(2)= medianIndxP - ((UsrmdlocP(1)-1)*24);  %calc c value

meanKval= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3))));
meanrval= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4))));
else
    % Need to set L r K values to zeros or pick the first spot with zeros
    %Spot 1 could be other than zero as the median isn't calculated if fewer than some percent are nonzero
  medianCalcFailedD= 'To Few nonZero spots for valid median RF1 selection' 
  firstZeroDindx= find(((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
  firstZeroD= drfPindx((firstZeroDindx),dMPs(mm));
  %Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))=firstZeroD; 
  %Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm);   %RF1mp;   %Is this supposed to be the MP number or the ScanPlate number???
    
     
end  %~isempty(NZrefIndxP) && length(medianIndxPisp) > 3   ln584
catch   %try ln565
  medianCalcTryFailed1D= 'Failed! Failed!  {Dispersed RF1s}'
  try
      firstZeroindxD= find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first'); 
      firstZeroPindx= uu(firstZeroindxD,4);
  catch
  end
  end %try ~ln565
   end   %for d=0:DMnum 
  end    %for mm=1:length(dMPs)
%}

%{
%Code Template taken from EZlstBoxCmpExt.m
try
%if RFcmpGFlg==0    
smpSz= size(medianIndxP,1);
K= median(vvK(medianIndxP,dmSel)); Ks= num2str(K);  Kstd= std(vvK(medianIndxP,dmSel)); KstdStr= num2str(Kstd);
r= median(vvr(medianIndxP,dmSel)); rs= num2str(r);  rstd= std(vvr(medianIndxP,dmSel)); rstdStr= num2str(rstd);
l= median(vv(medianIndxP,dmSel)); Ls= num2str(l);   Lstd= std(vv(medianIndxP,dmSel));  LstdStr= num2str(Lstd);
Kl= K - std(vvK(medianIndxP,dmSel));   %K - Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Ku= K + std(vvK(medianIndxP,dmSel));   %K + Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
rl= r - std(vvr(medianIndxP,dmSel));   %r - Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
ru= r + std(vvr(medianIndxP,dmSel));   %r + Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;
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 rstr=rs(1:5); catch, rstr=rs(1:length(rs)); 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 )));
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
%tser=(scan(1,plateNum).plate(1).t0Series(:));
%rawData= scan(1,plateNum).plate(1).intens(indx,:)/scan(1,plateNum).plate(1).Ag(indx);

            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;
            traceN=Exp(1).traceN;
            end
            if zoneSel==2, plotAxes=ghandles.Paxes2; OLaxes=ghandles.OLaxes2;Daxes=ghandles.Daxes2;
                Dlaxes=ghandles.Dlaxes2;Dkaxes=ghandles.Dkaxes2;Draxes=ghandles.Draxes2;
            Exp(2).traceN=Exp(2).traceN+1;
            traceN=Exp(2).traceN;
            end
            if zoneSel==3, plotAxes=ghandles.Paxes3; OLaxes=ghandles.OLaxes3;Daxes=ghandles.Daxes3;
                Dlaxes=ghandles.Dlaxes3;Dkaxes=ghandles.Dkaxes3;Draxes=ghandles.Draxes3;
            Exp(3).traceN=Exp(3).traceN+1;
            traceN=Exp(3).traceN;
            end
plot(plotAxes,t,g);hold (plotAxes,'on');  %plot(plotAxes,tser,rawData,'g*');
plot(plotAxes,t,gSlow,'y'); plot(plotAxes,t,gFast,'r');hold (plotAxes,'off');
%************CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC**************************************
%Store L R and K valves for Composite [C] plots
Exp(expN).ll(traceN)= l; Exp(expN).rr(traceN)= r; Exp(expN).kk(traceN)= K;

Exp(expN).lstd(traceN)= std(vv(medianIndxP,dmSel));  %Exp(expN).Dexp(DexpN).RFcmpL(RFnum).dm(inDM).std;
Exp(expN).kstd(traceN)= std(vvK(medianIndxP,dmSel));  %Exp(expN).Dexp(DexpN).RFcmpK(RFnum).dm(inDM).std;
Exp(expN).rstd(traceN)= std(vvr(medianIndxP,dmSel)); %Exp(expN).Dexp(DexpN).RFcmpr(RFnum).dm(inDM).std;


Exp(expN).lslow(traceN)= lslow; Exp(expN).lfast(traceN)= lfast; 
Exp(expN).lKl(traceN)= Kl; Exp(expN).Ku(traceN)= Ku; 
Exp(expN).lrl(traceN)= rl; Exp(expN).Ku(traceN)= ru; 
%************************************************************************
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]) 
%Exp(zoneSel).hOLb(traceN)=plot(OLaxes,tser,rawData,'g*'); %No Raw Data, Ref Composite 17_1009   
catch  
    catchissue='Ln68 EZlstBoxCmpExt'
end  %trycatch

%Get the DM agar description
%if expN==1,DMstr=char(get(handles.DM1,'string'));end
%if expN==2,DMstr=char(get(handles.DM2,'string'));end
%if expN==3,DMstr=char(get(handles.DM3,'string'));end
DMstr= num2str(dmSel);

%spec=MP(1,LBmp).specifics{1,1}(indx); %orfrep=MP(1,plateNum).orfRep{1,1}(indx);
%tPtStr=strcat('T=', num2str(scan(1,plateNum).plate(1).t0Series(tPtSel)));
%graphStr= strcat(usrGnSp,'_','L=',Lstr,'_','Lstd=',LstdStr,'_','r=',rstr,'_','rstd=',rstdStr,'_','K=',Kstr,'Kstd=',KstdStr);
graphStr= strcat(usrGnSp,'_','L=',Lstr,'_','Lstd=',LstdStr,'_','r=',rstr,'_','rstd=',rstdStr,'_','K=',Kstr,'Kstd=',KstdStr);
spotDescrip=strcat(graphStr,'DMS->',DMstr);

xp=char(Exp(zoneSel).Dexp(DexpN).resDir);
if ispc,
    slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'\');
else
    slashPos=strfind(char(Exp(zoneSel).Dexp(DexpN).resDir),'/');
end
    
startPos=slashPos(length(slashPos)-1) +1;
endPos=slashPos(length(slashPos)) -1
expStr= {xp(startPos:endPos)}

Exp(zoneSel).hOLname(traceN)= usrGnSp; %spotDescrip;  %graphStr;  %ghandles.Exp(zoneSel).hOLname(traceN)= graphStr;
Exp(zoneSel).hOLexpNm(traceN)= expStr;  %ghandles.Exp(expN).hOLexpNm(traceN)= expStr;
Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
%Exp(zoneSel).hOLplateNum(traceN)= plateNum; 

%traceData= vertcat(get(Exp(OLay).hOL(traceN),'XData'),get(ghandles.Exp(OLay).hOL(traceN),'YData'));  

%if zoneSel==1,set(ghandles.GeneOrfLoc1,'string',geneOrfstr);end  % Displays the value.
%if zoneSel==2,set(ghandles.GeneOrfLoc2,'string',geneOrfstr);end
%if zoneSel==3,set(ghandles.GeneOrfLoc3,'string',geneOrfstr);end
%if zoneSel==1,set(ghandles.graphStrLoc1,'string',spotDescrip);end  %graphStr);end % Displays the value.
%if zoneSel==2,set(ghandles.graphStrLoc2,'string',spotDescrip);end  %graphStr);end    
%if zoneSel==3,set(ghandles.graphStrLoc3,'string',spotDescrip);end  %graphStr);end
catch
    catchissue='Ln33 EZlstBoxCmpExt'
        msg='Error'
end % trycatch zoneSel<4  datatip selection from Image (not from an OverLay Plot)
%**************Write Spot and Exp Info to OLay title areas****************************************************************************

    if zoneSel==1,  %&& get(ghandles.rotPB1,'value')~=1
        if length(char(Exp(zoneSel).hOLname(traceN)))>40,set(ghandles.OLay1,'FontSize',8);end
        set(ghandles.OLay1,'string', Exp(zoneSel).hOLname(traceN)); 
        if length(char(Exp(zoneSel).hOLexpNm(traceN)))>40,set(ghandles.OLexp1,'FontSize',8);end
        set(ghandles.OLexp1,'string',Exp(zoneSel).hOLexpNm(traceN));
    end
    if zoneSel==2 %&& get(ghandles.rotPB2,'value') ~=1
        if length(char(Exp(zoneSel).hOLname(traceN)))>40,set(ghandles.OLay2,'FontSize',8);end
        set(ghandles.OLay2,'string', Exp(zoneSel).hOLname(traceN)); 
        if length(char(Exp(zoneSel).hOLexpNm(traceN)))>40,set(ghandles.OLexp2,'FontSize',8);end
        set(ghandles.OLexp2,'string',Exp(zoneSel).hOLexpNm(traceN));
    end
    if zoneSel==3 %&& get(ghandles.rotPB3,'value') ~=1 
        if length(char(Exp(zoneSel).hOLname(traceN)))>40,set(ghandles.OLay3,'FontSize',8);end
        set(ghandles.OLay3,'string', Exp(OLay).hOLname(traceN)); 
        if length(char(Exp(zoneSel).hOLexpNm(traceN)))>40,set(ghandles.OLexp3,'FontSize',8);end
        set(ghandles.OLexp3,'string',Exp(OLay).hOLexpNm(traceN));
    end
  %}  
%********************************************************************** 

%{
%elseif RFcmpGFlg==1
K= Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).med; Ks= num2str(K);
r= Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).med; rs= num2str(r);
l= Exp(expN).Dexp(DexpN).RFcmpGL.dm(inDM).med; Ls= num2str(l);
Kl= K - Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
Ku= K + Exp(expN).Dexp(DexpN).RFcmpGK.dm(inDM).std;
rl= r - Exp(expN).Dexp(DexpN).RFcmpGr.dm(inDM).std;
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
%}
%Exp(expN).Dexp(n).UsrmdPindx= [];
%Exp(expN).Dexp(n).UsrmdPpltN= [];
%Exp(expN).Dexp(n).UsrmdPscanN= [];
%Exp(expN).Dexp(n).UsrMedianP= [];
%Exp(expN).Dexp(n).stdP= [];
%Exp(expN).Dexp(n).meanP= [];
%Exp(expN).Dexp(n).minP= [];
%Exp(expN).Dexp(n).maxP= [];

%Exp(expN).Dexp(n).RFmdGLB= {[]};
%Exp(expN).Dexp(n).RFmdGindx= [];
%Exp(expN).Dexp(n).RFmdGpltN= [];
%Exp(expN).Dexp(n).RFmdGscanN= [];

%UsrmdDGloc(d,1)= uu(nzPosIndxDG,1);  %MP of distributedGlobal Median value
%UsrmdDGloc(d,2)= uu(nzPosIndxDG,2);   %calc r value
%UsrmdDGloc(d,3)= uu(nzPosIndxDG,3);  %calc c value
%lstindx=lstindx+1;
%lstindxOrf= lstindxOrf+1;
%{
usrGLbl= strcat(usrGnSp,'UmdG(');  %accomodate User Ref Selection
aa(lstindx,1)= strcat(usrGLbl,num2str(d),')');  %remove string2cell brackets {...}
aa(lstindx,2)= {strcat(':',num2str(UsrmdDGloc(d,1)),':',num2str(UsrmdDGloc(d,2)),':',num2str(UsrmdDGloc(d,3)))};  %,'std_',num2str(std2))};
bb(lstindxOrf,1)= strcat(usrGLbl,num2str(d),')');  %remove string2cell brackets {...}
bb(lstindxOrf,2)= {strcat(':',num2str(UsrmdDGloc(d,1)),':',num2str(UsrmdDGloc(d,2)),':',num2str(UsrmdDGloc(d,3)))};  %,'std_',num2str(std2))};
 %Composite Reference Amalgum Plot ******************
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= strcat(usrGnSp,'UcmpG(',num2str(d),')'); 
aa(lstindx,2)={''};
bb(lstindxOrf,1)= strcat(usrGnSp,'UcmpG(',num2str(d),')'); 
bb(lstindxOrf,2)={''};
%*****************************************************
%}
%{
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
usrPLbl= strcat(usrGnSp,'UmdP('); %accomodate User Ref Selection
aa(lstindx,1)= strcat(usrPLbl,num2str(d),')'); 
aa(lstindx,2)= {strcat(':',num2str(dMPs(mm)),':',num2str(UsrmdlocP(1)),':',num2str(UsrmdlocP(2)))};  
bb(lstindxOrf,1)= strcat(usrPLbl,num2str(d),')');   %remove string2cell brackets {...}
bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(UsrmdlocP(1)),':',num2str(UsrmdlocP(2)))};

Exp(expN).Dexp(n).UsrmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))= medianIndxP;
Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm);   %This is a storage of the MasterPlate used NOT the ScanPlate?  WeMight wish to store the ScanPlateNumber also???
Exp(expN).Dexp(n).UsrmdPscanN(d,dMPs(mm))=usrScNdisp;
Exp(expN).Dexp(n).UsrMedianP(d,dMPs(mm))= mval1Disp;
Exp(expN).Dexp(n).stdP(d,dMPs(mm))= std1Disp;
Exp(expN).Dexp(n).meanP(d,dMPs(mm))= mean1Disp; 
Exp(expN).Dexp(n).minP(d,dMPs(mm))= minDisp;
Exp(expN).Dexp(n).maxP(d,dMPs(mm))= maxDisp;

Exp(expN).Dexp(n).UsrCmpPL.dm(d).med= mval1Disp;  %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPL.dm(d).mean= mean1Disp; %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPL.dm(d).std= std1Disp;  %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPL.dm(d).min= minDisp;  %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPL.dm(d).max= maxDisp;  %For Ref Composite 17_1026
Exp(expN).Dexp(n).UsrCmpPK.dm(d).med= median(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPK.dm(d).mean= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPK.dm(d).std= std(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPK.dm(d).min= min(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPK.dm(d).max= max(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,3)))); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPr.dm(d).med= median(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPr.dm(d).mean= mean(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPr.dm(d).std= std(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPr.dm(d).min= min(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026 
Exp(expN).Dexp(n).UsrCmpPr.dm(d).max= max(nonzeros((Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZrefIndxP,4)))); %For Ref Composite 17_1026 
%}
%Exp(expN).Dexp(n).UsrmdGindx(d)= nzPosIndxDG;
%Exp(expN).Dexp(n).UsrmdGpltN(d)= UsrmdDGloc(d,1);  
%Exp(expN).Dexp(n).UsrmdGscanN(d)= uu(nzPosIndxDG,4);
  %{
    try
      firstZeroindxD= find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first'); 
      firstZeroPindx= uu(firstZeroindxD,4);
      %Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm);
      %Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))=firstZeroPindx;
      
    catch
        catchissue='try at Ln565'
        %Exp(expN).Dexp(n).UsrmdPpltN(d,dMPs(mm))= dMPs(mm);
        %Exp(expN).Dexp(n).UsrmdPindx(d,dMPs(mm))=384; %if crapout,Then use spot384 as default to keep going  
    end
     try
        % Exp(expN).Dexp(n).UsrmdPpltN= dMPs(mm);  
     catch
         catchissue='Ln619'
         %Exp(expN).Dexp(n).UsrmdPpltN= 1;  %This might keep from breaking BUT ??? 
     end
    error='EZexpSel lineAfter 565'   
 end %try ~ln565
%}