% 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      
      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
    mp 
  end

  % 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
end

Exp(expN).UgeneCnt=Exp(expN).UgeneCnt +1;
Exp(expN).UgeneSpLst(Exp(expN).UgeneCnt)=usrGnSp;

% PLOT Values Selected Gene-Specifics Composite
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');
    % 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

  % 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 ME
  msg='ME.message';
end % trycatch zoneSel<4  datatip selection from Image (not from an OverLay Plot)


% Deprecated functions
%{
% 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
%}