%***********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


traceN=Exp(expN).traceN;
DexpN= Exp(expN).DexpN;  %Temp input for development

patrnN=strfind(selGnOrf{1},':');  %Extract Gene-Orf Name
patrndash= strfind(selGnOrf{1},'-');
selStrNm= char(selGnOrf)
if strcmpi(selStrNm(1:3),'RF-')
    usrGene= selStrNm(4:(patrndash(2)-1));    
else
    usrGene= 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
    
    
    
for n=1:Exp(expN).DexpLength   %LOOP Thru DayExps

MPnum=length(Exp(expN).Dexp(n).MP);
DMnum= length(Exp(expN).Dexp(n).DM.drug);

%Extract expDay from ExpName string
dayNpos= max(strfind(Exp(expN).Dexp(n).ExpFoldr, '_D'))
dayLbl= Exp(expN).Dexp(n).ExpFoldr(dayNpos+1:end);


%*********************************

dRF1indx=0;

usrSp= usrSpec;  %user entry of Specifics for Ref selection

%*******************************************************
for mp=1:length(Exp(expN).Dexp(n).MP) 
   
  for ind384=1:384   
     try  %         
         %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)={mp}; drfMP(dRF1indx,mp)= mp;
            drf(dRF1indx,3)={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
      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)
%*****************************************************
%************************************************************************************************

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    
  i=2;
  clear chgIndx
  chgIndx(1)=1;
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
      end
end
chgIndx(length(chgIndx)+1)= size(drf,1) +1;  %length(drf)+1;  

vvL= zeros(size(drf,1),1 );  %length(drf)+1;
%************************************
 dMPs= unique(cell2mat(drf(:,2))); 
 %*****************************************
 
 for mm=1:length(dMPs)    % length(chgIndx)
    usrScNdisp=((dMPs(mm)-1)*DMnum)+(dmSel); 
    NZusrIndx= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm));    medianIndxDisp= NZusrIndx;
    vvL(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,5);
    %For Global Ref Composite 17_1009 %**************************************************************************
    vvK(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,3);
    vvr(chgIndx(mm):(chgIndx(mm+1)-1))=Exp(expN).Dexp(n).scan(usrScNdisp).plate(1).CFout(NZusrIndx,4);
    %*****************************************************************************************************
  end    %for mm=1:length(dMPs)

%****************CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES******************************************************************

for d=dmSel:dmSel
    NZusrIndxG=[];
    NZusrIndxG= find(vvL);   
 
  if isempty(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(:);
    if ~isempty(NZusrIndxG) && length(NZusrIndxG) > 0 %(.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero 

UsrLvals{n}= vvL(NZusrIndxG);
UsrKvals{n}= vvK(NZusrIndxG);
Usrrvals{n}= vvr(NZusrIndxG);
     end
end 

end  % if exist('drf','var')

%END OF DISPERSE Gene data collection  
%*********************************************************************
%####################################################################
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), 
    warndlg('No Growth condition found for Gene-Specifics combination. . ','No Growth warning');
    NoGrowthflg=1;
end
    

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


%***********PLOT Values Selected Gene-Specifics Composite  ******************************************try
if NoGrowthflg==0
smpSz= size(NZusrIndxG,1);
K= median(cell2mat((UsrKvals(DexpN)))); Ks= num2str(K);  Kstd= std(cell2mat((UsrKvals(DexpN)))); KstdStr= num2str(Kstd);
r= median(cell2mat((Usrrvals(DexpN)))); rs= num2str(r);  rstd= std(cell2mat((Usrrvals(DexpN)))); rstdStr= num2str(rstd);
l= median(cell2mat((UsrLvals(DexpN)))); Ls= num2str(l);  Lstd= std(cell2mat((UsrLvals(DexpN))));  LstdStr= num2str(Lstd);
Kl= K - Kstd;  %std(UsrKvals(DexpN));  
Ku= K + Kstd;  %std(UsrKvals(DexpN));  
rl= r - rstd;  %std(Usrrvals(DexpN));  
ru= r + rstd;  %std(UsrKvals(DexpN));  
lfast= l - Lstd;
lslow= l + Lstd;
elseif NoGrowth==1   %if all data is zero (NoGrowth)
   smpSz= size(NZusrIndxG,1);
K= 0; Ks= num2str(K);  Kstd= 0; KstdStr= num2str(0);
r= 0; rs= num2str(r);  rstd= 0; rstdStr= num2str(0);
l= 0; Ls= num2str(l);  Lstd= 0;  LstdStr= num2str(0);
Kl= K - Kstd;  
Ku= K + Kstd;  
rl= r - rstd;  
ru= r + rstd;  
lfast= l - Lstd;
lslow= l + Lstd;
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 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;
            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');

Exp(expN).Trace(traceN).UsrGLB= usrGnSp;
Exp(expN).Trace(traceN).dmSel= dmSel;
for n=1:Exp(expN).DexpLength   %LOOP Thru DayExps
Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).UsrLvals= UsrLvals(n);
Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).UsrKvals= UsrKvals(n);
Exp(expN).Trace(traceN).Dexp(n).DM(dmSel).Usrrvals= Usrrvals(n);
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  
    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,'_');

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;  
Exp(zoneSel).hOLexpNm(traceN)= expStr;  
Exp(zoneSel).hOLresDir(traceN)= {Exp(zoneSel).Dexp(DexpN).resDir};
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==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)