server-scripts/qhtcp-workflow/apps/matlab/easy/DgenResults.m

global projectScansDir
global projectName
global matFile
global defImParMat
global printResultsDir
global fotosResultsDir
global pointMapsFile
global pointMapsResultsDir

ln=1;

% Version compatability fixes
if verLessThan('matlab','8.3')
  fd4=diff(sym('K / (1 +  exp(-r* (t - l )))'),4);
  sols=solve(fd4);
else % accomodate new matlab changes after 2014a
  syms t K r l;
  fd4=diff(K / (1 +  exp(-r* (t - l ))),t,4);
  sols=solve(fd4);
  tmpswap=sols(1);
  sols(1)=sols(3);
  sols(3)=tmpswap;
end

% MPnum=ImParMat(1);
% opt=questdlg('Print Results Only (RES), DB Only (DB), or Both','Results Printout Options','Res','DB','Both','Both');
opt='Res';
if ~exist('defImParMat','var') || isempty(defImParMat) % TODO needs explanation
  load(pointMapsFile);
end
destPerMP=ImParMat(2); % TODO this is weird, needs explanation
load(matFile);
load(mpdmFile)
numOfDrgs=length(DM.drug);
numOfMeds=length(DM.media);
destPerMP=numOfDrgs;

% TODO this should be rewritten or is unnecessary, what is this for
% Determine the longest set of intensity(tPts) for the Experiment Data Set
maxNumIntens=0;
for n=1:size(scan,2)
  for m=1:size(scan(n).plate,2)
    maxNumIntens=max(maxNumIntens,size(scan(n).plate(m).intens,2));
  end
end

% if length(projectScansDir) == max(strfind(projectScansDir,'\'))
%   localprojectScansDir=projectScansDir(1:end-1);
% else
%   localprojectScansDir=projectScansDir;
% end

% DBupload=fullfile(drive,'EZdbFiles','DBupLOADfiles');

resultsFilename=fullfile(printResultsDir, 'results_elr.txt');
DBfilename=fullfile(printResultsDir, 'DbaseELr.txt');

if isequal(opt,'Res')||isequal(opt,'Both'),fid=fopen(resultsFilename,'w');end
if isequal(opt,'DB')||isequal(opt,'Both'),fid2=fopen(DBfilename,'w');end

if isequal(opt,'Res')||isequal(opt,'Both')
  fprintf(fid,'%d\t',ln); % Results header
  fprintf(fid,'%s\t\n',projectScansDir);
  ln=ln+1;
  fprintf(fid,'%d\t',ln);
end

mpCnt=0;
totPlCnt=0;
drgCnt=0;
medCnt=0;

try
  load(fullfile(fotosResultsDir,'Nbdg')) % Convolute scan array data into plates
catch
  load(fullfile(pointMapsResultsDir,'Nbdg')) % Convolute scan array data into plates
end

for s=1:size(scan,2)
  % Convolute scan array data into plates DconB for DBcombo
  clear Diag
  try
    Diag(:,:,:,1)=sbdg{s}(1:1:24,16:-1:1,:);
  catch
    sbdg{s};
  end

  for p=1:size((scan(s).plate),2)
    totPlCnt=totPlCnt+1;
    if destPerMP>1 && rem(totPlCnt,destPerMP)==1
      mpCnt=mpCnt+1;
    end
    if destPerMP==1
      mpCnt=mpCnt+1;
    end
    pertCnt=rem(totPlCnt,destPerMP);
    if pertCnt==0
      pertCnt=destPerMP;
    end
    pert=strcat('Perturb_',num2str(pertCnt));
    s % TODO seems wrong
    p % TODO seems wrong
    clear outCmat
    outCmat=scan(s).plate(p).CFout;

    % Print Time Point HEADER for each plate for newly added intensity data
    if isequal(opt,'Res')||isequal(opt,'Both')
      fprintf(fid, '\n'); 
      ln=ln+1;
      fprintf(fid,'%d\t',ln);
      fprintf(fid,'Scan\tPlate\tRow\tCol\t');
      try
        asd=cell2mat(scan(s).plate(1).CFparameters(1));
        aucEndPt=strcat('AUC',num2str(asd(9)));
      catch
        asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384));
        aucEndPt=strcat('AUC',num2str(asd(9)));
      end
      
      fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene');
      fprintf(fid, '\t %s',aucEndPt);
      fprintf(fid, '\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm');
  
      if size(outCmat,2)==27     
        fprintf(fid, '\ttc11Cut\ttc12Cut\ttc21Cut\ttc22Cut');  % '\tEarly1\tEarly2\tLate1\tLate2'); 17_0629 MinBaseIntens update for MedianBase label
      end
      fprintf(fid, '\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd');
    end

    clear outTseries
    outTseries=[];
    outTseries=scan(s).plate(p).tSeries;
    TseriesSize=size(outTseries,1);
                    
    clear outIntens
    outIntens=[];
    RawIntens=[];
    RawIntens=scan(s).plate(p).intens;
    RawIntensSize=size(RawIntens,2)
    
    clear Ag;  %Ag is Growth Area
    Ag=scan(s).plate(p).Ag;
    AgSize=size(Ag);
  
    dataLength=min(TseriesSize,RawIntensSize);
    if isequal(opt,'Res')||isequal(opt,'Both')   
      for j=1:dataLength
        fprintf(fid, '\t%.5f', outTseries(j));
      end
    end   

    numBlkCol=(maxNumIntens - dataLength); % size(outTseries,1));
    if isequal(opt,'Res')||isequal(opt,'Both')  
      for nn=1:numBlkCol  % extend to col beyond longest rawDataSet    
        fprintf(fid, '\t');
      end
      fprintf(fid,'\tOrfRep');        
      fprintf(fid,'\tSpecifics');
      fprintf(fid,'\tStrainBkGrd');
      fprintf(fid, '\n');
      ln=ln+1;
      fprintf(fid,'%d\t',ln);
    end

    % Data
    n=0;
    for r=1:16      
      for c=1:24
        n=n+1; 
        clear selcode;
        Kval=outCmat(n,3);
        rSq=outCmat(n,6);
        lval=outCmat(n,5);
        if Kval>160, selcode='K_Hi'; else selcode=' ';end
        if Kval<40, selcode=strcat(selcode,' K_Lo');end
        if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo');end
        if lval>(0.85*(max(outTseries))), selcode=strcat(selcode,' late');end
        if isnan(outCmat(n,7))||isnan(outCmat(n,8))||isnan(outCmat(n,9))...
          || isnan(outCmat(n,10))||isnan(outCmat(n,11))...
          || isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN');
        end
        
        % RiseTime Calculation
        K=(outCmat(n,3));  
        R=(outCmat(n,4));  
        L=(outCmat(n,5));  
        if R>0 && L>0 && K>0
          rr=R; ll=L; 
          tc1=eval(sols(2));
          tc2=eval(sols(3));
          LL=eval(sols(1));
          riseTm=LL-tc1;
        else
          riseTm=0;    
        end
    
        if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end        
        if outCmat(n,3)==0,selcode=strcat('0 ',selcode);end
        
        orf=cell2mat(MP(mpCnt).orf{1}(n));
        gene=cell2mat(MP(mpCnt).genename{1}(n));
        orfRep=cell2mat(MP(mpCnt).orfRep{1}(n));
        specifics=cell2mat(MP(mpCnt).specifics{1}(n));
        strain=cell2mat(MP(mpCnt).strain{1}(n));
        drug=char(DM.drug{pertCnt}); 
        conc=char(DM.conc{pertCnt});
        media=char(DM.media{pertCnt});
        try
          mod1=char(DM.mod1{pertCnt});
          conc1=char(DM.conc1{pertCnt});
        catch
          mod1=' ';
          conc1=' ';
        end
        try
          mod2=char(DM.mod2{pertCnt});
          conc2=char(DM.conc2{pertCnt});
        catch
          mod2=' ';
          conc2=' ';    
        end
        
        if ~isempty(outCmat)  
          if isequal(opt,'Res')||isequal(opt,'Both')  
            fprintf(fid,'%d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
            fprintf(fid, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
              outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
              outCmat(n,5),outCmat(n,6),outCmat(n,7),outCmat(n,8),...
              outCmat(n,9),outCmat(n,10),outCmat(n,11),outCmat(n,12),...
              outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
            
            fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
              outCmat(n,17),outCmat(n,18),outCmat(n,19),...
              outCmat(n,20),outCmat(n,21));

            % Added for data cut times used in 'r'optomized method 06/14/2018
            if (size(outCmat,2) == 27)
              fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f',...
                outCmat(n,24),outCmat(n,25),outCmat(n,26),outCmat(n,27));
            end

            fprintf(fid, '\t%d\t%d\t%d\t%d\t%d\t%d',...    
              outCmat(n,22),outCmat(n,23),Diag(c,r,1,p),Diag(c,r,2,p),Diag(c,r,3,p),Diag(c,r,4,p)); %,Diag(r,c,3,p),Diag(r,c,4,p));
          end 

          % DBfile
          if isequal(opt,'DB')||isequal(opt,'Both')
            dbRsq=0;dbKup=0; dbKlo=0; dbrup=0; dbrlo=0; dbLlo=0; dbLup=0;
            if isnumeric(outCmat(n,6)), dbRsq=outCmat(n,6);end
            if isnumeric(outCmat(n,7)), dbKup=outCmat(n,7);end
            if isnumeric(outCmat(n,8)), dbKlo=outCmat(n,8);end
            if isnumeric(outCmat(n,9)), dbrup=outCmat(n,9);end
            if isnumeric(outCmat(n,10)), dbrlo=outCmat(n,10);end
            if isnumeric(outCmat(n,11)), dbLlo=outCmat(n,11);end
            if isnumeric(outCmat(n,12)), dbLup=outCmat(n,12);end
          end 

          if isequal(opt,'DB')||isequal(opt,'Both')
            fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',projectName,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
            fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
                outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
                outCmat(n,5),dbRsq,dbKup,dbKlo,dbrup,dbrlo,dbLlo,dbLup);   %\t%.5f\t%.5f\t%.5f\t%.5f
          end

          % Add Intensities series to end of curve fit data
          outIntens=[];
          outIntens=zeros(384,dataLength);
          intensBlob='';
          tmBlob='';
        
          for j=1:dataLength  %size(RawIntens,2)  %size(outTseries,1)
            if Ag(n)==0,Ag(n)=scan(s).Awindow;end
            outIntens(n,j)=RawIntens(n,j)/Ag(n);
              if isequal(opt,'Res')||isequal(opt,'Both')
                fprintf(fid, '\t%.5f', outIntens(n,j));  % Results print Intens
              end
            if isequal(opt,'DB')||isequal(opt,'Both') 
              if j<dataLength
                intensBlob=strcat(intensBlob,num2str(outIntens(n,j)),';');  
              else
                intensBlob=strcat(intensBlob,num2str(outIntens(n,j)));
              end
              if outTseries(j)<.0001,outTseries(j)=0;end
              if j<dataLength
                tmBlob=strcat(tmBlob,num2str(outTseries(j)),';');
              else
                tmBlob=strcat(tmBlob,num2str(outTseries(j))); 
              end
            end
          end

          % Results
          if isequal(opt,'Res')||isequal(opt,'Both')
            for nn=1:numBlkCol  %extend to col beyond longest rawDataSet    
              fprintf(fid, '\t');
            end
            % Masterplate sheet
            if ~isnan(orfRep)
              fprintf(fid, '\t%s', orfRep);  %print OrfRep
            else
              fprintf(fid, '\t%s', ' ');
            end
            if ~isnan(specifics)    
              fprintf(fid, '\t%s', specifics);  
            else
              fprintf(fid, '\t%s', ' ');  
            end
            if ~isnan(strain)
              fprintf(fid, '\t%s', strain);  
            else
              fprintf(fid, '\t%s', ' '); 
            end
            fprintf(fid, '\n');
            ln=ln+1;
            fprintf(fid,'%d\t',ln);
          end

          % DB Raw Intensities and Timepoints
          if isequal(opt,'DB')||isequal(opt,'Both')
            fprintf(fid2, '\t%s\t%s',intensBlob,tmBlob );
            % Masterplate sheet
            if ~isnan(orfRep)
              fprintf(fid2, '\t%s',orfRep );
            else
              fprintf(fid2, '\t%s', ' '); 
            end
            if ~isnan(specifics)
              fprintf(fid2, '\t%s',specifics );
            else
              fprintf(fid2, '\t%s', ' '); 
            end
            if ~isnan(strain)
              fprintf(fid2, '\t%s',strain );
            else
              fprintf(fid2, '\t%s', ' '); 
            end
            fprintf(fid2, '\n');
          end
        end
      end
    end
  end
end

if isequal(opt,'Res')||isequal(opt,'Both')
  fclose(fid); 
end

% if isequal(opt,'DB')||isequal(opt,'Both')
%   fclose(fid2);
%   try
%     copyfile(DBfilename,DBupload)
%   catch ME
%     fprintf('DB upload failed with error: %s\n', getReport(ME, 'basic'));
%     rep=sprintf('Failed copyfile to %s - %s', DBupload, rep);
%     errordlg(rep);
%   end
% end

% Print results using the standard method
try
  scan(1).plate(1).CFoutStd(1,1) %Test for 2018 r_refined version 

  ln=1;
  resultsFilename=fullfile(printResultsDir, 'results_std.txt');
  DBfilename=fullfile(printResultsDir, 'DbaseStd.txt');
  if isequal(opt,'Res')||isequal(opt,'Both'),fid=fopen(resultsFilename,'w');end
  if isequal(opt,'DB')||isequal(opt,'Both'),fid2=fopen(DBfilename,'w');end  %121012 Combo
  if isequal(opt,'Res')||isequal(opt,'Both') %print Results
    fprintf(fid,'%d\t',ln); %Results header
    fprintf(fid,'%s\t\n',projectScansDir);
    ln=ln+1;
    fprintf(fid,'%d\t',ln);
  end

  mpCnt=0;
  totPlCnt=0;
  drgCnt=0;
  medCnt=0;

  for s=1:size(scan,2)
    %Convolute scan array data into plates DconB for DBcombo
    clear Diag
    try
      Diag(:,:,:,1)= sbdg{s}(1:1:24,16:-1:1,:);
    catch
      sbdg{s};
    end

    for p=1:size((scan(s).plate),2)
      totPlCnt=totPlCnt+1;
      if destPerMP>1 &&rem(totPlCnt,destPerMP)==1, mpCnt=mpCnt+1; end
      if destPerMP==1,mpCnt=mpCnt+1; end
      pertCnt=rem(totPlCnt,destPerMP);
      if pertCnt==0, pertCnt= destPerMP;end
      pert=strcat('Perturb_',num2str(pertCnt));
      s % BCR seems wrong
        
      %Print Time Point HEADER for each plate for newly added intensity data
      if isequal(opt,'Res')||isequal(opt,'Both')
        fprintf(fid, '\n'); 
        ln=ln+1;
        fprintf(fid,'%d\t',ln);
        fprintf(fid,'Scan\tPlate\tRow\tCol\t');
        
        try
          asd=cell2mat(scan(s).plate(1).CFparameters(1));
          aucEndPt=strcat('AUC',num2str(asd(9)));
        catch
          asd=cell2mat(scan(s).plate(1).CFparameters{1,1}(1,384));
          aucEndPt=strcat('AUC',num2str(asd(9)));
        end
        fprintf(fid, 'Num.\tDiagnostics\tDrug\tConc\tMedia\tModifier1\tConc1\tModifier2\tConc2\tORF\tGene');
        fprintf(fid, '\t %s',aucEndPt);
        fprintf(fid, '\triseTm\tK\tr\tl\tR-squared\tK-lower\tK-upper\tr-lower\tr-upper\tl-lower\tl-upper\tArea\tLastInten\tSplineMaxRateTm\tLastFitTm\t1stFitTm\tMedianBase\tFitBase\tMinTm\tThreshTm\tTotFitPts\tPostThreshFitPts\t1stBackgrd\tLstBackgrd\t1stMeanTotBackgrd\tLstMeanTotBackgrd'); %17_0629 MinBaseIntens update for MedianBase label
      end     
      clear outTseries
      outTseries=[];
      outTseries=scan(s).plate(p).tSeries;
      TseriesSize= size(outTseries,1);
      clear outCmat
      outCmat=scan(s).plate(p).CFoutStd;
      clear outIntens
      outIntens=[];
      RawIntens=[];
      RawIntens=scan(s).plate(p).intens;
      RawIntensSize=size(RawIntens,2);
      clear Ag;  %Ag is Growth Area
      Ag=scan(s).plate(p).Ag;
      AgSize= size(Ag);
      
      dataLength= min(TseriesSize,RawIntensSize);
      if isequal(opt,'Res')||isequal(opt,'Both')   
        for j=1:dataLength
          fprintf(fid, '\t%.5f', outTseries(j));
        end
      end   

      numBlkCol=(maxNumIntens - dataLength); %size(outTseries,1));

      if isequal(opt,'Res')||isequal(opt,'Both')  
        for nn=1:numBlkCol  %extend to col beyond longest rawDataSet    
          fprintf(fid, '\t');
        end
        fprintf(fid,'\tOrfRep');        
        fprintf(fid,'\tSpecifics');
        fprintf(fid,'\tStrainBkGrd');
        fprintf(fid, '\n');
        ln=ln+1;
        fprintf(fid,'%d\t',ln);
      end

      % Data  
      n=0;     
      for r=1:16      
        for c=1:24
          n=n+1; 
          clear selcode;
          Kval=outCmat(n,3);
          rSq=outCmat(n,6);
          lval=outCmat(n,5);
          if Kval>160, selcode='K_Hi'; else selcode=' ';end
          if Kval<40, selcode=strcat(selcode,' K_Lo');end  % TODO sprintf if you want a space
          if rSq<.97 && rSq>0, selcode=strcat(selcode,' rSqLo');end
          if lval>(0.85*(max(outTseries))), selcode=strcat(selcode,' late');end
          if isnan(outCmat(n,7))||isnan(outCmat(n,8))||isnan(outCmat(n,9))...
            ||isnan(outCmat(n,10))||isnan(outCmat(n,11))...
            ||isnan(outCmat(n,12)), selcode=strcat(selcode,' NaN');
          end
              
          % RiseTime Calculation
          K=(outCmat(n,3));
          R=(outCmat(n,4));
          L=(outCmat(n,5));
          if R>0 && L>0 && K>0
            rr=R; ll=L;
            tc1=eval(sols(2));
            tc2=eval(sols(3));
            LL=eval(sols(1));
            riseTm= LL-tc1;
          else
            riseTm=0;    
          end
         
          if Ag(n)< .30*(scan(s).Awindow),selcode=strcat(selcode,' smArea'); end  % same, need sprintf for space       
          if outCmat(n,3)==0,selcode=strcat('0 ',selcode); end
          orf=cell2mat(MP(mpCnt).orf{1}(n));
          gene=cell2mat(MP(mpCnt).genename{1}(n));
          orfRep=cell2mat(MP(mpCnt).orfRep{1}(n));
          specifics=cell2mat(MP(mpCnt).specifics{1}(n));
          strain=cell2mat(MP(mpCnt).strain{1}(n));
          drug=char(DM.drug{pertCnt}); 
          conc=char(DM.conc{pertCnt});
          media=char(DM.media{pertCnt});
          try
            mod1=char(DM.mod1{pertCnt});
            conc1=char(DM.conc1{pertCnt});
          catch
            mod1=' ';
            conc1=' ';
          end
          try
            mod2=char(DM.mod2{pertCnt});
            conc2=char(DM.conc2{pertCnt});
          catch
            mod2=' ';
            conc2=' ';    
          end
              
          if ~isempty(outCmat)  
            if isequal(opt,'Res')||isequal(opt,'Both')  
              fprintf(fid,'%d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
              fprintf(fid, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
                outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
                outCmat(n,5),outCmat(n,6),outCmat(n,7),outCmat(n,8),...
                outCmat(n,9),outCmat(n,10),outCmat(n,11),outCmat(n,12),...
                outCmat(n,13),outCmat(n,14),outCmat(n,15),outCmat(n,16));
            
              fprintf(fid, '\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%d\t%d',...
                outCmat(n,17),outCmat(n,18),outCmat(n,19),...
                outCmat(n,20),outCmat(n,21),outCmat(n,22),outCmat(n,23));
            
              fprintf(fid, '\t%d\t%d\t%d\t%d',...    
                Diag(c,r,1,p),Diag(c,r,2,p),Diag(c,r,3,p),Diag(c,r,4,p)); %,Diag(r,c,3,p),Diag(r,c,4,p));
            end

            % DBFile
            % RiseTime calculation
            if isequal(opt,'DB')||isequal(opt,'Both')
              dbRsq= 0;dbKup= 0; dbKlo= 0; dbrup= 0; dbrlo= 0; dbLlo= 0; dbLup= 0;
              if isnumeric(outCmat(n,6)), dbRsq= outCmat(n,6);end
              if isnumeric(outCmat(n,7)), dbKup= outCmat(n,7);end
              if isnumeric(outCmat(n,8)), dbKlo= outCmat(n,8);end
              if isnumeric(outCmat(n,9)), dbrup= outCmat(n,9);end
              if isnumeric(outCmat(n,10)), dbrlo= outCmat(n,10);end
              if isnumeric(outCmat(n,11)), dbLlo= outCmat(n,11);end
              if isnumeric(outCmat(n,12)), dbLup= outCmat(n,12);end
            end

            if isequal(opt,'DB')||isequal(opt,'Both')
              fprintf(fid2,'%s\t %d\t %d\t %d\t %d\t %d\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t %s\t',projectName,s,p,r,c,n,selcode,drug,conc,media,mod1,conc1,mod2,conc2,orf,gene);
              fprintf(fid2, '%.5f\t %.5f\t %.5f\t %.5f\t %.5f\t %.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f\t%.5f',...
                outCmat(n,1),riseTm,outCmat(n,3),outCmat(n,4),...
                outCmat(n,5),dbRsq,dbKup,dbKlo,...
                dbrup,dbrlo,dbLlo,dbLup);
            end

            % DB Analysis      
            % Add Intensities series to end of curve fit data
            outIntens=[];
            outIntens=zeros(384,dataLength);
            intensBlob='';
            tmBlob='';

            for j=1:dataLength  %size(RawIntens,2)  %size(outTseries,1)
              if Ag(n)==0,Ag(n)=scan(s).Awindow;end
              outIntens(n,j)= RawIntens(n,j)/Ag(n);
              if isequal(opt,'Res')||isequal(opt,'Both')
                fprintf(fid, '\t%.5f', outIntens(n,j));  % Results print Intens
              end
              if isequal(opt,'DB')||isequal(opt,'Both') 
                if j<dataLength
                  intensBlob=strcat(intensBlob,num2str(outIntens(n,j)),';');  
                else
                  intensBlob=strcat(intensBlob,num2str(outIntens(n,j)));
                end
                if outTseries(j)<.0001,outTseries(j)=0;end
                if j<dataLength
                  tmBlob=strcat(tmBlob,num2str(outTseries(j)),';');
                else
                  tmBlob=strcat(tmBlob,num2str(outTseries(j))); 
                end
              end
            end

            % Results fprint
            if isequal(opt,'Res')||isequal(opt,'Both')
              for nn=1:numBlkCol  %extend to col beyond longest rawDataSet    
                fprintf(fid, '\t');
              end

              % Masterplate sheet
              if ~isnan(orfRep)
                fprintf(fid, '\t%s', orfRep);  %print OrfRep
              else
                fprintf(fid, '\t%s', ' ');
              end
              if ~isnan(specifics)    
                fprintf(fid, '\t%s', specifics);  
              else
                fprintf(fid, '\t%s', ' ');  
              end
              if ~isnan(strain)
                fprintf(fid, '\t%s', strain);  
              else
                fprintf(fid, '\t%s', ' '); 
              end

              fprintf(fid, '\n');
              ln=ln+1;
              fprintf(fid,'%d\t',ln);
            end

            % Raw Intensities and Timepoints
            if isequal(opt,'DB')||isequal(opt,'Both')
              fprintf(fid2, '\t%s\t%s',intensBlob,tmBlob );

              % Masterplate sheet
              if ~isnan(orfRep)
                fprintf(fid2, '\t%s',orfRep );
              else
                fprintf(fid2, '\t%s', ' '); 
              end
              if ~isnan(specifics)
                fprintf(fid2, '\t%s',specifics );
              else
                fprintf(fid2, '\t%s', ' '); 
              end
              if ~isnan(strain)
                fprintf(fid2, '\t%s',strain );
              else
                fprintf(fid2, '\t%s', ' '); 
              end
              fprintf(fid2, '\n');
            end  %DB print
          end %if ~isempty(outCmat)
        end  %c
      end  %r   
    end  %p
  end  %s

  if isequal(opt,'Res')||isequal(opt,'Both')
    fclose(fid); 
  end

  % if isequal(opt,'DB')||isequal(opt,'Both')
  %   fclose(fid2);
  %   try
  %     copyfile(DBfilename,DBupload)
  %   catch ME
  %     fsprintf('DB upload failed with error: %s\n', getReport(ME, 'basic'));
  %     rep=sprintf('Failed copyfile to %s - %s\n', DBupload, rep);
  %     errordlg(rep)
  %   end
  % end

  msgbox([sprintf('Printing script complete. Check results sheets in %s for results.', printResultsDir)])

catch ME
  fprintf('Printing script failed with error: %s\n', getReport(ME, 'basic'));
end