%% CALLED BY EASYconsole.m %%
w=pwd
numOfMPs=0;
%GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select Master Plate File','File Selection','OK', struct('Default','OK','Interpreter','tex'))
[Scanfiles, pathname]=uigetfile('*.*','MultiSelect','off');
if ispc
 MPdir= fullfile(pathname,'\');
else
  MPdir=fullfile(pathname,'/');
end

infile= Scanfiles(1,:);
cd(MPdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
if ispc
  [num, txt, raw] = xlsread(infile);  %,'Yor1HitsMPsetFinal');
  fields= {txt(2,1:15)}; %or 1:17 for later but dont wish to exceed and cause error ? if used
  
else
  clear MPtbl
  opts = detectImportOptions(infile);
  MPtbl = readtable(infile,opts);
  MPtbl= readtable(infile);
  fields= {opts.VariableNames};  %? if used anywhere although 'saved' to MPDMmat
  MPcell= readcell(infile);
end


cd(w)
numb= 0;
clear MP;
try
    
  if ispc
    excLnNum=3;
    while (isequal(txt{excLnNum,1},'###'))
numb=numb+1;    
 MP(numb).head = {raw(excLnNum,2:6)};
 MP(numb).recNum = {raw((excLnNum+1):(excLnNum+384),1)};
 MP(numb).orf = {raw((excLnNum+1):(excLnNum+384),2)};
 MP(numb).strain = {raw((excLnNum+1):(excLnNum+384),3)};
 MP(numb).genename= {raw((excLnNum+1):(excLnNum+384),12)};
 MP(numb).drug= {raw((excLnNum+1):(excLnNum+384),8)};
 MP(numb).media= {raw((excLnNum+1):(excLnNum+384),7)};
if size(raw,2)>15
  MP(numb).orfRep= {raw((excLnNum+1):(excLnNum+384),16)};  %added 12_1005 to specify replicates Orfs in MP
  MP(numb).specifics= {raw((excLnNum+1):(excLnNum+384),17)};  %added 12_1008 to specify replicates Specific details in MP
else
 MP(numb).orfRep= ' ';   
 MP(numb).specifics= ' ';
end
%{
if size(raw,2)>17 ; Future MP field
 MP(numb).specifics2= {raw((excLnNum+1):(excLnNum+384),18)};  %added 12_1008 to specify strain Bkground in MP
else
 MP(numb).specifics2= ' ';
end
%}
excLnNum=excLnNum+385;

msg=strcat('NumberOfMP = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum));

    end % end if ispc
 else  %if not ispc
   excLnNum=1;
   while (isequal(MPcell{(excLnNum+2),1},'###'))
    numb=numb+1;    
    MP(numb).head = {MPtbl(excLnNum,2:6)};
     MP(numb).head{1}= table2cell(MP(numb).head{1});
    MP(numb).recNum = {MPtbl((excLnNum+1):(excLnNum+384),1)};
     MP(numb).recNum{1}= table2cell(MP(numb).recNum{1});
    MP(numb).orf = {MPtbl((excLnNum+1):(excLnNum+384),2)};
     MP(numb).orf{1}= table2cell(MP(numb).orf{1});
    MP(numb).strain = {MPtbl((excLnNum+1):(excLnNum+384),3)};
     MP(numb).strain{1}= table2cell(MP(numb).strain{1});
    MP(numb).genename= {MPtbl((excLnNum+1):(excLnNum+384),12)};
     MP(numb).genename{1}= table2cell(MP(numb).genename{1});
    MP(numb).media= {MPtbl((excLnNum+1):(excLnNum+384),7)};
     MP(numb).media{1}= table2cell(MP(numb).media{1});
      if size(MPtbl,2)>15
        MP(numb).orfRep= {MPtbl((excLnNum+1):(excLnNum+384),16)};  %added 12_1005 to specify replicates Orfs in MP
         MP(numb).orfRep{1}= table2cell(MP(numb).orfRep{1});
        MP(numb).specifics= {MPtbl((excLnNum+1):(excLnNum+384),17)};  %added 12_1008 to specify replicates Specific details in MP
         MP(numb).specifics{1}= table2cell(MP(numb).specifics{1});
      else
        MP(numb).orfRep= ' ';   
        MP(numb).specifics= ' ';
      end

excLnNum=excLnNum+385;
msg=strcat('NumberOfMP = ',num2str(numb), 'lastLineNo. = ',num2str(excLnNum))
  end
 
  end %end of if ispc for MP while loop choice PC or Linux-other (ln~48)

catch ME
   h = msgbox(msg,'Check Number of Master Plates and Excel Lines')
   uiwait(h);
end %end for try MP excel sheet input

%*********************************************************************
%DMupload
%Drug and Media Plate setup  Upload from Excel
%scan().plate().LocInd().gene
cd(MPdir);
excLnNum=1;
%w=pwd
%cd('D:\EASY\Experiments\');  %cd(ExpPath);  %
numOfDrugs=0;
numOfMedias=0;
%GUI input for selecting a MasterPlate Excel file
questdlg('\fontsize{20} Select DrugMedia File','File Selection','OK', struct('Default','OK','Interpreter','tex'));
[Scanfiles, pathname]=uigetfile('*.*', 'MultiSelect','off');
if ispc
 DMdir= fullfile(pathname,'\');
else
    DMdir=fullfile(pathname,'/');
end

clear infile;
infile= Scanfiles(1,:);
cd(DMdir)
%fid=fopen(infile)%('exp23PrintTimes.xls'); % textread puts date and time sequentially into vector
if ispc
   [num, txt, raw] = xlsread(infile);  %,'Yor1HitsMPsetFinal');
   fields= {txt(2,1:5)};
   Linked= num(1,1);
else
   opts = detectImportOptions(infile); 
   DMtbl= readtable(infile,opts);
   fields= opts.VariableOptions;   
   Linked= DMtbl{1,1};
   DMcell= readcell(infile);
end
cd(w)
numb=0;

%fields= {txt(2,1:5)};
%Linked= num(1,1);


if isequal(Linked,1)   %Drugs and Media are linked 1 to 1; else they are combinatorial
clear DM;
%try
excLnNum=2;
if ispc
while (~isequal(txt{excLnNum,2},'###'))
  numb=numb+1;    
  DM.drug(numb) = {raw(excLnNum,2)};
  DM.conc(numb) = {raw(excLnNum,3)};
  DM.media(numb) = {raw(excLnNum,4)};
  DM.mod1(numb) = {raw(excLnNum,5)};
  DM.conc1(numb) = {raw(excLnNum,6)};
  DM.mod2(numb) = {raw(excLnNum,7)};
  DM.conc2(numb) = {raw(excLnNum,8)};
  excLnNum=excLnNum+1;
  msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum))
end
else
    clear DM
    excLnNum=1;
    while (~isequal(DMcell{excLnNum+1,2},'###'))
      numb=numb+1;    
      DM.drug(numb) = {DMtbl(excLnNum,2)};
       DM.drug(numb)= table2cell(DM.drug{numb});
      DM.conc(numb) = {DMtbl(excLnNum,3)};
       DM.conc(numb)= table2cell(DM.conc{numb});
      DM.media(numb) = {DMtbl(excLnNum,4)};
       DM.media(numb)= table2cell(DM.media{numb});
      DM.mod1(numb) = {DMtbl(excLnNum,5)};
       DM.mod1(numb)= table2cell(DM.mod1{numb});
      DM.conc1(numb) = {DMtbl(excLnNum,6)};
       DM.conc1(numb)= table2cell(DM.conc1{numb});
      DM.mod2(numb) = {DMtbl(excLnNum,7)};
       DM.mod2(numb)= table2cell(DM.mod2{numb});
      DM.conc2(numb) = {DMtbl(excLnNum,8)};
       DM.conc2(numb)= table2cell(DM.conc2{numb});
      excLnNum=excLnNum+1;
      msg=strcat('NumberOf1:1DrugMediaPlates = ',num2str(numb), '   lastLineNo. = ',num2str(excLnNum))
    end
end



end
%Legacy contengency  -Not ever used!!
if isequal(Linked,0)   %0 indicates Drugs and Media are combinatorial
clear DM;
excLnNum=2;
drgCnt=0;
medCnt=0;
if ispc
  while (~isequal(txt{excLnNum,2},'###'))
   drgCnt=drgCnt+1;    
   DM.drug(drgCnt) = {raw(excLnNum,2)};
   DM.conc(drgCnt) = {raw(excLnNum,3)};
   excLnNum=excLnNum+1;
  end

  while (~isequal(txt{excLnNum,4},'###'))
   medCnt=medCnt+1;    
   DM.media(medCnt) = {raw(excLnNum,4)};
   excLnNum=excLnNum+1;
  end
else %else if not PC (Then linux or other)
  excLnNum=1;
  while (~isequal(DMcell{excLnNum+1,2},'###'))
   drgCnt=drgCnt+1;    
   DM.drug(drgCnt) = {DMtbl(excLnNum,2)};
   DM.conc(drgCnt) = {DMtbl(excLnNum,3)};
   excLnNum=excLnNum+1;
  end

  while (~isequal(DMcel{excLnNum+1,4},'###'))
   medCnt=medCnt+1;    
   DM.media(medCnt) = {DMtbl(excLnNum,4)};
   excLnNum=excLnNum+1;
  end
end
 
msg=strcat('NumberOfDrugs = ',num2str(drgCnt), '     NumberOfMedias = ',num2str(medCnt)  )

end

save (fullfile(MPdir,'MPDMmat'), 'fields','MP','DM','Linked');

cd(w)
msgbox(['Drug-Media-MasterPlate Annotation File   Generation Complete'])