global Expaa
global Expbb
global expType
global usrExpJobsDir
global zonePB

% Initialize some variables from matlab
ezPath=which(mfilename);
[ezDir,ezFileName]=fileparts(ezPath);
ezDir=fullfile(easyDir);
[parentDir, ~]=fileparts(ezDir);
parentDir=fullfile(parentDir); % ../easy/apps

debug=1;
if debug
  disp('Running in debug mode');
  disp('Initialized variables:');
  whos;
end

% Set scansDir (project scans directory) intelligently
if exist('PROJECT', 'var') && ~isempty(getenv('PROJECT'))
  scansDir=getenv('PROJECT');
  fprintf('Using project path: %s from environment variable PROJECT\n', scansDir);
  disp('This usually indicates that we are in standalone mode');
elseif exist('PROJECT_SCANS_DIR', 'var') && ~isempty(getenv('PROJECT_SCANS_DIR'))
  scansDir=getenv('PROJECT_SCANS_DIR');
  fprintf('Using scans directory: %s from environment variable PROJECT_SCANS_DIR\n', scansDir);
  disp('This usually indicates that we are in module mode');
else
  % TODO Lots of this is hardcoded logic, this TODO is just a reminder to change this block
  % when changing EASY and other variables in the parent script
  fprintf('Beginning parent scans directory search\n');
  fprintf('This usually indicates that we are in stand-alone mode without PROJECT or PROJECT_SCANS_DIR environment variables\n');
  dirsToScan={
    fullfile(parentDir,'..', '..', 'scans'),
    fullfile(parentDir, '..', '..', 'ExpJobs'),
    fullfile('/mnt/data/scans'),
    fullfile('/mnt/data/ExpJobs'),
    fullfile(parentDir, '..', '..', 'templates', 'scans-demo')
  };
  for d=dirsToScan
    if exist(d, 'dir')
      subDirs=dir(d);
      if ~isempty(subDirs)
        fprintf('Found a non-empty parent scans directory in our list: %s\n', d);
        fprintf('Scanning inside for a project scan directory\n');
        [~, sortedIndices]=sort(datenum({dirs.date}), 'descend'); % sort by newest first
        sortedDirs=dirs{sortedIndices};
        scansDir=sortedDirs{1};
        fprintf('Selected newest project scans directory: %s\n', scansDir);
      end
    end
  end
end

% User sanity check and warning
if exist('PROJECT_USER', 'var') && ~isempty(getenv('PROJECT_USER'))
  if ~equal(getenv('PROJECT_USER'), userName)
    disp("WARNING: PROJECT_USER does not match the current namespace");
  end
end

% Allow module to override hardcoded default EZview directory
if exist('EZVIEW_DIR','var') && ~isempty(getenv('EZVIEW_DIR'))
  EZVIEW_DIR=fullfile(getenv('EZVIEW_DIR'));
  if ~strcmp(ezDir, EZVIEW_DIR) % sanity check
    disp("WARNING: EZVIEW_DIR does not match this script's hardcoded EZview location");
    disp("This is probably OK but if strange beahvior arises, we'll need to fix it in code");
    ezDir=EZVIEW_DIR;
  end
  fprintf('Using EZview script directory: %s from environment variable EZVIEW_DIR\n', ezDir);
else
  fprintf('Using EZview script directory: %s from hardcoded default\n', ezDir);
end

w=pwd;

% Single Exp or Chronological Study
% Construct a questdlg with three options

Exp(expN).expLoadCnt= 0;

% Initiation for composite plotting cPlots
Exp(expN).cTraceN= 1;
Exp(expN).cTraceIndx= 1;
Exp(expN).CompositPlot= 0;

choice='Cancel';
expType=0;
choice=questdlg('Choose Single Exp, Chronological Study OR Multi Exp', ...
  'Experiment Type Menu', ...
  'Single Exp','Chronological Study','Multi Exp','Single Exp');

% Handle response
switch choice
  case 'Single Exp'
    disp([choice 'Single Exp Selected'])
    expType=1;
  case 'Chronological Study'
    disp([choice 'Chronological Study Selected'])
    expType=2;
  case 'Multi Exp'
    disp([choice 'Multi Exp Selected'])
    expType=3;
  case 'Cancel'
    disp('Cancel Load Exp')
    expType=0
end

fprintf('expType=%d\n',expType);
if expType==0, return; end
zonePB=expN;

% Pre Load setup incase failure to Load occurs
% updated 230818 to migrate to AppDesigner
if expN==1
  set(handles.zonePB1,'value',1);
  set(handles.zonePB2,'value',0);
  set(handles.zonePB3,'value',0);
  set(handles.zonePB1,'BackgroundColor',[1.0 0.6 0.6]);
  set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0]);
  set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0]);
end

if expN==2
  set(handles.zonePB2,'value',1);
  set(handles.zonePB1,'value',0);
  set(handles.zonePB3,'value',0);
  set(handles.zonePB2,'BackgroundColor',[1.0 0.6 0.6]);
  set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0]);
  set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0]);
end

if expN==3
  set(handles.zonePB3,'value',1);
  set(handles.zonePB1,'value',0);
  set(handles.zonePB2,'value',0);
  set(handles.zonePB3,'BackgroundColor',[1.0 0.6 0.6]);
  set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0]);
  set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0]);
end

Exp(expN).htmapRFanswer= {'G','L'};  %ZoneData

if expType==1
  Exp(expN).DexpType= 'single';

  % Test for Bad MP cell array (usually 384 [NaN}'s)
  % replaced length(Exp(expN).Dexp(1).MP) with MPnum 
  for mx=1:length(Exp(expN).Dexp(1).MP)
    try
      char((Exp(expN).Dexp(1).MP(mx).genename{1}(384)))      
      MPnum=mx;
    catch
      break
    end
  end

  % TODO don't want to cd here
  try
    cd(usrExpJobsDir);
  catch
    if ispc
      cd(fullfile('C:\')); %end  % \Easy\Experiments'));
    else
      cd(fullfile('/mnt/data/scans'))
    end
  end

  datacursormode off;

  if ispc
      try
          cd(usrExpJobsDir);
      catch    
          cd(fullfile('C:\')); %end  % \Easy\Experiments'));
      end
  else
      try
          cd(usrExpJobsDir);
      catch
          cd(fullfile('~'));
      end
  end
  try
      [openExpfile,openExppath] = uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off')
  catch ME
      catchissue='Ln50'
      ME
      cd(w)
      return
  end
%Return without execution if user cancels or doesn't select a .mat file
try 
    if openExpfile==0 || openExppath==0, cd(w), return, end
catch
end
if expN==1
    orfLstSel=get(handles.GeneOrfTog,'value')
end

if expN==2
    orfLstSel=get(handles.GeneOrfTog,'value')
end

if expN==3
    orfLstSel=get(handles.GeneOrfTog,'value')
end
Exp(expN).Dexp(1).srtGnLst={('CheckMP/MPDMfile')};
Exp(expN).Dexp(1).srtOrfLst={('CheckMP/MPDMfile')};
set(handles.listboxGnOrf,'value',1)  %Fix accomodation for bug in App Designer .. .wlapp converter 230906
set(handles.listboxGnOrf,'string',cellstr([{'Failed To Load'}; {' '}]));
%try
 ExpOutmat= fullfile(openExppath,openExpfile);
 load(ExpOutmat);
    cd(openExppath)
    cd ..;
    resDir=pwd;
    Exp(expN).Dexp(1).resDir=resDir;
    cd ..;
    try   %This try-catch is to go up one more dir if the images aren't found (from /OtherResults)
        test4imageDir= imread(fullfile(pwd,'1','1.bmp'));
       ExpPath=pwd;
       Exp(expN).Dexp(1).ExpFoldr=ExpPath;
    catch
        try
        cd ..
        test4imageDir= imread(fullfile(pwd,'1','1.bmp'));
        ExpPath=pwd;
        Exp(expN).Dexp(1).ExpFoldr=ExpPath;
        catch
            cd(w)
        end
    end
    cd(w)
%Experiment LOADs 
%load (fullfile(ExpFoldr,'MasterPlateFiles','MPDMmat.mat')) 
load (fullfile(Exp(expN).Dexp(1).ExpFoldr,'MasterPlateFiles','MPDMmat.mat')) 
load(fullfile(resDir,'Fotos','Coordinates')) 
load(fullfile(resDir,'Fotos','anlZones'))
load(fullfile(resDir,'Fotos','BGatTpts'))
load(fullfile(resDir,'PTmats','NImParameters'))
%Backup for cond. sothat failure to load is recovered back prev. ExpJob data 
%test in temp 

Exp(expN).Dexp(1).temp.DM=DM;
Exp(expN).Dexp(1).temp.MP=MP;
Exp(expN).Dexp(1).temp.scan=scan;
Exp(expN).Dexp(1).temp.FexpScanSpots=FexpScanSpots;
Exp(expN).Dexp(1).temp.FexpScanBMtp=FexpScanBMtp;
Exp(expN).Dexp(1).temp.anlZoneRefs=anlZoneRefs;
Exp(expN).Dexp(1).temp.ImParMat=ImParMat;

Exp(expN).Dexp(1).DM=Exp(expN).Dexp(1).temp.DM;
Exp(expN).Dexp(1).MP= Exp(expN).Dexp(1).temp.MP;
Exp(expN).Dexp(1).scan= Exp(expN).Dexp(1).temp.scan;
Exp(expN).Dexp(1).FexpScanSpots= Exp(expN).Dexp(1).temp.FexpScanSpots;
Exp(expN).Dexp(1).FexpScanBMtp= Exp(expN).Dexp(1).temp.FexpScanBMtp;
Exp(expN).Dexp(1).anlZoneRefs=Exp(expN).Dexp(1).temp.anlZoneRefs;
Exp(expN).Dexp(1).ImParMat=Exp(expN).Dexp(1).temp.ImParMat;

Exp(expN).DexpLength= 1;
Exp(expN).Dexp((Exp(expN).DexpLength+1):end)= [];



% Load new ExpJob
if expN==1,
% Exp(1).traceN=0;
tPtsSize=size(FexpScanBMtp{1,1},3);
set(handles.MPsldr1,'max',length(MP));
set(handles.DMsldr1,'max',length(DM.drug));
set(handles.Tptsldr1,'max',tPtsSize);

% MPnum=length(Exp(expN).Dexp(1).MP);
set(handles.MPsldr1,'min',1)  %,'max',MPnum+.1)
DMnum= length(Exp(expN).Dexp(1).DM.drug);
set(handles.DMsldr1,'min',1,'max',DMnum)  
tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr1,'min',1,'max',tPtsSize)

set(handles.MPsldr1,'value',1)
set(handles.DMsldr1,'value',1)
set(handles.Tptsldr1,'value',1)
set(handles.MPed1,'string','1')
set(handles.DMed1,'string','1')
set(handles.Tpted1,'string','1')
set(handles.MPsldr1,'SliderStep',[1/length(MP) 1/length(MP)]);
set(handles.DMsldr1,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
set(handles.Tptsldr1,'SliderStep',[1/tPtsSize 1/tPtsSize]);

set(handles.DN1,'value',1)
set(handles.DN1,'string',1)
end
if expN==2,
%Exp(2).traceN=0;
tPtsSize=size(FexpScanBMtp{1,1},3);
set(handles.MPsldr2,'max',length(MP));
set(handles.DMsldr2,'max',length(DM.drug));
set(handles.Tptsldr2,'max',tPtsSize);
%MPnum=length(Exp(expN).Dexp(1).MP);
set(handles.MPsldr2,'min',1)  %,'max',MPnum)
DMnum= length(Exp(expN).Dexp(1).DM.drug);
set(handles.DMsldr2,'min',1,'max',DMnum)  
tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr2,'min',1,'max',tPtsSize)

set(handles.MPsldr2,'value',1)
set(handles.DMsldr2,'value',1)
set(handles.Tptsldr2,'value',1)
set(handles.MPed2,'string','1')
set(handles.DMed2,'string','1')
set(handles.Tpted2,'string','1')
set(handles.MPsldr2,'SliderStep',[1/length(MP) 1/length(MP)]);
set(handles.DMsldr2,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
set(handles.Tptsldr2,'SliderStep',[1/tPtsSize 1/tPtsSize]);

set(handles.DN2,'value',1)
set(handles.DN2,'string',1)
end

if expN==3,
%Exp(3).traceN=0;
tPtsSize=size(FexpScanBMtp{1,1},3);
set(handles.MPsldr3,'max',length(MP));
set(handles.DMsldr3,'max',length(DM.drug));
set(handles.Tptsldr3,'max',tPtsSize);
%MPnum=length(Exp(expN).Dexp(1).MP);
set(handles.MPsldr3,'min',1)  %,'max',MPnum)
DMnum= length(Exp(expN).Dexp(1).DM.drug);
set(handles.DMsldr3,'min',1,'max',DMnum)  
tPtsSize=size(Exp(expN).Dexp(1).FexpScanBMtp{1,1},(3));
set(handles.Tptsldr3,'min',1,'max',tPtsSize)

set(handles.MPsldr3,'value',1)
set(handles.DMsldr3,'value',1)
set(handles.Tptsldr3,'value',1)
set(handles.MPed3,'string','1')
set(handles.DMed3,'string','1')
set(handles.Tpted3,'string','1')
set(handles.MPsldr3,'SliderStep',[1/length(MP) 1/length(MP)]);
set(handles.DMsldr3,'SliderStep',[1/length(DM.drug) 1/length(DM.drug)]);
set(handles.Tptsldr3,'SliderStep',[1/tPtsSize 1/tPtsSize]);

set(handles.DN3,'value',1)
set(handles.DN3,'string',1)
end

if expN==1,set(handles.GeneOrfLoc1,'string',{''});
           set(handles.graphStrLoc1,'string',{''});
           cla(handles.Paxes1)
end 
if expN==2,set(handles.GeneOrfLoc2,'string',{''});
           set(handles.graphStrLoc2,'string',{''});
           cla(handles.Paxes2)
end
if expN==3,set(handles.GeneOrfLoc3,'string',{''});
           set(handles.graphStrLoc3,'string',{''})
           cla(handles.Paxes3)
end
Exp(expN).Dexp(1).srtGnLst={('CheckMP/MPDMfile')};
Exp(expN).Dexp(1).srtOrfLst={('CheckMP/MPDMfile')};
set(handles.listboxGnOrf,'string',Exp(expN).Dexp(1).srtGnLst)
set(handles.listboxGnOrf,'string',Exp(expN).Dexp(1).srtOrfLst)


EZVimDisplay

% Capture Exp Name
try
 xp=char(Exp(expN).Dexp(1).resDir);
   if ispc,
    slashPos=strfind(char(Exp(expN).Dexp(1).resDir),'\');
   else
    slashPos=strfind(char(Exp(expN).Dexp(1).resDir),'/');
   end 
 startPos=slashPos(length(slashPos)-2) +1;
 endPos=(slashPos(length(slashPos)) -1);
 expStrn= xp(startPos:end);
 if expN==1,set(handles.expName1,'string',expStrn);end
 if expN==2,set(handles.expName2,'string',expStrn);end
 if expN==3,set(handles.expName3,'string',expStrn);end
catch
    catchissue='Ln198'
end % nested try-catch-end


% Compile GeneList and OrfList
% Sort and add the medians of Ref Plates if RF1,RF2 exist
% Added 17-1023 For User Addition of Gene Composites to ListBox 
Expaa{expN,1}= [];   Expbb{expN,1}= [];
lstindx=0;
lstindxOrf=0;
spN=0;
rfcnt=0;
dRF1indx=0;
RF1mp=[];  RF2mp=[];
for mp=1:MPnum  %length(Exp(expN).Dexp(1).MP) 
   
  for ind384=1:384   
      spN=spN+1;
    
     try % Temp find data error
          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(1).MP(mp).genename{1}(ind384))==38991,
                 Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)={'OCT1_'}; 
             elseif isnumeric(cell2mat(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))
                 Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)={' '}; 
             end
    %****Check for full(384spot) Reference Plates (RF1 or/and RF2)**************          
    RF1fullPlate=0;
    try RF1fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF1'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
    RF2fullPlate=0;
    try RF2fullPlate=sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF2'))==384; catch, mp, msg=strcat(num2str(mp),' genename ERROR'), end
             
       if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384))),'blank'))...     %'\<blank\>'
                   && ~isnumeric(Exp(expN).Dexp(1).MP(mp).orf{1}(ind384))...
                   && ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),' ')...
                   && ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'  ')...
                   && ~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'')...
                   && ~isempty((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)))...
                   && (~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'RF1'))... %||~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1'))... %&& mp==1)...
                   && (~strcmpi((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),'RF2'))... %||~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))... %&& mp==length(Exp(expN).Dexp(1).MP))...
                   && iscellstr((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)))
                   
            lstindxOrf=lstindxOrf+1;
            Exp(expN).Dexp(1).MP(mp).orf{1}(ind384) =strrep((Exp(expN).Dexp(1).MP(mp).orf{1}(ind384)),':',' ');
            bb(lstindxOrf,1)= (Exp(expN).Dexp(1).MP(mp).orf{1}(ind384));
            bb(lstindxOrf,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
            bb(lstindxOrf,3)={mp};
            bb(lstindxOrf,4)={r};
            bb(lstindxOrf,5)={c};
            
            mutorfs(lstindxOrf)=spN;  %16_0318 added for Interaction EZinteract
            %Exp(expN).Dexp(1).mutSpotIndx(lstindxOrf)=spN;  %16_0318 added for Interaction EZinteract
        end    
           
    if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))),'blank'))...      %'\<blank\>'  
                   && ~isnumeric(Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))...
                   && ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),' ')...
                   && ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'  ')...
                   && ~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'')...
                   && ~isempty((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))...
                   && (~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1'))...  %&& ~RF1fullPlate)...
                   && (~strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))...  %&& ~RF2fullPlate)...
                   && iscellstr((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)))
                   
            lstindx=lstindx+1;
           Exp(expN).Dexp(1).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),':',' ');
            aa(lstindx,1)= (Exp(expN).Dexp(1).MP(mp).genename{1}(ind384));
            aa(lstindx,2)={strcat(':',num2str(mp),':',num2str(r),':',num2str(c))};
            aa(lstindx,3)={mp};
            aa(lstindx,4)={r};
            aa(lstindx,5)={c};
            
            mutgenes(lstindx)=spN;
           
           
          elseif (RF1fullPlate==1 ||...   %sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}),'RF1'))==384 || ...
                   (((length(unique(Exp(expN).Dexp(1).MP(mp).genename{1}(1:384)))) ==1 && mp==1 ) && ...   %(isequal((Exp(expN).Dexp(1).MP(mp).genename{1}(1:384)), (Exp(expN).Dexp(1).MP(mp).genename{1}(384:-1:1)))&& mp==1 )) && ...
                    ~exist('RF1scanN','var')))
               rfcnt=rfcnt+1;
               RFs(spN:spN+383)= spN:spN+383;
               RF1mp=mp
               RF1scanN=(mp*DMnum)-(DMnum-1)     
               
           elseif (RF2fullPlate==1||...          %sum(ismember((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF2'))==384 ||... 
                  (((length(unique(Exp(expN).Dexp(1).MP(mp).genename{1}(1:384)))) ==1 && mp== MPnum ) && ... 
                  ~exist('RF2scanN','var')))
                  rfcnt=rfcnt+1;
                  RFs(spN:spN+383)= spN:spN+383;
                  RF2mp=mp              
                  RF2scanN= (mp*DMnum)-(DMnum-1)   
               
               %Dispersed Reference capture and find Medians                
         elseif  strcmpi((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),'RF1') && ...
                   (RF1fullPlate~=1)
           
               dRF1indx=dRF1indx+1;
           Exp(expN).Dexp(1).MP(mp).genename{1}(ind384) =strrep((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384)),':',' ');
            drf(dRF1indx,1)= (Exp(expN).Dexp(1).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;
          
    end   %if isempty(regexpi(char((Exp(expN).Dexp(1).MP(mp).genename{1}(ind384))),'blank'))...  
    %*******************************************************************************       
      catch
      error='EZexpSel lineAfter 236 EZexpSel.m'   
      mp
      ind384
      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(1).MP)
%*****************************************************
   %Cover case if mutorfs RFs are labeled RF1 or RF2
   try
     Exp(expN).Dexp(1).mutSpotIndx.wRFs= union(RFs, mutorfs);
     catch
       msg= 'No RFs Found in Exp! wRFs'
       Exp(expN).Dexp(1).mutSpotIndx.wRFs=  mutorfs;
   end
   try
     Exp(expN).Dexp(1).mutSpotIndx.woRFs= setdiff(mutorfs,RFs);
   catch
       Exp(expN).Dexp(1).mutSpotIndx.woRFs= mutorfs;
       msg= 'No RFs Found in Exp! woRFs'
   end
   
%&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& 




Exp(expN).Dexp(1).RFmd1indx=[];
Exp(expN).Dexp(1).RFmd1LB= {[]};
Exp(expN).Dexp(1).RFmd1pltN={}; 
Exp(expN).Dexp(1).RFmd1val= [];
Exp(expN).Dexp(1).mean1= []; 
Exp(expN).Dexp(1).std1= [];
Exp(expN).Dexp(1).min1= [];
Exp(expN).Dexp(1).max1= [];

Exp(expN).Dexp(1).RFcmpK= []; %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpr= []; %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpL= []; %For Ref Composite 17_1009 

Exp(expN).Dexp(1).RFmd2indx= [];
Exp(expN).Dexp(1).RFmd2LB= {[]};
Exp(expN).Dexp(1).RFmd2pltN= {};
Exp(expN).Dexp(1).RFmd2val= [];
Exp(expN).Dexp(1).mean2= []; 
Exp(expN).Dexp(1).std2= []; 
Exp(expN).Dexp(1).min2= []; 
Exp(expN).Dexp(1).max2= [];

Exp(expN).Dexp(1).RFmean= [];
Exp(expN).Dexp(1).RFstd= [];
Exp(expN).Dexp(1).RFmin= [];
Exp(expN).Dexp(1).RFmax= [];

Exp(expN).Dexp(1).RFmdPLvals= [];  %17_1201 TrendOL
Exp(expN).Dexp(1).RFmdPLB= {[]};
Exp(expN).Dexp(1).RFmdPindx= [];
Exp(expN).Dexp(1).RFmdPpltN= [];
Exp(expN).Dexp(1).RFmdPscanN= [];
Exp(expN).Dexp(1).RFmedianP= [];
Exp(expN).Dexp(1).stdP= [];
Exp(expN).Dexp(1).meanP= [];
Exp(expN).Dexp(1).minP= [];
Exp(expN).Dexp(1).maxP= [];
Exp(expN).Dexp(1).RFcmpPK= []; %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpPr= []; %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpPL= []; %For Ref Composite 17_1009 

Exp(expN).Dexp(1).RFmdGLB= {[]};
Exp(expN).Dexp(1).RFmdGindx= [];
Exp(expN).Dexp(1).RFmdGpltN= [];
Exp(expN).Dexp(1).RFmdGscanN= [];
Exp(expN).Dexp(1).RFmedianG= [];
Exp(expN).Dexp(1).RFmeanG= [];
Exp(expN).Dexp(1).RFstdG= [];
Exp(expN).Dexp(1).RFminG= [];
Exp(expN).Dexp(1).RFmaxG= [];
Exp(expN).Dexp(1).RFcmpGK= []; %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGr= []; %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGL= []; %For Ref Composite 17_1009 

%{
Exp(expN).Dexp(1).RFmeanGK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFstdGK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFminGK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFmaxGK= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFmeanGr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFstdGr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFminGr= []; %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFmaxGr= []; %For Ref Composite 17_1009
%}



if exist('RF1scanN','var')     
  for d=0:(DMnum-1)
      medianIndx=[];
      nonZeroIndx=[];
      medValList=[];
      rf1scN=RF1scanN+d;

try  %if RF1scanN doesn't exist this addition to list will be skipped
    nonZeroIndx= find(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5));
    
     if isempty(nonZeroIndx), nonZeroCnt=0; medianIndx= nonZeroIndx; 
     else nonZeroCnt=length(nonZeroIndx); 
     end
        %                          
     if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)==0, medianIndx=  nonZeroIndx(1:nonZeroCnt-1); end
     if ~isempty(nonZeroIndx) && mod(nonZeroCnt,2)~=0, medianIndx= nonZeroIndx; end 
  clear medValLst
  clear kValLst
  clear rValLst     
if ~isempty(nonZeroIndx) && length(medianIndx) > (.15*384) %To calc. a median, more than 15% of spots must be nonZero
    medValLst= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5);
    medValList1{d+1}= medValLst;
    min1= min(medValLst);
    max1= max(medValLst);
    std1= std(medValLst);
    mean1= mean(medValLst);
    
    kValLst= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,3); %For Ref Composite 17_1009
    rValLst= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,4); %For Ref Composite 17_1009
    
mval1=median(medValLst);  %mval1=median(Exp(expN).Dexp(1).scan(RF1mps).plate(1).CFout(1:384,5));  %CFout(1:383,5));
RFmd1pos=find(mval1==(Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5)));
RFmd1loc(1)= ceil(RFmd1pos/24); %calc r value
RFmd1loc(2)= RFmd1pos - ((RFmd1loc(1)-1)*24);  %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF1md(',num2str(d+1),')')};  %{'RF1md'};
aa(lstindx,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))};  %,'std_',num2str(std1))};
bb(lstindxOrf,1)= {strcat('RF1md(',num2str(d+1),')')};  %{'RF1md'};
bb(lstindxOrf,2)={strcat(':',num2str(RF1mp),':',num2str(RFmd1loc(1)),':',num2str(RFmd1loc(2)))};  %,'std_',num2str(std1))};
%Composite Reference Amalgum Plot  *********************
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF1cmp(',num2str(d+1),')')}; 
aa(lstindx,2)={''};
bb(lstindxOrf,1)= {strcat('RF1cmp(',num2str(d+1),')')};
bb(lstindxOrf,2)={''};
%*******************************************************

Exp(expN).Dexp(1).RFmd1LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(1).RFmd1indx(d+1)= RFmd1pos;
Exp(expN).Dexp(1).RFmd1pltN= RF1mp;
Exp(expN).Dexp(1).RFmd1val(d+1)= mval1;
Exp(expN).Dexp(1).RFmd1Lvals= medValLst;  %17_1201 TrendOL
Exp(expN).Dexp(1).mean1(d+1)= mean1; 
Exp(expN).Dexp(1).std1(d+1)= std1;
Exp(expN).Dexp(1).min1(d+1)= min1;
Exp(expN).Dexp(1).max1(d+1)= max1;
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).Lvals= medValLst;  %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).med= median(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).mean= mean(medValLst); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).std= std(medValLst); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).min= min(medValLst); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpL(1).dm(d+1).max= max(medValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).Kvals= kValLst;  %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).med= median(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).mean= mean(kValLst); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).std= std(kValLst); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).min= min(kValLst); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpK(1).dm(d+1).max= max(kValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).rvals= rValLst;  %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).med= median(rValLst); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).mean= mean(rValLst); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).std= std(rValLst); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).min= min(rValLst); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpr(1).dm(d+1).max= max(rValLst); %For Ref Composite 17_1009 

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
  medianCalcFailed= 'To Few nonZero spots for valid median RF1 selection' 
  firstZero= find(((Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first') 
  Exp(expN).Dexp(1).RFmd1indx(d+1)=firstZero; 
  Exp(expN).Dexp(1).RFmd1pltN= RF1mp; 
    
   try medValList1{d+1}= Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(medianIndx,5); nonZeroCnt; 
   catch, catcherror = 'Ln356',
   end
     
end  %~isempty(nonZeroIndx) && length(medianIndx) > (.15*384)
catch   %try ~ln375
  medianCalcTryFailed1= 'Failed! Failed! Ln362 But process continued with bogus P1ind384 spot value!'
  
    try
      firstZero= find(((Exp(expN).Dexp(1).scan(rf1scN).plate(1).CFout(1:384,5))==0),1,'first')  
      Exp(expN).Dexp(1).RFmd1indx(d+1)=firstZero;
    catch
        catchissue='Ln366'
      Exp(expN).Dexp(1).RFmd1indx(d+1)=384; %if crapout,Then use spot384 as default to keep going  
    end
     try
         Exp(expN).Dexp(1).RFmd1pltN= RF1mp;  
     catch
         catchissue='Ln372'
         Exp(expN).Dexp(1).RFmd1pltN= 1; 
     end
 
    error='EZexpSel lineAfter 258'
    
 
end %try ~ln375

 end   %for d=0:DMnum
end  % if exist('RF1scanN','var')
%**********************************************************************************
%Calc RF2 median if a full plate of RF2s exist**************************
Exp(expN).Dexp(1).RFmd2indx=[];
Exp(expN).Dexp(1).RFmd2pltN=[];


if exist('RF2scanN','var')
  for d=0:(DMnum-1)
      medianIndx2=[];
      nonZeroIndx2=[];
      medValList2=[];
      rf2scN=RF2scanN+d;
    
try  %if RF2scanN doesn't exist this addition to list will be skipped  
     nonZeroIndx2= find(Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5));
     if isempty(nonZeroIndx2), nonZeroCnt2=0; medianIndx2= nonZeroIndx2; 
     else nonZeroCnt2=length(nonZeroIndx2); 
     end
        %                          
     if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)==0, medianIndx2=  nonZeroIndx2(1:nonZeroCnt2-1); end
     if ~isempty(nonZeroIndx2) && mod(nonZeroCnt2,2)~=0, medianIndx2= nonZeroIndx2; end
clear medValLst2   
clear kValLst2
clear rValLst2
if ~isempty(nonZeroIndx2) && length(medianIndx2) > (.15*384) %To calc. a median, more than 15% of spots must be nonZero   
  medValLst2= Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,5);
  medValList2{d+1}= medValLst2;
    min2= min(medValLst2);
    max2= max(medValLst2);
    std2= std(medValLst2);
    mean2= mean(medValLst2);
    
  kValLst2= Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,3); %For Ref Composite 17_1009
  rValLst2= Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,4); %For Ref Composite 17_1009

mval2=median(medValLst2);  %mval2=median(Exp(expN).Dexp(1).scan(RF2mps).plate(1).CFout(1:383,5));
RFmd2pos=find(mval2==(Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5)));
RFmd2loc(1)= ceil(RFmd2pos/24); %calc r value
RFmd2loc(2)= RFmd2pos - ((RFmd2loc(1)-1)*24);  %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF2md(',num2str(d+1),')')};  %{'RF2md'};
aa(lstindx,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))};  %,'std_',num2str(std2))};
bb(lstindxOrf,1)= {strcat('RF2md(',num2str(d+1),')')};   %{'RF2md'};
bb(lstindxOrf,2)={strcat(':',num2str(RF2mp),':',num2str(RFmd2loc(1)),':',num2str(RFmd2loc(2)))};  %,'std_',num2str(std2))};
 %Composite Reference Amalgum Plot   (CRAP)
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF2cmp(',num2str(d+1),')')}; 
aa(lstindx,2)={''};
bb(lstindxOrf,1)= {strcat('RF2cmp(',num2str(d+1),')')}; 
bb(lstindxOrf,2)={''};

Exp(expN).Dexp(1).RFmd2LB(d+1)= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(1).RFmd2indx(d+1)=RFmd2pos;
Exp(expN).Dexp(1).RFmd2pltN= RF2mp;
Exp(expN).Dexp(1).RFmd2val(d+1)= mval2;
Exp(expN).Dexp(1).RFmd1Lvals= medValLst2;  %17_1201 TrendOL
Exp(expN).Dexp(1).mean2(d+1)= mean2;
Exp(expN).Dexp(1).std2(d+1)= std2;
Exp(expN).Dexp(1).min2(d+1)= min2;
Exp(expN).Dexp(1).max2(d+1)= max2;
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).Lvals= medValLst2;  %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).med= median(medValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).mean= mean(medValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).std= std(medValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).min= min(medValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpL(2).dm(d+1).max= max(medValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).Kvals= kValLst2;  %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).med= median(kValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).mean= mean(kValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).std= std(kValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).min= min(kValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpK(2).dm(d+1).max= max(kValLst2); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).rvals= rValLst2;  %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).med= median(rValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).mean= mean(rValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).std= std(rValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).min= min(rValLst2); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpr(2).dm(d+1).max= max(rValLst); %For Ref Composite 17_1009 

  else
    % Pick the first spot with zeros
    % Use that position to satisfy and keep process OK
  medianCalcFailed2= 'Too Few nonZero spots for valid median RF2 selection'
  firstZero2= find(((Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first')   
  Exp(expN).Dexp(1).RFmd2indx(d+1)=firstZero2; 
  Exp(expN).Dexp(1).RFmd2pltN= RF2mp; 
    
   try medValList2{d+1}= Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(medianIndx2,5);  nonZeroCnt2; catch, catchissue='Ln431', end
      
end

catch
         medianCalcTryFailed2= 'Failed! Failed! Ln436 No RF1median But process continued with bogus P1ind384 spot value!'
    
     try
      firstZero2= find(((Exp(expN).Dexp(1).scan(rf2scN).plate(1).CFout(1:384,5))==0),1,'first');
      Exp(expN).Dexp(1).RFmd2indx(d+1)=firstZero2;
     catch
        catchissue='Ln442'
      Exp(expN).Dexp(1).RFmd2indx(d+1)=384;  %if crapout,Then use spot384 as default to keep going  
    end
     try
         Exp(expN).Dexp(1).RFmd2pltN= RF2mp; 
     catch
         catchissue='Ln448'
         Exp(expN).Dexp(1).RFmd2pltN= 1;
     end
    
     error='EZexpSel lineAfter 279'
 
end   %if RF2scanN doesn't exist this addition to list will be skipped  
   clear RFcombValList
   RFcombValList= cat(1,medValList1{d+1},medValList2{d+1});
   Exp(expN).Dexp(1).RFmean(d+1)= mean(RFcombValList);
   Exp(expN).Dexp(1).RFstd(d+1)=std(RFcombValList);
   try, Exp(expN).Dexp(1).RFmin(d+1)=min(RFcombValList);
   catch, Exp(expN).Dexp(1).RFmin(d+1)= 0; end
   try, Exp(expN).Dexp(1).RFmax(d+1)=max(RFcombValList);
   catch, Exp(expN).Dexp(1).RFmax(d+1)= 0; end
   
 end   %for d=0:DMnum   ln446
 
elseif exist('RF1scanN','var')  
   Exp(expN).Dexp(1).RFmean= Exp(expN).Dexp(1).mean1;
   Exp(expN).Dexp(1).RFstd= Exp(expN).Dexp(1).std1;
   Exp(expN).Dexp(1).RFmin= Exp(expN).Dexp(1).min1;
   Exp(expN).Dexp(1).RFmax= Exp(expN).Dexp(1).max1;
end  %if exist('RF2scanN','var')  ln445

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%*************************************************************************************************
%***********DISPERSE REFERENCE PLATES
Exp(expN).Dexp(1).RFmdPindx=[];
Exp(expN).Dexp(1).RFmdPpltN=[];
if exist('drf','var')       
%Det. index of change from one MP to the next    

  i=2;
  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),DMnum);
%************************************
 dMPs= unique(cell2mat(drf(:,3))); 
 %*****************************************
    
  for mm=1:length(dMPs)    % length(chgIndx)
      
    for d=1:(DMnum)
      medianIndxDisp=[];
      NZrefIndxP=[];
      nonZeroValsP=[];
      medValLstDisp=[];
     rf1scNdisp=((dMPs(mm)-1)*DMnum)+(d);

try  % Determine the dispersed RFs median mean and std if such exist
    NZrefIndxP= drfPindx((find(drfPindx(:,dMPs(mm)))),dMPs(mm));   %find(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(drf(chgIndx(cI):chgIndx(cI+1)),5));
    %vv= Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
    vv(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
    %For Global Ref Composite 17_1009 %**************************************************************************
    vvK(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,3);
    vvr(chgIndx(mm):(chgIndx(mm+1)-1),d)=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,4);
    %*****************************************************************************************************
    nonZeroValsP= nonzeros(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5));
    std1Disp= std(nonZeroValsP);
    mean1Disp= mean(nonZeroValsP);
    minDisp= min(nonZeroValsP);
    maxDisp= max(nonZeroValsP);
    drfVals=Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5);
    
    %MEDIAN Determination for PLATES with Dispersed RFs
    %NZrefIndxP= NZrefIndxP %find(Exp(expN).Dexp(1).scan(rf1scNdisp).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) > 3 %(.15*384) %To calc. a median, more than 15% of spots must be nonZero
    medValLstDisp= Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(medianIndxDisp,5);
    %medValList1Disp{d}= medValLstDisp;
    mval1Disp=median(medValLstDisp);  %mval1=median(Exp(expN).Dexp(1).scan(RF1mps).plate(1).CFout(1:384,5));  %CFout(1:383,5));
    nonZeroMedPosIndx=find(mval1Disp==nonZeroValsP);  %(Exp(expN).Dexp(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5)));  %(nonZeroIndxDisp,5)));   %((nonZrfIndx.mp{dMPs(mm),:}),5)));
RFmd1posD= NZrefIndxP(nonZeroMedPosIndx);  %drfPindx((RFmd1posIndx),dMPs(mm));
RFmd1locD(1)= ceil(RFmd1posD/24); %calc r value
RFmd1locD(2)= RFmd1posD - ((RFmd1locD(1)-1)*24);  %calc c value

lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF1mdP(',num2str(d),')')};
aa(lstindx,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};  
bb(lstindxOrf,1)= {strcat('RF1mdP(',num2str(d),')')};
bb(lstindxOrf,2)={strcat(':',num2str(dMPs(mm)),':',num2str(RFmd1locD(1)),':',num2str(RFmd1locD(2)))};

Exp(expN).Dexp(1).RFmdPLvals(d,dMPs(mm))= mval1Disp;  %17_1201 TrendOL
Exp(expN).Dexp(1).RFmdPLB(d,dMPs(mm))= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))= RFmd1posD;
Exp(expN).Dexp(1).RFmdPpltN(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(1).RFmdPscanN(d,dMPs(mm))=rf1scNdisp;
Exp(expN).Dexp(1).RFmedianP(d,dMPs(mm))= mval1Disp;
Exp(expN).Dexp(1).stdP(d,dMPs(mm))= std1Disp;
Exp(expN).Dexp(1).meanP(d,dMPs(mm))= mean1Disp; 
Exp(expN).Dexp(1).minP(d,dMPs(mm))= minDisp;
Exp(expN).Dexp(1).maxP(d,dMPs(mm))= maxDisp;
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(1).scan(rf1scNdisp).plate(1).CFout(NZrefIndxP,5))==0),1,'first');
  firstZeroD= drfPindx((firstZeroDindx),dMPs(mm));
  Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=firstZeroD; 
  Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm);   %RF1mp;   %Is this supposed to be the MP number or the ScanPlate number???
    
     
end  %~isempty(NZrefIndxP) && length(medianIndxDisp) > 3   ln584
catch   %try ln565
  medianCalcTryFailed1D= 'Failed! Failed! Ln565 {Dispersed RF1s} "try" But process continued with bogus Plate spot value!'
  
    try
      firstZeroindxD= find(vv((chgIndx(d):chgIndx(d+1)-1),5)==0,1,'first'); 
      firstZeroPindx= uu(firstZeroindxD,4);
      Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
      Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=firstZeroPindx;
      
    catch
        catchissue='try at Ln565'
        Exp(expN).Dexp(1).RFmdPpltN(d,dMPs(mm))= dMPs(mm);
        Exp(expN).Dexp(1).RFmdPindx(d,dMPs(mm))=384; %if crapout,Then use spot384 as default to keep going  
    end
     try
         Exp(expN).Dexp(1).RFmdPpltN= dMPs(mm);  
     catch
         catchissue='Ln619'
         Exp(expN).Dexp(1).RFmdPpltN= 1;  %This might keep from breaking BUT ??? 
     end
    error='EZexpSel lineAfter 565'   
end %try ~ln565

   end   %for d=0:DMnum 
  end    %for mm=1:length(dMPs)

%****************CALC. GLOBAL MEAN, STD, AND MEDIAN FOR DISTRIBUTED REFERENCES******************************************************************
uu= horzcat(uu,vv);
for d=1:DMnum
    medianIndxG=[];
    NZrfIndxG=[];
    minG = min(nonzeros(vv(:,d)));
    maxG = max(nonzeros(vv(:,d)));
    RFmeanG= mean(nonzeros(vv(:,d)));
    RFstdG= std(nonzeros(vv(:,d)));
    NZrfIndxG= find(vv(:,d));  %find(nonzeros(vv(:,d)));  WWRONG FOR A WHILE! 
 
  if isempty(RFmeanG), nonZeroCntD=0,    %medianIndxDisp= RFmeanG(d); 
     else nonZeroCntD= length(nonzeros(vv(:,d))); 
  end
  %Calc. of median requires an odd number of indx items 
     if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)==0, medianIndxD=  NZrfIndxG(1:(size(NZrfIndxG,1)-1)); end
     if ~isempty(NZrfIndxG) && mod(nonZeroCntD,2)~=0, medianIndxD= NZrfIndxG(:); end 

     if ~isempty(NZrfIndxG) && length(medianIndxD) > (.15*size(drf,1)) %To calc. a median, more than 15% of spots must be nonZero 
  
   mvalsDG= median(vv(medianIndxD,d));                  %(nonzeros(vv(:,d))); 
   nzPosIndxDG=find(mvalsDG==vv(:,d)); 
RFmdDGloc(d,1)= uu(nzPosIndxDG,1);  %MP of distributedGlobal Median value
RFmdDGloc(d,2)= uu(nzPosIndxDG,2);   %calc r value
RFmdDGloc(d,3)= uu(nzPosIndxDG,3);  %calc c value
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RF1mdG(',num2str(d),')')}; 
aa(lstindx,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))};  %,'std_',num2str(std2))};
bb(lstindxOrf,1)= {strcat('RF1mdG(',num2str(d),')')}; 
bb(lstindxOrf,2)={strcat(':',num2str(RFmdDGloc(d,1)),':',num2str(RFmdDGloc(d,2)),':',num2str(RFmdDGloc(d,3)))};  %,'std_',num2str(std2))};
 %Composite Reference Amalgum Plot ******************
lstindx=lstindx+1;
lstindxOrf= lstindxOrf+1;
aa(lstindx,1)= {strcat('RFcmpG(',num2str(d),')')}; 
aa(lstindx,2)={''};
bb(lstindxOrf,1)= {strcat('RFcmpG(',num2str(d),')')}; 
bb(lstindxOrf,2)={''};
%*****************************************************
%Exp(expN).Dexp(1).RFmdGLvals= vv(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(1).RFmdGLB(d)= strcat(aa(lstindx,1),aa(lstindx,2));
Exp(expN).Dexp(1).RFmdGindx(d)= nzPosIndxDG;
Exp(expN).Dexp(1).RFmdGpltN(d)= RFmdDGloc(d,1);  
Exp(expN).Dexp(1).RFmdGscanN(d)= uu(nzPosIndxDG,4);
Exp(expN).Dexp(1).RFmedianG(d)= mvalsDG;
Exp(expN).Dexp(1).RFminG(d)= minG;
Exp(expN).Dexp(1).RFmaxG(d)= maxG;
Exp(expN).Dexp(1).RFstdG(d)= RFstdG;
Exp(expN).Dexp(1).RFmeanG(d)= RFmeanG; 

Exp(expN).Dexp(1).RFcmpGL.dm(d).Lvals= vv(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpGL.dm(d).med= median(vv(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGL.dm(d).mean= mean(vv(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGL.dm(d).std= std(vv(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGL.dm(d).min= min(vv(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGL.dm(d).max= max(vv(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGK.dm(d).Kvals= vvK(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpGK.dm(d).med= median(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGK.dm(d).mean= mean(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGK.dm(d).std= std(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGK.dm(d).min= min(vvK(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGK.dm(d).max= max(vvK(medianIndxD,d)); %For Ref Composite 17_1009
Exp(expN).Dexp(1).RFcmpGr.dm(d).rvals= vvr(medianIndxD,d); %17_1201 TrendOL
Exp(expN).Dexp(1).RFcmpGr.dm(d).med= median(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGr.dm(d).mean= mean(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGr.dm(d).std= std(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGr.dm(d).min= min(vvr(medianIndxD,d)); %For Ref Composite 17_1009 
Exp(expN).Dexp(1).RFcmpGr.dm(d).max= max(vvr(medianIndxD,d)); %For Ref Composite 17_1009 

     end  %if ~isempty(NZrfIndxG) && length(medianIndxD) > (.15*size(drf,1)) %To calc. a median, more than 15%
end  

end  % if exist('drf','var')
%END OF DISPERSE REFERENCE PLATAES CALCULATIONS AND LIST ADDITIONS   
 %*********************************************************************
%Added 17-1023 For User Addition of Gene Composites to ListBox
%Expaa{ic,1}= aa;   Expbb{ic,1}= bb;
%**********************************************************************
 
 
 
 
 







%>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

%try
for mp=1:MPnum  %length(Exp(expN).Dexp(1).MP)
  for ind384=1:384   
      spN=spN+1;


  end

%catch
%end  %try   for user selected Reference routine
end

%****************************************************************************************************
gnLstRaw= strcat(aa(:,1),aa(:,2));
Exp(expN).Dexp(1).srtGnLst= sort(gnLstRaw);

orfLstRaw=strcat(bb(:,1),bb(:,2));
Exp(expN).Dexp(1).srtOrfLst= sort(orfLstRaw);
%********Auto select Zone and load listboxGnOrf data**********
zeroCLn= zeros(1,DMnum);
Exp(expN).expLoadCnt= Exp(expN).expLoadCnt+1; expLdCnt= Exp(expN).expLoadCnt;
zonePB= expN;
if expN==1
    set(handles.zonePB1,'value',1)
    set(handles.zonePB2,'value',0)
    set(handles.zonePB3,'value',0)
    set(handles.zonePB1,'BackgroundColor',[1.0 0.6 0.6])
    set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0])
    set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0]) 
    orfLstSel=get(handles.GeneOrfTog,'value')
  if orfLstSel==1
   set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtOrfLst)   
  else
   set(handles.listboxGnOrf,'string',Exp(1).Dexp(1).srtGnLst)
  end
  DNLaxes1= handles.DNLaxes1; %ZoneRelated
  Exp(1).hzeroCLn(expLdCnt) = plot(DNLaxes1,zeroCLn,1:DMnum,'y');
end

if expN==2
    set(handles.zonePB1,'value',0)
    set(handles.zonePB3,'value',0)
    set(handles.zonePB2,'value',1)
    set(handles.zonePB2,'BackgroundColor',[1.0 0.6 0.6])
    set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0])
    set(handles.zonePB3,'BackgroundColor',[1.0 1.0 1.0])
    orfLstSel= get(handles.GeneOrfTog,'value');
  if orfLstSel==1
   set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtOrfLst)   
  else
   set(handles.listboxGnOrf,'string',Exp(2).Dexp(1).srtGnLst)
  end
  DNLaxes2= handles.DNLaxes2;  %ZoneRelated
  Exp(2).hzeroCLn(expLdCnt) = plot(DNLaxes2,zeroCLn,1:DMnum,'y');
  
end

if expN==3
    set(handles.zonePB1,'value',0)
    set(handles.zonePB2,'value',0)
    set(handles.zonePB3,'value',1)
    set(handles.zonePB3,'BackgroundColor',[1.0 0.6 0.6]);
    set(handles.zonePB1,'BackgroundColor',[1.0 1.0 1.0]);
    set(handles.zonePB2,'BackgroundColor',[1.0 1.0 1.0]);
    orfLstSel=get(handles.GeneOrfTog,'value');
  if orfLstSel==1
   set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtOrfLst)   
  else
   set(handles.listboxGnOrf,'string',Exp(3).Dexp(1).srtGnLst)
  end
  DNLaxes3= handles.DNLaxes3; %ZoneRelated
  Exp(3).hzeroCLn(expLdCnt) = plot(DNLaxes3,zeroCLn,1:DMnum,'y');
end

if Exp(4).interacPBsel==0  %if interaction "raw" don't show a center line
  for i=1:Exp(expN).expLoadCnt,
      try set(Exp(expN).hzeroCLn(i),'visible','off'); 
      catch
          catchissue= strcat('Ln521',i)
      end, 
  end %ZoneRelated
end
%*********************************************************
EZdiagRFsSheet %**
%*****************

%*********************************************************
RFconfig=0;
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean'))&&...
        ~isempty(Exp(expN).Dexp(1).RFmean)&&...
    sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG'))&&...
        isempty(Exp(expN).Dexp(1).RFmeanG)
    RFconfig=1;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean'))==0 ||...
        isempty(Exp(expN).Dexp(1).RFmean)&&...
    sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG'))&&...
        ~isempty(Exp(expN).Dexp(1).RFmeanG)
    RFconfig=2;
end
if sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmean'))&&...
        ~isempty(Exp(expN).Dexp(1).RFmean)&&...
    sum(ismember(fieldnames(Exp(expN).Dexp(1)),'RFmeanG'))&&...
        ~isempty(Exp(expN).Dexp(1).RFmeanG)
    RFconfig=3;
end
Exp(expN).RFconfig= RFconfig;  %ZoneRelated
%******************************************
if RFconfig~=0
   Exp(expN).Dexp(1).RFrnames=rnames;
   Exp(expN).Dexp(1).RFdata= data;
   Exp(expN).Dexp(1).resetHtmpTg =5;  %ZoneRelated    

   % HtMapTog 'string', 'Current user L/N' selection'
   Exp(expN).Dexp(1).spotIndx= [];
   if expN==1,
    Exp(1).htmapPBsel=0;
    set(handles.HtMapTog1,'string','L')
    %*********
    EZhtMap %*
    %*********
   end
   if expN==2,
    Exp(2).htmapPBsel=0;
    set(handles.HtMapTog2,'string','L')
    %*********
    EZhtMap %*
    %*********
   end
   if expN==3,
    Exp(3).htmapPBsel=0;
    set(handles.HtMapTog3,'string','L')
    %*********
    EZhtMap %*
    %*********
   end
   htMapTogPBfg=0;

elseif RFconfig==0,
        RFconfigMsg= 'No RF1 references in this Experiment Job'
        try
          %*********************
          EZsingleExUserRF
           %EZmultiDayGui     %*
           %cd(w)             %*
           %EZmultiDay        %*
           %EZmultiExLoad     %*
          %*********************
        catch
            RFconfigMsg= 'No RF1 or User selected references in this Experiment Job'
            Exp(expN).Dexp(1).resetHtmpTg =3;  %ZoneRelated
        end
            
       % Exp(expN).Dexp(1).resetHtmpTg =3;  %ZoneRelated
end
%*****************************************
%**********************************************
%{
try msgBadGeneName,  catch, end
try
    
    if RFconfig==0,
        RFconfigMsg= 'No RF1 references in this Experiment Job'
        Exp(expN).Dexp(1).resetHtmpTg =3;  %ZoneRelated
    end
catch
end
%***************************
%}
%*******************************************************************
elseif expType==2  %Multiple Experiment from in one Folder extraction
    Exp(expN).DexpType= 'chrono'; 
     %*********************
     %Test for Bad MP cell array (usually 384 [NaN}'s)
     %replaced length(Exp(expN).Dexp(1).MP) with MPnum 
    for mx=1:length(Exp(expN).Dexp(1).MP)
     try
      char((Exp(expN).Dexp(1).MP(mx).genename{1}(384)))      
    MPnum=mx;
     catch
        break
     end
    end
%*************************************************
       ww=pwd;
       try EZmultiDayGui; catch ME
       msg = ME.message, cd(ww); end     %*            %*
       try EZmultiDay; catch ME
       msg = ME.message, cd(ww); end       %*
       try EZmultiExLoad; catch ME
       msg = ME.message, cd(ww); end     %*
      %*********************
elseif expType==3
    Exp(expN).DexpType= 'multi';
      %*********************
      %Test for Bad MP cell array (usually 384 [NaN}'s)
      %replaced length(Exp(expN).Dexp(1).MP) with MPnum 
    for mx=1:length(Exp(expN).Dexp(1).MP)
     try
      char((Exp(expN).Dexp(1).MP(mx).genename{1}(384)))      
    MPnum=mx;
     catch
        break
     end
    end
%*************************************************
       ww=pwd;
       try EZmultiDayGui; catch ME
       msg = ME.message,cd(ww); end     %*            %*
       try EZmultiDay; catch ME
       msg = ME.message, cd(ww); end        %*
       try EZmultiExLoad;  catch ME
       msg = ME.message, cd(ww); end   %*
      %*********************
else
    disp('Cancel Load Exp')
end
        


%__________________________________________________________________________
%Bone Yard***********************************
%Exp(expN).Dexp(1).RF1cmpK.[]; %For Ref Composite 17_1009 
%Exp(expN).Dexp(1).std1K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min1K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max1K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1)RF1cmpr= [];  %For Ref Composite 17_1009
%Exp(expN).Dexp(1).std1r= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min1r= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max1r= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).RF= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).std2K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min2K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max2K= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).RF2cmpr= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).std2r= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).min2r= []; %For Ref Composite 17_1009
%Exp(expN).Dexp(1).max2r= []; %For Ref Composite 17_1009

%kValList1{d+1}= kValLst; %For Ref Composite 17_1009
    %kmin1= min(kValLst); %For Ref Composite 17_1009
    %kmax1= max(kValLst); %For Ref Composite 17_1009
    %kstd1= std(kValLst); %For Ref Composite 17_1009
    %kmean1= mean(kValLst); %For Ref Composite 17_1009
    %rValList1{d+1}= rValLst; %For Ref Composite 17_1009
    %rmin1= min(rValLst); %For Ref Composite 17_1009
    %rmax1= max(rValLst); %For Ref Composite 17_1009
    %rstd1= std(rValLst); %For Ref Composite 17_1009
    %rmean1= mean(rValLst); %For Ref Composite 17_1009
  %kValList2{d+1}= kValLst2; %For Ref Composite 17_1009
    %kmin2= min(kValLst2); %For Ref Composite 17_1009
    %kmax2= max(kValLst2); %For Ref Composite 17_1009
    %kstd2= std(kValLst2); %For Ref Composite 17_1009
    %kmean2= mean(kValLst2); %For Ref Composite 17_1009  
  %rValList2{d+1}= rValLst2; %For Ref Composite 17_1009
   % rmin2= min(rValLst2); %For Ref Composite 17_1009
    %rmax2= max(rValLst2); %For Ref Composite 17_1009
    %rstd2= std(rValLst2); %For Ref Composite 17_1009
    %rmean2= mean(rValLst2); %For Ref Composite 17_1009    


%{

%User Reference Input Dialog Box used in the multiExperiment Chrono setup

   prompt = {'Enter GeneName to use as Reference:',...
       'Enter Specifics Term if used to futher specify Reference '}       
    dlg_title = 'User Reference Input';
    num_lines = 1;
    def = {'RF1','None'};
    answer = inputdlg(prompt,dlg_title,num_lines,def);
    rfGene= cell2mat(answer(1));
    if ~strcmpi(rfGene,'RF1')|| ~strcmpi(rfGene,'RF2'), usrRefFg=1; end
    rfSpec= answer(2); %if strcmpi(answer(2),'None'), rfSpec= ''; end
    rfGnSp= strcat(rfGene,rfSpec);

    
%+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
%First user input prototype code
if ~exist('RF1scanN','var') && ~exist('RF2scanN','var')  %change || &&
    prompt = {'Enter Masterplate Number(s) of Your Reference GeneName spots:',...
              'Enter GeneName of Your Reference:'};
    dlg_title = 'User Reference Input';
    num_lines = 1;
    def = {'Ref MP(s)','USRrefGeneName'};
    answer = inputdlg(prompt,dlg_title,num_lines,def);
    rfMPstr= cell2mat(answer(1));
    rfMPcomas=strfind((cell2mat(answer(1))),',');
    n=0;
    if isempty(rfMPcomas)|| max(rfMPcomas)== length(rfMPstr)
        usrMPs= rfMPstr
    else
    for i= rfMPcomas,
        n=n+1
        usrMPs(n)= str2double(rfMPstr(i-1:i))
    if i== max(rfMPcomas)
        usrMPs(n+1)= str2double(rfMPstr(i:end))
    end 
    end
    end
    usrMPs= answer(1); 
    refGene= answer(2);

end
%}