COPSkcloop

function COPSkcloop(infile)

%channels
%={'0Ed412','0Ed443','0Ed490','0Ed510','0Ed555','0Ed665','1Lu412','1Lu443',
%'1Lu490','1Lu510','1Lu555','1Lu665'}; %prr channels
rqfid = fopen('/home/oceancolor/Plumes_and_Blooms/workspace/eriks/C-OPS/Copsrqclist.txt')
chin = 1;
while ~feof(rqfid)
    chline = fgets(rqfid);
    channels2(chin,:) = {chline(1:6)};
    chin = chin + 1;
    if chin > 36
        break
    end
end
channels2 = channels2';
depth_width = [10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10,10];
%interval = [12,12,12,12,12,10,12,12,12,12,12,10];
% -r 1ed412 1 12
% -r 1ed443 1 12
% -r 1ed490 1 12
% -r 1ed510 1 12
% -r 1ed555 1 12
% -r 1ed665 1 10
% -r 1lu412 1 12
% -r 1lu443 1 12
% -r 1lu490 1 12
% -r 1lu510 1 12
% -r 1lu555 1 12
% -r 1lu665 1 10
%infile = 'bsakrmP101216B.lcd.1';
s = struct('channel',channels2,'depthwidth',depth_width);
valac = [];
donebefore =0;


%=============main loop============
for L = 1:size(depth_width,2)

%vars
%=%bscalcE(s(L).channel,s(L).scale(L),s(L).interval(L),'bananKrqcmmP101216B.l%cd.1')
%-------------end changed 12-4-12
%valac = valac; %changed 12-4-12 from ' to not

%===generate new file and checking what input files to use=======
%========

newfile = strcat('kc',infile);
infp = fopen(newfile,'r+');
if infp ~= -1
    infile = newfile;
end
 if infp ==-1 && donebefore == 0 %if first time through using "mbs" file
     nf = fopen(newfile,'w+');  %open a new file for writing as usual
     infp = fopen(infile,'r+'); %open original as usual
 else
     if infp == -1 && donebefore == 1 
         newfile = infile;
     end
     temp = strcat('tempkclcd',newfile); %write stuff to this and then rename... to "kc"
     nf = fopen(temp,'w+');%open a temp file that will be renaimed 'kc..'
     if donebefore ==1 && L < 2 ;
         infile = newfile;%just need to assign this once otherwise infile will keep having an extra kc on it.(kckckc..)   
     end
     infp = fopen(infile,'r+');
 end 
if donebefore ==1
    %disp('done before')
end
donebefore =1;
vars = [];


%=======================================================================
%=====runs the kc stuff=================================================
%=====================================

vars = CPSbopkc(s(L).channel,s(L).depthwidth(L),infile);
vars = vars';% changed 12-4-12
valac = [valac,vars];
%=======================================================================
%======================================================================= 


%===========print filters to 
while ~feof(infp)
    linep = fgets(infp);
    if strncmp(linep,'<data>',6) == 1
        fprintf(nf,'%s\n',['kcr-',s(L).channel]);
        fprintf(nf,'%s\n','<data>');
        break
    end
    fprintf(nf,linep); %moved to after channel print 12-4-12
    
end

%==========================================================================
%-----open temp data file for reading and add new data columns to it.
%==========================================================================
   mname = strcat('temp',infile); %this is the same temp data file generated by bopkc
   tn = load(mname);

   if L ==1
    tempm = [tn,valac]; %added 12-4-12 ' making first line of data to write
   else
       tempm = [tempm,vars];
   end
   %disp('keyboard in kcloop')
   %keyboard %#===++
    dlmwrite(mname,tempm,'delimiter',' ','precision',6); %overwrites data file with new columns
    matfile = fopen(mname);
    while ~feof(matfile)
        nln = fgets(matfile);
        fprintf(nf,'%s',nln); %writes matfile to new lcd
    end
    
    
%------add filters to end of file
while ~feof(infp)
    tl = fgets(infp);

    if strncmp(tl,'<filters_used>',14) == 1
        fprintf(nf,tl);
        while ~feof(infp)
            npf = fgets(infp);
            fprintf(nf,'%s',npf);
        end
    end
end


%===add stats line==
%for L = 1:size(depth_width,2) commented 12-4-12
fprintf(nf,'%s\n',['bopkc', s(L).channel,' ', num2str(s(L).depthwidth(L)),' ', infile]);
%fprintf(nf,'%s\n',char(valac(L)))
%fprintf(nf,'%s/n')
%end commented 12-4-12

fclose(nf);
fclose(infp);
if donebefore ==1 && L > 1
%movefile(tempname,newfile)
    movefile(temp,infile);
end
infile = newfile; %needs to update filename otherwise infile will always be the same.
end

fclose all

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