% MATLAB script to make 2x2 proofreading tiles
% for the TwoCounterSquareCapped tiles

N=59;   % number of original tile types
M=28;   % number of original bond types

origtiles={                                       % input from
{21 21 25 25}, '(white) % seed'                   ,' ' 
{16 1 26 0}, '(red) % hor  seed row 6'            ,'E'
{6 2 7 1},   '(red1) % hor  seed row 5'           ,'E'
{5 3 7 2},   '(red2) % hor  seed row 4'           ,'E'
{6 4 7 3},   '(red3) % hor  seed row 3'           ,'E'
{5 24 7 4},  '(red4) % hor  seed row 2'           ,'E'
{6 25 7 24}, '(red5) % hor  seed row 1'           ,'E'
{1 16 0 26}, '(red) % vert seed row 6'            ,'N'
{2 6 1 7},   '(red1) % vert seed row 5'           ,'N'
{3 5 2 7},   '(red2) % vert seed row 4'           ,'N'
{4 6 3 7},   '(red3) % vert seed row 3'           ,'N'
{24 5 4 7},  '(red4) % vert seed row 2'           ,'N'
{25 6 24 7}, '(red5) % vert seed row 1'           ,'N'
{7 7 7 7},   '[.9](pink1) % blank 0 (small square)'   ,'NE'
{8 8 8 8},   '[.9](pink2) % blank 1 (large square)'   ,'SW'
{5 12 17 12},' (blue3)  % -- vertical counter'      ,'SW'
{6 12 18 12},' (green)'                             ,'SW'
{17 10 6 10},' (blue2)'                             ,'SE'
{18 10 5 11},' (green2)'                            ,'SE'
{18 11 6 11},' (green3)'                            ,'SE'	
{17 11 5 11},' (blue1)'                             ,'SE'
{20 8 13 12},  '(magenta1)'                           ,'SW'
{21 8 14 12},  '(magenta2)'                           ,'SW'
{13 8 21 10},  '[1.5](magenta3)'                           ,'S from W'
{14 8 20 11},  '[1.5](magenta4)'                           ,'S from W'
{15 12 22 0},  '[1.5](grey20)'                             ,'S from E'
{16 12 23 0},  '[1.5](grey30)'                             ,'S from E'
{27 10 16 0},  '(grey40)'                             ,'SE'
{23 10 15 0},  '(grey50)'                             ,'SE'
{22 11 15 0},  '(grey60)'                             ,'SE'
{23 11 16 0},  '(grey70)'                             ,'SE'
{12 5 12 17},'  (blue3) % -- horizontal counter'    ,'SW'
{12 6 12 18},'  (green)'                            ,'SW'
{10 17 10 6},'  (blue2)'                            ,'NW'
{10 18 11 5},'  (green2)'                           ,'NW'
{11 18 11 6},'  (green3)'                           ,'NW'
{11 17 11 5},'  (blue1)'                            ,'NW'
{8 20 12 13},  '(magenta1)'                           ,'SW'
{8 21 12 14},  '(magenta2)'                           ,'SW'
{8 13 10 21},  '[1.5](magenta3)'                           ,'W from S'
{8 14 11 20},  '[1.5](magenta4)'                           ,'W from S'
{12 15 0 22},  '[1.5](grey20)'                             ,'W from N'
{12 16 0 23},  '[1.5](grey30)'                             ,'W from N'
{10 27 0 16},  '(grey40)'                             ,'NW'
{10 23 0 15},  '(grey50)'                             ,'NW'
{11 22 0 15},  '(grey60)'                             ,'NW'
{11 23 0 16},  '(grey70)'                             ,'NW'
{26 26 0 0},  '(yellow1) % cap keystone (small square)'      ,'NE'
{26 7 26 0},  '(green4)  % vert cap 1   (small square)'      ,'NE'
{7 26 0 26},  '(green4)  % hor  cap 1   (small square)'      ,'NE'
{0 28 27 0},  '[1.5](yellow3) % cap keystone for vert counter'    ,'S from E'
{0 28 17 28},  '(gold)    % cap 1 for vert counter'           ,'SW'
{0 28 13 28}, '(orange)  % cap 2 for vert counter'           ,'SW'
{28 0 0 27},  '[1.5](yellow3) % cap keystone for hori counter'    ,'W from N'
{28 0 28 17},  '(gold)    % cap 1 for hori counter'           ,'SW'
{28 0 28 13}, '(orange)  % cap 2 for hori counter'           ,'SW'
{0 28 8 28},  '(brown)   % hor  cap for blank (big square)'  ,'SW' 
{28 0 28 8},  '(brown)   % vert cap for blank (big square)'  ,'SW' 
{0 0 28 28},  '[2](yellow4) % cap keystone       (big square)'  ,'SW'
  }

origG = [2  2  2  2  1   1 1 1 1 1  1 1 1 1 1  1 1  1  2  2   2  2  2  2   2     1 2 1]
%% this isn't actually used for making the proofreading tiles. (it is used for orig) 
%% proofreadings looks at input directions. 

prooftiles = cell(4*N,3);
proofG     = zeros(1,2*M+4*N);

for n=1:N
  a=origtiles{n,1}{1};   if (a>0) ahat=a+M; else ahat=0; end
  b=origtiles{n,1}{2};   if (b>0) bhat=b+M; else bhat=0; end
  c=origtiles{n,1}{3};   if (c>0) chat=c+M; else chat=0; end
  d=origtiles{n,1}{4};   if (d>0) dhat=d+M; else dhat=0; end
  prooftiles{4*n-3,1} = {a         2*M+4*n-3 2*M+4*n-0 dhat     };  prooftiles{4*n-3,2} = origtiles{n,2};
  prooftiles{4*n-2,1} = {ahat      bhat      2*M+4*n-2 2*M+4*n-3};  prooftiles{4*n-2,2} = origtiles{n,2};  
  prooftiles{4*n-1,1} = {2*M+4*n-2 b         chat      2*M+4*n-1};  prooftiles{4*n-1,2} = origtiles{n,2};
  prooftiles{4*n-0,1} = {2*M+4*n-0 2*M+4*n-1 c         d        };  prooftiles{4*n-0,2} = origtiles{n,2};

  %% funky colors for one tile
  pL=find(origtiles{n,2}=='[');  pR=find(origtiles{n,2}==']');
  if isempty(pL)
    prooftiles{4*n-2,2} = ' ';
  else
   prooftiles{4*n-2,2} = origtiles{n,2}(pL:pR);
  end

  % For each tile, we know the direction of growth.  Set internal bond strengths based on input strengths.
  % Output sticky end strengths are set by the tile that reads this one.
  inputdir = origtiles{n,3}; 
  if strcmp(inputdir,'NE')
    proofG([a a+M b b+M 2*M+4*n-3 2*M+4*n-2 2*M+4*n-1 2*M+4*n-0]) = [1 1 1 1 1 1 1 1];   
    for i=0:3, prooftiles{4*n-i,3}=inputdir; end
  elseif strcmp(inputdir,'NW')
    proofG([a a+M d d+M 2*M+4*n-3 2*M+4*n-2 2*M+4*n-1 2*M+4*n-0]) = [1 1 1 1 1 1 1 1];   
    for i=0:3, prooftiles{4*n-i,3}=inputdir; end
  elseif strcmp(inputdir,'SE')
    proofG([c c+M b b+M 2*M+4*n-3 2*M+4*n-2 2*M+4*n-1 2*M+4*n-0]) = [1 1 1 1 1 1 1 1];   
    for i=0:3, prooftiles{4*n-i,3}=inputdir; end
  elseif strcmp(inputdir,'SW')
    proofG([c c+M d d+M 2*M+4*n-3 2*M+4*n-2 2*M+4*n-1 2*M+4*n-0]) = [1 1 1 1 1 1 1 1];   
    for i=0:3, prooftiles{4*n-i,3}=inputdir; end
  elseif inputdir(1)=='S'
    proofG([c c+M 2*M+4*n-3 2*M+4*n-2 2*M+4*n-1 2*M+4*n-0]) = [2 1 1 2 1 1];   
    prooftiles{4*n-3,3}='SE'; prooftiles{4*n-2,3}='S'; prooftiles{4*n-1,3}='SW'; prooftiles{4*n-0,3}='S';
  elseif inputdir(1)=='N'
    proofG([a a+M 2*M+4*n-3 2*M+4*n-2 2*M+4*n-1 2*M+4*n-0]) = [2 1 1 2 1 1];   
    prooftiles{4*n-3,3}='N'; prooftiles{4*n-2,3}='NW'; prooftiles{4*n-1,3}='N'; prooftiles{4*n-0,3}='NE';
  elseif inputdir(1)=='E'
    proofG([b b+M 2*M+4*n-3 2*M+4*n-2 2*M+4*n-1 2*M+4*n-0]) = [2 1 2 1 1 1];   
    prooftiles{4*n-3,3}='E'; prooftiles{4*n-2,3}='SE'; prooftiles{4*n-1,3}='E'; prooftiles{4*n-0,3}='NE';
  elseif inputdir(1)=='W'
    proofG([d d+M 2*M+4*n-3 2*M+4*n-2 2*M+4*n-1 2*M+4*n-0]) = [2 1 2 1 1 1];   
    prooftiles{4*n-3,3}='SW'; prooftiles{4*n-2,3}='W'; prooftiles{4*n-1,3}='NW'; prooftiles{4*n-0,3}='W';
  else %% seed tile
    proofG([2*M+4*n-3 2*M+4*n-2 2*M+4*n-1 2*M+4*n-0]) = [2 1 1 2];   
    prooftiles{4*n-3,3}=' '; prooftiles{4*n-2,3}='W'; prooftiles{4*n-1,3}='NW'; prooftiles{4*n-0,3}='N';
  end
end

%% Output origtiles and prooftiles to a file  (thus, this file is real source)

oname='TwoCounterSquareCapped.tiles';
fname='TwoCounterSquareCapped2x2.tiles';

f=fopen(oname,'w');

fprintf(f,'%% %s  output from source make2x2tiles.m \n', oname);
fprintf(f,['%%  Modifies binarycap.tiles to use two perpendicular counters.\n' ...
           '%%  This avoids prolonged facet exposure, and should yield\n' ...
           '%%  lower error rates.  Counter tiles are at higher concentration\n' ...
           '%%  to make counter growth and blank growth rates similar.\n' ...
           '%%  Also, using unique bonds for the two layers of the counter growth\n' ...
           '%%  (forward and backward) eliminates some spurious growth on those facets.\n']);

fprintf(f,'tile edges matches {{N E S W}*}\n');
fprintf(f,'num tile types=%d\n', N);
fprintf(f,'num binding types=%d\n', M);
fprintf(f,'tile edges={\n');
for n=1:N
  fprintf(f,'{%d %d %d %d}%s \n', ...
     origtiles{n,1}{1}, origtiles{n,1}{2}, origtiles{n,1}{3}, origtiles{n,1}{4}, ...
     origtiles{n,2} );
end
fprintf(f,'}\n');
fprintf(f,'binding strengths=\n{');
for i=1:M, fprintf(f,'%d ', origG(i)); end
fprintf(f,'}\n'); 
fprintf(f,'size=64\nblock=10\nseed=50,8,1\nupdate_rate=50000\nGse=9\nGmc=17.7\n');

fclose(f);


f=fopen(fname,'w');

fprintf(f,'%% %s  generated by make2x2tiles.m from %s\n', fname,oname);
fprintf(f,'tile edges matches {{N E S W}*}\n');
fprintf(f,'num tile types=%d\n', 4*N);
fprintf(f,'num binding types=%d\n', 2*M+4*N);
fprintf(f,'tile edges={\n');
for n=1:(4*N)
  fprintf(f,'{%d %d %d %d}%s \n', ...
     prooftiles{n,1}{1}, prooftiles{n,1}{2}, prooftiles{n,1}{3}, prooftiles{n,1}{4}, ...
     prooftiles{n,2} );
end
fprintf(f,'}\n');
fprintf(f,'binding strengths=\n{');
for i=1:(2*M+4*N), fprintf(f,'%d ', proofG(i)); end
fprintf(f,'}\n'); 
fprintf(f,'size=128\nblock=5\nseed=108,20,1\nupdate_rate=50000\nGse=9\nGmc=17.7\n');

fclose(f);