From 2d5ce7564d6238dc643f5166c8e1209df45d466e Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Thu, 8 Aug 2024 13:02:15 +0200
Subject: [PATCH] Replaced dialog windows with console inputs (#8)

---
 greedyMix/process_FASTA_data.m | 14 +++++-------
 spatial/handleIndiFastaCase.m  | 41 ++++++++++++++++------------------
 2 files changed, 24 insertions(+), 31 deletions(-)

diff --git a/greedyMix/process_FASTA_data.m b/greedyMix/process_FASTA_data.m
index e5d71fd..a6793ea 100644
--- a/greedyMix/process_FASTA_data.m
+++ b/greedyMix/process_FASTA_data.m
@@ -36,15 +36,13 @@
   clear h0; clear inp;
   clear file; clear filename2; clear pathname1; clear pathname2;
 
-  input_pops = questdlg(['When using data which are in FASTA-format, '...
+  input_pops = input(['When using data which are in FASTA-format, '...
   'you can specify the sampling populations of the individuals by '...
   'giving two additional files: one containing the names of the '...
   'populations, the other containing the indices of the first '...
   'individuals of the populations. Do you wish to specify the '...
-  'sampling populations?'], ...
-  'Specify sampling populations?',...
-  'Yes', 'No', 'No');
-  if isequal(input_pops,'Yes')
+  'sampling populations? (y/N)'], 's');
+  if isequal(input_pops,'y')
     [namefile, namepath] = uigetfile('*.txt', 'Load population names');
     if namefile==0
       kysyToinen = 0;
@@ -79,10 +77,8 @@
   cc.coordinates = coordinates;
   format_type = 'FASTA';
 
-  save_preproc = questdlg('Do you wish to save pre-processed data?',...
-  'Save pre-processed data?',...
-  'Yes','No','Yes');
-  if isequal(save_preproc,'Yes')
+  save_preproc = input('Do you wish to save pre-processed data? (y/N)', 's');
+  if isequal(save_preproc,'y')
     [filename, pathname] = uiputfile('*.mat','Save pre-processed data as');
     kokonimi = [pathname filename];
     save(kokonimi,'cc','dist','Z','format_type','-v7.3'); % added by Lu Cheng, 08.06.2012
diff --git a/spatial/handleIndiFastaCase.m b/spatial/handleIndiFastaCase.m
index da1424d..0871b72 100644
--- a/spatial/handleIndiFastaCase.m
+++ b/spatial/handleIndiFastaCase.m
@@ -4,10 +4,9 @@ function handleIndiFastaCase(cc,dist,Z)
 
 OUTPUT_FILE = 'baps6_output.baps';
 
-teksti = 'Input upper bound to the number of populations (only one value): ';
-npopstextExtra = inputdlg(teksti ,'Input maximum number of populations',1,{'20'});
+npopstextExtra = input('Input maximum number of populations', 's');
 if isempty(npopstextExtra)  % Painettu Cancel:ia
-    return
+    nMaxPops = 20;
 else
     nMaxPops = str2num(npopstextExtra{1});
     nMaxPops = nMaxPops(1);
@@ -75,16 +74,15 @@ function handleIndiFastaCase(cc,dist,Z)
        names{i} = namesInCell;
    end
 end
-vorPlot(vorPoints, vorCells, partition, pointers, coordinates, names);    
+vorPlot(vorPoints, vorCells, partition, pointers, coordinates, names);
 
-talle = questdlg(['Do you want to save the mixture populations ' ...
+talle = input(['Do you want to save the mixture populations ' ...
     'so that you can use them later in admixture analysis or plot ' ...
-    'additional images?'], ...
-    'Save results?','Yes','No','Yes');
-if isequal(talle,'Yes')
+    'additional images? (y/N) '], 's');
+if isequal(talle,'y')
     %%waitALittle;    % Hetki odotusta, jotta muistaa kysy?..
     [filename, pathname] = uiputfile('*.mat','Save results as');
-    
+
     if (filename == 0) & (pathname == 0)
         % Cancel was pressed
         return
@@ -94,7 +92,7 @@ function handleIndiFastaCase(cc,dist,Z)
             delete(OUTPUT_FILE)
         end
     end
-       
+
     %  added by Lu Cheng, 05.12.2012
     tmpFile = [pathname filename '.mapfile.txt'];
     fid = fopen(tmpFile,'w+');
@@ -111,7 +109,7 @@ function handleIndiFastaCase(cc,dist,Z)
         end
     end
     fclose(fid);
-    
+
 %     save([pathname filename], 'c');
     format_type = 'FASTA';
     save([pathname filename], 'cc','dist','Z','format_type','-v7.3');
@@ -168,20 +166,20 @@ function writeMixtureInfo(c)
 end
 for m=1:npops
     indsInM = find(partition==m);
-    
+
     if isempty(indsInM)
         continue;
     end
-    
+
     length_of_beginning = 11 + floor(log10(m));
     cluster_size = length(indsInM);
-    
+
     text = ['Cluster ' num2str(m) ': {' char(popnames{indsInM(1)})];
     for k = 2:cluster_size
         text = [text ', ' char(popnames{indsInM(k)})];
     end;
     text = [text '}'];
-    
+
     while length(text)>58
         %Take one line and display it.
         new_line = takeLine(text,58);
@@ -196,7 +194,7 @@ function writeMixtureInfo(c)
             text = [];
         end;
     end;
-    
+
     if ~isempty(text)
         disp(text);
         if (fid ~= -1)
@@ -214,7 +212,7 @@ function writeMixtureInfo(c)
     disp(' ');
     disp(' ');
     disp('Changes in log(marginal likelihood) if indvidual i is moved to cluster j:');
-        
+
     if (fid ~= -1)
         fprintf(fid, '%s \n', ' '); fprintf(fid, '\n');
         fprintf(fid, '%s \n', 'Changes in log(marginal likelihood) if indvidual i is moved to cluster j:'); fprintf(fid, '\n');
@@ -225,19 +223,19 @@ function writeMixtureInfo(c)
         tmpstr = sprintf('\t%10s',num2str(ii));
         text = [text tmpstr];
     end
-    
+
     disp(text);
     if (fid ~= -1)
         fprintf(fid, '%s \n', text);
     end
-        
+
     for ii = 1:ninds
         text = sprintf('%10s',popnames{ii});
         for jj = 1:npops
             tmpstr = sprintf('\t%10s',num2str(logmldiff(ii,jj),'%10.6f'));
             text = [text tmpstr];
         end
-        
+
         if ii<100
             disp(text);
         elseif ii==101
@@ -246,7 +244,7 @@ function writeMixtureInfo(c)
         end
         if (fid ~= -1)
             fprintf(fid, '%s \n', text);
-        end   
+        end
         text = [];
     end
 end
@@ -304,4 +302,3 @@ function writeMixtureInfo(c)
     n = n+1;
 end;
 newline = description(1:n);
-