Added MATLAB code from original greedyMix() (#25)

R/greedyMix.R

@@ -12,6 +12,78 @@
 #' @examples
 #' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
 #' greedyMix(data)
-greedyMix <- function(data, format, verbose = TRUE) {
+greedyMix <- function(data, format, fixedK = FALSE, partition_compare = FALSE, verbose = TRUE) {
   data <- importFile(data, format, verbose)
+  if (partition_compare) {
+    # nsamplingunits = size(c.rows,1);
+    # partitions = partitionCompare.partitions;
+    # npartitions = size(partitions,2);
+    # partitionLogml = zeros(1,npartitions);
+    # for i = 1:npartitions
+    #     % number of unique partition lables
+    #     npops = length(unique(partitions(:,i)));
+
+    #     partitionInd = zeros(ninds*rowsFromInd,1);
+    #     partitionSample = partitions(:,i);
+    #     for j = 1:nsamplingunits
+    #         partitionInd([c.rows(j,1):c.rows(j,2)]) = partitionSample(j);
+    #     end
+    #     partitionLogml(i) = ...
+    #         initialCounts(partitionInd, data(:,1:end-1), npops, c.rows, noalle, adjprior);
+
+    # end
+    # % return the logml result
+    # partitionCompare.logmls = partitionLogml;
+    # set(h1, 'userdata', partitionCompare);
+    # return
+  }
+
+  if (fixedK) {
+      # [logml, npops, partitionSummary]=indMix_fixK(c);
+  } else {
+      # [logml, npops, partitionSummary]=indMix(c);
+  }
+  stopifnot(logml != 1)
+
+  # data = data(:,1:end-1);
+
+  # h0 = findobj('Tag','filename1_text');  inp = get(h0,'String');
+  # h0 = findobj('Tag','filename2_text');
+  # outp = get(h0,'String');
+  # changesInLogml = writeMixtureInfo(logml, rowsFromInd, data, adjprior, priorTerm, ...
+  #     outp,inp,partitionSummary, popnames, fixedK);
+
+  # viewMixPartition(PARTITION, popnames);
+
+  talle <- questdlg(
+    c(
+      'Do you want to save the mixture populations ',
+      'so that you can use them later in admixture analysis?'
+    ),
+    'Save results?',
+    defbtn = 'n'
+  );
+  if (talle == "y") {
+  #     [filename, pathname] = uiputfile('*.mat','Save results as');
+  #     if (sum(filename)==0) || (sum(pathname)==0)
+  #         % Cancel was pressed
+  #         return;
+  #     else
+  #         % copy 'baps4_output.baps' into the text file with the same name.
+  #         if exist('baps4_output.baps','file')
+  #         copyfile('baps4_output.baps',[pathname filename '.txt'])
+  #         delete('baps4_output.baps')
+  #         end
+  #     end;
+  #     c.PARTITION = PARTITION; c.COUNTS = COUNTS; c.SUMCOUNTS = SUMCOUNTS;
+  #     c.alleleCodes = alleleCodes; c.adjprior = adjprior; c.popnames = popnames;
+  #     c.rowsFromInd = rowsFromInd; c.data = data; c.npops = npops;
+  #     c.noalle = noalle; c.mixtureType = 'mix';
+  #     c.logml = logml; c.changesInLogml = changesInLogml;
+  #     save([pathname filename], 'c', '-v7.3'); % added by Lu Cheng, 08.06.2012
+  } else {
+  #     if exist('baps4_output.baps','file')
+  #     delete('baps4_output.baps')
+  #     end
+  }
 }