changes while testing

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 3eeeae292e674dbc7823522ce8e35d8d531ab70e..2542431f111f85b5bc344d93388662364045a509 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -27,7 +27,7 @@ vector<string> TreeGroupCommand::setParameters(){
                CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
                
         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-        CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
+//CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
                

diff --git a/trialSwap2.cpp b/trialSwap2.cpp
index c580436b3b3d542150502d2b771f426bc4aed8a7..9a5232b526851d704ac9e7d738cf18a4f6326945 100644 (file)
--- a/trialSwap2.cpp
+++ b/trialSwap2.cpp
@@ -4,28 +4,6 @@
 //The sum_of_squares, havel_hakimi and calc_c_score algorithms have been adapted from I. Miklos and J. Podani. 2004. Randomization of presence-absence matrices: comments and new algorithms. Ecology 85:86-92.
 
 
-/**************************************************************************************************
-int TrialSwap2::intrand(int n){
-    try {
-        double z;
-        
-        z = (double)random() * (double)n / (double)RAND_MAX;
-        if(z>=n)
-            z=n-1;
-        if(z<0)
-            z=0;
-        return((int)floor(z));
-    }
-       catch(exception& e) {
-               m->errorOut(e, "TrialSwap2", "intrand");
-               exit(1);
-       }
-}
-/**************************************************************************************************/
-/* completely random matrix, all column and row totals are variable, matrix size is the same
- *
- *
- */
 /**************************************************************************************************/
 int TrialSwap2::sim1(vector<vector<int> > &co_matrix){ 
     try {