From c24be04180aacf08ce518d02a5402d23e53d0b73 Mon Sep 17 00:00:00 2001 From: Sarah Westcott Date: Mon, 30 Apr 2012 11:19:07 -0400 Subject: [PATCH] changes while testing --- treegroupscommand.cpp | 2 +- trialSwap2.cpp | 22 ---------------------- 2 files changed, 1 insertion(+), 23 deletions(-) diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp index 3eeeae2..2542431 100644 --- a/treegroupscommand.cpp +++ b/treegroupscommand.cpp @@ -27,7 +27,7 @@ vector 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 c580436..9a5232b 100644 --- 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 > &co_matrix){ try { -- 2.39.2