X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.h;h=e3dd214446d31d187148de2be7dbf2ffbfebe96e;hb=0cefb55a2616975bd4a144fc345693695ffc9bb6;hp=23f728755aadb4c4f878e299790ed8669790034a;hpb=e150b0b0664caec517485ee6d69dcdade6dcae77;p=mothur.git diff --git a/clustercommand.h b/clustercommand.h index 23f7287..e3dd214 100644 --- a/clustercommand.h +++ b/clustercommand.h @@ -14,7 +14,7 @@ #include "sabundvector.hpp" #include "listvector.hpp" #include "cluster.hpp" -#include "sparsematrix.hpp" +#include "sparsedistancematrix.h" /* The cluster() command: The cluster command outputs a .list , .rabund and .sabund files. @@ -34,15 +34,17 @@ public: vector setParameters(); string getCommandName() { return "cluster"; } string getCommandCategory() { return "Clustering"; } + string getOutputFileNameTag(string, string); string getHelpString(); - string getCitation() { return "http://www.mothur.org/wiki/Cluster"; } + string getCitation() { return "Schloss PD, Westcott SL (2011). Assessing and improving methods used in OTU-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. \nhttp://www.mothur.org/wiki/Cluster"; } + string getDescription() { return "cluster your sequences into OTUs using a distance matrix"; } int execute(); void help() { m->mothurOut(getHelpString()); } private: Cluster* cluster; - SparseMatrix* matrix; + SparseDistanceMatrix* matrix; ListVector* list; RAbundVector* rabund; RAbundVector oldRAbund;