X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.h;h=29dc69a05ad20ad7a19b7956fc3c55928ac5db35;hb=529ec122f7cac4af987e121d150b878d7c7a0d5d;hp=a82d02270ecc37f1c85e93c9fe51b70e29288081;hpb=15b252e317fde72ce0a5de8776cb88112e0ed2b6;p=mothur.git diff --git a/clustersplitcommand.h b/clustersplitcommand.h index a82d022..29dc69a 100644 --- a/clustersplitcommand.h +++ b/clustersplitcommand.h @@ -15,7 +15,7 @@ #include "sabundvector.hpp" #include "listvector.hpp" #include "cluster.hpp" -#include "sparsematrix.hpp" +#include "sparsedistancematrix.h" #include "readcluster.h" #include "splitmatrix.h" #include "readphylip.h" @@ -35,6 +35,7 @@ public: vector setParameters(); string getCommandName() { return "cluster.split"; } string getCommandCategory() { return "Clustering"; } + string getOutputFileNameTag(string, string); string getHelpString(); 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.split"; } string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; } @@ -46,7 +47,7 @@ private: vector processIDS; //processid vector outputNames; - string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile; + string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, countfile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile; double cutoff, splitcutoff; int precision, length, processors, taxLevelCutoff; bool print_start, abort, hard, large, classic; @@ -61,6 +62,7 @@ private: int mergeLists(vector, map, ListVector*); map completeListFile(vector, string, set&, ListVector*&); int createMergedDistanceFile(vector< map >); + int createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund); }; /////////////////not working for Windows////////////////////////////////////////////////////////////