#include "sabundvector.hpp"
#include "listvector.hpp"
#include "cluster.hpp"
-#include "sparsematrix.hpp"
+#include "sparsedistancematrix.h"
#include "readcluster.h"
#include "splitmatrix.h"
#include "readphylip.h"
vector<string> 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 getOutputPattern(string);
+ 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 77:3219. \nhttp://www.mothur.org/wiki/Cluster.split"; }
string getDescription() { return "splits your sequences by distance or taxonomy then clusters into OTUs"; }
int execute();
vector<int> processIDS; //processid
vector<string> 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;
+ bool print_start, abort, hard, large, classic, runCluster;
time_t start;
ofstream outList, outRabund, outSabund;
int mergeLists(vector<string>, map<float, int>, ListVector*);
map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
int createMergedDistanceFile(vector< map<string, string> >);
+ int createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund);
};
/////////////////not working for Windows////////////////////////////////////////////////////////////
// anything to do with mothur's use of copy constructors in many of our data structures. ie. listvector
// is copied by nameassignment and passed to read which passes to the thread? -westcott 2-8-12
////////////////////////////////////////////////////////////////////////////////////////////////////
-/**************************************************************************************************/
+/**************************************************************************************************
//custom data structure for threads to use.
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
}
};
-/**************************************************************************************************/
+/**************************************************************************************************
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
static DWORD WINAPI MyClusterThreadFunction(LPVOID lpParam){
}
#endif
-
+*/
#endif