1 #ifndef CLUSTERSPLITCOMMAND_H
2 #define CLUSTERSPLITCOMMAND_H
5 * clustersplitcommand.h
8 * Created by westcott on 5/19/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "rabundvector.hpp"
15 #include "sabundvector.hpp"
16 #include "listvector.hpp"
17 #include "cluster.hpp"
18 #include "sparsematrix.hpp"
19 #include "globaldata.hpp"
22 class ClusterSplitCommand : public Command {
25 ClusterSplitCommand(string);
26 ~ClusterSplitCommand();
31 GlobalData* globaldata;
32 vector<int> processIDS; //processid
33 vector<string> outputNames;
35 string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
36 double cutoff, splitcutoff;
37 int precision, length, processors, taxLevelCutoff;
38 bool print_start, abort, hard, large;
40 ofstream outList, outRabund, outSabund;
42 void printData(ListVector*);
43 int createProcesses(vector < vector < map<string, string> > >);
44 vector<string> cluster(vector< map<string, string> >, set<string>&);
45 int mergeLists(vector<string>, map<float, int>, ListVector*);
46 map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);