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"
21 class ClusterSplitCommand : public Command {
24 ClusterSplitCommand(string);
25 ClusterSplitCommand();
26 ~ClusterSplitCommand() {}
28 vector<string> setParameters();
29 string getCommandName() { return "cluster.split"; }
30 string getCommandCategory() { return "Clustering"; }
31 string getHelpString();
34 void help() { m->mothurOut(getHelpString()); }
37 vector<int> processIDS; //processid
38 vector<string> outputNames;
40 string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
41 double cutoff, splitcutoff;
42 int precision, length, processors, taxLevelCutoff;
43 bool print_start, abort, hard, large;
45 ofstream outList, outRabund, outSabund;
47 void printData(ListVector*);
48 int createProcesses(vector < vector < map<string, string> > >);
49 vector<string> cluster(vector< map<string, string> >, set<string>&);
50 int mergeLists(vector<string>, map<float, int>, ListVector*);
51 map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
52 int createMergedDistanceFile(vector< map<string, string> >);