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();
27 ~ClusterSplitCommand();
28 vector<string> getRequiredParameters();
29 vector<string> getValidParameters();
30 vector<string> getRequiredFiles();
31 map<string, vector<string> > getOutputFiles() { return outputTypes; }
36 GlobalData* globaldata;
37 vector<int> processIDS; //processid
38 vector<string> outputNames;
39 map<string, vector<string> > outputTypes;
41 string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile;
42 double cutoff, splitcutoff;
43 int precision, length, processors, taxLevelCutoff;
44 bool print_start, abort, hard, large;
46 ofstream outList, outRabund, outSabund;
48 void printData(ListVector*);
49 int createProcesses(vector < vector < map<string, string> > >);
50 vector<string> cluster(vector< map<string, string> >, set<string>&);
51 int mergeLists(vector<string>, map<float, int>, ListVector*);
52 map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
53 int createMergedDistanceFile(vector< map<string, string> >);