#include "command.hpp"
#include "globaldata.hpp"
-#include "sparsematrix.hpp"
#include "listvector.hpp"
#include "inputdata.h"
#include "readotu.h"
#include "fastamap.h"
#include "groupmap.h"
+#include "readmatrix.hpp"
+#include "formatmatrix.h"
typedef list<PCell>::iterator MatData;
typedef map<int, float> SeqMap;
private:
GlobalData* globaldata;
- SparseMatrix* matrix;
ListVector* list;
ReadOTUFile* read;
InputData* input;
FastaMap* fasta;
GroupMap* groupMap;
- string filename, fastafile, listfile, namesfile, groupfile, label, sorted;
+ ReadMatrix* readMatrix;
+ FormatMatrix* formatMatrix;
+ NameAssignment* nameMap;
+ string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format, outputDir;
ofstream out;
- ifstream in, inNames;
- bool groupError;
-
- bool abort, allLines;
+ ifstream in, inNames, inRow;
+ bool abort, allLines, groupError, large;
set<string> labels; //holds labels to be used
map<string, int> nameToIndex; //maps sequence name to index in sparsematrix
-
+ vector<string> outputNames;
+ map<string, string> outputNameFiles;
+ float cutoff;
+ int precision;
vector<SeqMap> seqVec; // contains maps with sequence index and distance
// for all distances related to a certain sequence
-
+ vector<int> rowPositions;
void readNamesFile();
int process(ListVector*);
- string findRep(int, string&, ListVector*, int&); // returns the name of the "representative" sequence of given bin,
- // fills a string containing the groups in that bin if a groupfile is given,
- // and returns the number of sequences in the given bin
+ SeqMap getMap(int);
+ string findRep(int, ListVector*); // returns the name of the "representative" sequence of given bin
+ int processNames(string, string);
+
};