added pca command

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index d92df1a4045adbabd768210a628353d9b61383b3..58fec8d4f3e3aaaf148a9ff8455c4fba93c6b35f 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -13,7 +13,6 @@
 
 #include "command.hpp"
 #include "globaldata.hpp"
-#include "sparsematrix.hpp"
 #include "listvector.hpp"
 #include "inputdata.h"
 #include "readotu.h"
@@ -44,25 +43,18 @@ public:
 
 private:
        GlobalData* globaldata;
-       SparseMatrix* matrix;
        ListVector* list;
        ReadOTUFile* read;
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
-       string filename, fastafile, listfile, namesfile, groupfile, label, sorted;
+       string filename, fastafile, listfile, namesfile, groupfile, label, sorted, phylipfile, columnfile, namefile;
        ofstream out;
        ifstream in, inNames;
-       bool groupError;
-
-       bool abort, allLines;
+       bool abort, allLines, groupError;
        set<string> labels; //holds labels to be used
        map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
 
-       vector<SeqMap> seqVec;                  // contains maps with sequence index and distance
-                                                                       // for all distances related to a certain sequence
-
-
        void readNamesFile();
        int process(ListVector*);
        string findRep(int, string&, ListVector*, int&);        // returns the name of the "representative" sequence of given bin,