added formatmatrix, formatcolumn, and formatphylip classes. Used these classes in...

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 58fec8d4f3e3aaaf148a9ff8455c4fba93c6b35f..0e8a121793823677186d67e5d3cd255dd7ec47d1 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -18,6 +18,8 @@
 #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;
@@ -48,15 +50,24 @@ private:
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
-       string filename, fastafile, listfile, namesfile, groupfile, label, sorted, phylipfile, columnfile, namefile;
+       ReadMatrix* readMatrix;
+       FormatMatrix* formatMatrix;
+       NameAssignment* nameMap;
+       string filename, fastafile, listfile, namefile, groupfile, label, sorted, phylipfile, columnfile, distFile, format;
        ofstream out;
-       ifstream in, inNames;
-       bool abort, allLines, groupError;
+       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
+       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*);
+       SeqMap getMap(int);
        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