removed line option

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 8153c3645fc5de028a6a9812426889297991ab85..a48cbf1d7fd195264dacf9c43ee12b27867a8ff4 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -20,40 +20,43 @@
 #include "fastamap.h"
 #include "groupmap.h"
 
-class GlobalData;
-
 typedef list<PCell>::iterator MatData;
+typedef map<int, float> SeqMap;
 
 class GetOTURepCommand : public Command {
-       
+
 public:
-       GetOTURepCommand();     
+       GetOTURepCommand(string);
        ~GetOTURepCommand();
-       int execute();  
-       
+       int execute();
+       void help();
+
 private:
        GlobalData* globaldata;
        SparseMatrix* matrix;
        ListVector* list;
-       ListVector* listOfNames;
        ReadOTUFile* read;
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
-       string filename, fastafile, namesfile, groupfile;
+       string filename, fastafile, listfile, namesfile, groupfile, label;
        ofstream out;
        ifstream in, inNames;
        bool groupError;
-       
-        
+
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
        map<string, int> nameToIndex;  //maps sequence name to index in sparsematrix
-       map<int, string>::iterator it;
-       map<int, string>::iterator it2;
-       map<string, int>::iterator it3;
-       
+
+       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*); // returns name of "representative" sequence of given bin. //and fill a string containing the groups in that bin if a groupfile is given
+       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
 
 };