broke up globaldata and moved error checking and help into commands

[mothur.git] / getoturepcommand.h

diff --git a/getoturepcommand.h b/getoturepcommand.h
index 8153c3645fc5de028a6a9812426889297991ab85..f413d4f51f2a9c45e3a5d17dd0243a825eb71679 100644 (file)
--- a/getoturepcommand.h
+++ b/getoturepcommand.h
@@ -27,25 +27,29 @@ typedef list<PCell>::iterator MatData;
 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, line, label;
        ofstream out;
        ifstream in, inNames;
        bool groupError;
-       
-        
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it4;
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       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;