broke up globaldata and moved error checking and help into commands

[mothur.git] / binsequencecommand.h

diff --git a/binsequencecommand.h b/binsequencecommand.h
index bc2f883fe5f3e232d935780f7660e5a53647b18b..aceba65da17315de31515750a62fc53f4b7b9a48 100644 (file)
--- a/binsequencecommand.h
+++ b/binsequencecommand.h
@@ -24,9 +24,10 @@ class GlobalData;
 class BinSeqCommand : public Command {
        
 public:
-       BinSeqCommand();        
+       BinSeqCommand(string);  
        ~BinSeqCommand();
-       int execute();  
+       int execute();
+       void help();    
        
 private:
        GlobalData* globaldata;
@@ -35,7 +36,13 @@ private:
        InputData* input;
        FastaMap* fasta;
        GroupMap* groupMap;
-       string filename, fastafile, namesfile, groupfile;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string filename, fastafile, namesfile, groupfile, line, label;
        ofstream out;
        ifstream in, inNames;