broke up globaldata and moved error checking and help into commands

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 2cb653f790aeb970f2a8f9ba7e1122d2f8ef4c57..446be04a2a3972976b7e67aba9a97cb277d928a8 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -25,9 +25,10 @@ struct linePair {
 class DistanceCommand : public Command {
 
 public:
-       DistanceCommand();      
+       DistanceCommand(string);        
        ~DistanceCommand() {};
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -36,13 +37,19 @@ private:
        SequenceDB* seqDB;
        ofstream out, outFile;
        ifstream in;
-       string countends, phylip;
+       string countends, phylip, fastafile, calc;
        int processors;
        float cutoff;
        map<int, int> processIDS;   //end line, processid
        map<int, int>::iterator it;
        vector<linePair*> lines;
        
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it2;
+       bool abort;
+       vector<string>  Estimators; //holds estimators to be used
+       
        void appendFiles(string, string);
        void createProcesses(string);
        int driver(Dist*, SequenceDB*, int, int, string, float);