merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / distancecommand.h

diff --git a/distancecommand.h b/distancecommand.h
index 446be04a2a3972976b7e67aba9a97cb277d928a8..6a7ac93fa1d7b28d9fe03e1e27f1e4a1ec3ef491 100644 (file)
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -12,47 +12,40 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
 #include "validcalculator.h"
 #include "dist.h"
 #include "sequencedb.h"
 
-struct linePair {
-       int start;
-       int end;
-};
 
 class DistanceCommand : public Command {
 
 public:
        DistanceCommand(string);        
-       ~DistanceCommand() {};
+       ~DistanceCommand();
        int execute();  
        void help();
        
 private:
-       GlobalData* globaldata;
-       ValidCalculators* validCalculator;
+       struct linePair {
+               int start;
+               int end;
+       };
+       
        Dist* distCalculator;
-       SequenceDB* seqDB;
-       ofstream out, outFile;
-       ifstream in;
+       SequenceDB alignDB;
+
        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);
+       int driver(/*Dist*, SequenceDB, */int, int, string, float);
 
 };