added an alignreport option to screen seqs

[mothur.git] / collectcommand.h

diff --git a/collectcommand.h b/collectcommand.h
index 64362ef61cdfdc18da9cb5b170a88ff9713d93c9..04dcc602628695c5381048dbb67f4bad8be682e3 100644 (file)
--- a/collectcommand.h
+++ b/collectcommand.h
@@ -9,16 +9,13 @@
  *
  */
 
-#include <iostream>
-#include <fstream>
-#include <vector>
 #include "command.hpp"
 #include "ordervector.hpp"
 #include "inputdata.h"
 #include "groupmap.h"
 #include "collect.h"
 #include "display.h"
-#include "readmatrix.hpp"
+#include "readotu.h"
 #include "validcalculator.h"
 
 /*The collect() command:
@@ -40,19 +37,28 @@ class GlobalData;
 class CollectCommand : public Command {
        
 public:
-       CollectCommand();       
+       CollectCommand(string); 
        ~CollectCommand();
        int execute();  
+       void help();
        
 private:
        GlobalData* globaldata;
-       ReadMatrix* read;
+       ReadOTUFile* read;
        OrderVector* order;
+       OrderVector* lastOrder;
        InputData* input;
        Collect* cCurve;
        ValidCalculators* validCalculator;
        vector<Display*> cDisplays;
-       int freq, abund;
+       int freq, abund, size;
+
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string line, label, calc;
+       vector<string>  Estimators;
+
 
 };