changed sequence class so that when constructor is called aligned and unaligned value...

[mothur.git] / getsabundcommand.h

diff --git a/getsabundcommand.h b/getsabundcommand.h
index 27d25c2f2c3d2739bb6cfecd85f7b059b4867442..2612b7daa6c178f8ae0468893c49c2c9c613a38c 100644 (file)
--- a/getsabundcommand.h
+++ b/getsabundcommand.h
@@ -20,9 +20,10 @@ class GlobalData;
 
 class GetSAbundCommand : public Command {
 public:
-       GetSAbundCommand();
+       GetSAbundCommand(string);
        ~GetSAbundCommand();
        int execute();
+       void help();
        
 private:
        GlobalData* globaldata;
@@ -30,9 +31,14 @@ private:
        ofstream out;
        ReadOTUFile* read;
        OrderVector* order;
-       OrderVector* lastOrder;
        InputData* input;
        SAbundVector* sabund;
+
+       bool abort, allLines;
+       set<int> lines; //hold lines to be used
+       set<string> labels; //holds labels to be used
+       string line, label;
+
 };
 
 #endif