broke up globaldata and moved error checking and help into commands

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index b5ff7825c7ae06fb8351a2ed9b398379d6abbc9a..a3ec827c80e1dfa229bf228eb45df61499aef265 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -13,20 +13,29 @@
 #include "command.hpp"
 #include "globaldata.hpp"
 
+
+
 class AlignCommand : public Command {
        
 public:
-       AlignCommand(); 
+       AlignCommand(string);   
        ~AlignCommand();
-       int execute();  
+       int execute(); 
+       void help();    
 
 private:
        GlobalData* globaldata;
-       string candidateFileName, templateFileName, distanceFileName;
+       OptionParser* parser;
+       map<string, string> parameters;
+       map<string, string>::iterator it;
+       bool abort;
+       string candidateFileName, templateFileName, distanceFileName, search, align;
        int kmerSize;
        float match, misMatch, gapOpen, gapExtend;
        ofstream out;
        ifstream in;
+       int ableToOpen;
+       
 
 };