fixing bugs while testing

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index d519e9154fecadd04d3e535c3cfe6916e03cabba..ef5a92e4b8aad04651ded1ed8caf58dc58c16b30 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -15,7 +15,6 @@
 #include "database.hpp"
 #include "alignment.hpp"
 #include "alignmentdb.h"
-#include "mothurfiles.h"
 
 class AlignCommand : public Command {
        
@@ -23,12 +22,14 @@ public:
        AlignCommand(string);   
        AlignCommand();
        ~AlignCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "align.seqs";                  }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       
        int execute(); 
-       void help();    
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        struct linePair {
@@ -39,7 +40,6 @@ private:
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        bool MPIWroteAccnos;
-       map<string, vector<string> > outputTypes;
        
        AlignmentDB* templateDB;
        Alignment* alignment;
@@ -60,7 +60,6 @@ private:
        vector<string> outputNames;
        
        bool abort, flip, calledHelp;
-       CurrentFile* currentFiles;
 
 };