removed read.dist, read.otu, read.tree and globaldata. added current to defaults...

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 169b43512375aef99a22029b35425d87d6360afb..ef5a92e4b8aad04651ded1ed8caf58dc58c16b30 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -22,12 +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 {
@@ -38,7 +40,6 @@ private:
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        bool MPIWroteAccnos;
-       map<string, vector<string> > outputTypes;
        
        AlignmentDB* templateDB;
        Alignment* alignment;