some alterations to chimera.slayer

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 1410626a42e3a407289f18565dd0e64a3d4d3cd4..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;
@@ -58,7 +59,8 @@ private:
        vector<string> candidateFileNames;
        vector<string> outputNames;
        
-       bool abort, flip;
+       bool abort, flip, calledHelp;
+
 };
 
 #endif