1.19.0

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index b58c3f29bcc653e48c2d30fc9ae4a57344c4330e..ef5a92e4b8aad04651ded1ed8caf58dc58c16b30 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -20,9 +20,16 @@ class AlignCommand : public Command {
        
 public:
        AlignCommand(string);   
+       AlignCommand();
        ~AlignCommand();
+       
+       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 {
@@ -43,15 +50,17 @@ private:
        void appendReportFiles(string, string);
        
        #ifdef USE_MPI
-       int driverMPI(MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
        #endif
        
        string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
        float match, misMatch, gapOpen, gapExtend, threshold;
        int processors, kmerSize;
        vector<string> candidateFileNames;
+       vector<string> outputNames;
        
-       bool abort, flip;
+       bool abort, flip, calledHelp;
+
 };
 
 #endif