reworked amova / homova / anosim

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index b58c3f29bcc653e48c2d30fc9ae4a57344c4330e..169b43512375aef99a22029b35425d87d6360afb 100644 (file)
--- a/aligncommand.h
+++ b/aligncommand.h
@@ -20,7 +20,12 @@ class AlignCommand : public Command {
        
 public:
        AlignCommand(string);   
+       AlignCommand();
        ~AlignCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute(); 
        void help();    
        
@@ -33,6 +38,7 @@ private:
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        bool MPIWroteAccnos;
+       map<string, vector<string> > outputTypes;
        
        AlignmentDB* templateDB;
        Alignment* alignment;
@@ -43,15 +49,17 @@ 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