added pipeline commands which involved change to command factory and command class...

[mothur.git] / aligncommand.h

diff --git a/aligncommand.h b/aligncommand.h
index 1167c938708bcce7bb54755229bfceef00379822..1410626a42e3a407289f18565dd0e64a3d4d3cd4 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;
@@ -50,6 +56,7 @@ private:
        float match, misMatch, gapOpen, gapExtend, threshold;
        int processors, kmerSize;
        vector<string> candidateFileNames;
+       vector<string> outputNames;
        
        bool abort, flip;
 };