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

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 84f5f9f04d6752728c5f3bf72d5688cafd73b723..16549135aacbe25e36d89f21c503f1baae2fe659 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -29,7 +29,12 @@ class ClassifySeqsCommand : public Command {
        
 public:
        ClassifySeqsCommand(string);
+       ClassifySeqsCommand();
        ~ClassifySeqsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute(); 
        void help();    
        
@@ -45,8 +50,10 @@ private:
        vector<string> fastaFileNames;
        vector<string> namefileNames;
        vector<string> groupfileNames;
+       vector<string> outputNames;
        map<string, vector<string> > nameMap;
        map<string,  vector<string> >::iterator itNames;
+       map<string, vector<string> > outputTypes;
        
        Classify* classify;