some changes to trim.flows

[mothur.git] / classifyotucommand.h

diff --git a/classifyotucommand.h b/classifyotucommand.h
index 1077781e59b998892d699bf09b34c897a0a15375..e81c246201f36b7904d26b702748e1ba653dff66 100644 (file)
--- a/classifyotucommand.h
+++ b/classifyotucommand.h
@@ -19,7 +19,12 @@ class ClassifyOtuCommand : public Command {
 
 public:
        ClassifyOtuCommand(string);
+       ClassifyOtuCommand();
        ~ClassifyOtuCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
 
@@ -27,19 +32,20 @@ private:
 
        ListVector* list;
        InputData* input;
-       string listfile, namefile, taxfile, label, outputDir;
+       string listfile, namefile, taxfile, label, outputDir, refTaxonomy, groupfile, basis;
        bool abort, allLines, probs;
        int cutoff;
        set<string> labels; //holds labels to be used
        vector<string> outputNames;
        map<string, string> nameMap;
        map<string, string> taxMap;
+       map<string, vector<string> > outputTypes;
 
        int readNamesFile();
        int readTaxonomyFile();
        void removeConfidences(string&);
        int process(ListVector*);
-       string findConsensusTaxonomy(int, ListVector*, int&);   // returns the name of the "representative" taxonomy of given bin
+       vector<string> findConsensusTaxonomy(int, ListVector*, int&, string&);  // returns the name of the "representative" taxonomy of given bin
        
                                                                                                
 };