mods to trim.seqs

[mothur.git] / collectsharedcommand.h

diff --git a/collectsharedcommand.h b/collectsharedcommand.h
index e8b7b96a608453f5c5c7c6e510cd9b96bacd661b..327ce5d28832dbe7f25d69f6c0755f6e931c747d 100644 (file)
--- a/collectsharedcommand.h
+++ b/collectsharedcommand.h
@@ -27,7 +27,12 @@ class CollectSharedCommand : public Command {
        
 public:
        CollectSharedCommand(string);   
+       CollectSharedCommand(); 
        ~CollectSharedCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();  
        void help();
        
@@ -42,13 +47,14 @@ private:
        ValidCalculators* validCalculator;
        Collect* cCurve;
        vector<Display*> cDisplays;
-       int freq;
+       float freq;
        string format;
 
-       bool abort, allLines;
+       bool abort, allLines, all;
        set<string> labels; //holds labels to be used
-       string label, calc, groups;
-       vector<string>  Estimators, Groups;
+       string label, calc, groups, outputDir;
+       vector<string>  Estimators, Groups, outputNames;
+       map<string, vector<string> > outputTypes;
 
 
 };