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

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 2c31ba2245b523b7f18c0a3559ee9cd6f85890df..81b915efcbf97e4b91bfca3bf27353da8f9ea8e9 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -16,7 +16,12 @@ class ScreenSeqsCommand : public Command {
        
 public:
        ScreenSeqsCommand(string);
+       ScreenSeqsCommand();
        ~ScreenSeqsCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
@@ -44,8 +49,14 @@ private:
 
        bool abort;
        string fastafile, namefile, groupfile, alignreport, outputDir;
-       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
+       int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
        vector<string> outputNames;
+       vector<string> optimize;
+       map<string, vector<string> > outputTypes;
+       
+       int getSummary(vector<unsigned long int>&);
+       int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);
+       int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, linePair*);       
 };
 
 #endif