a few meaningless changes that are commented out

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 81b915efcbf97e4b91bfca3bf27353da8f9ea8e9..b8ab242e187b2f1b0fccc8b087e7c17f2cc0c903 100644 (file)
--- a/screenseqscommand.h
+++ b/screenseqscommand.h
@@ -17,13 +17,16 @@ 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();
+       ~ScreenSeqsCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "screen.seqs";                         }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
 
@@ -52,7 +55,8 @@ private:
        int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, criteria;
        vector<string> outputNames;
        vector<string> optimize;
-       map<string, vector<string> > outputTypes;
+       map<string, int> nameMap;
+       int readNames();
        
        int getSummary(vector<unsigned long int>&);
        int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string);