changes while setting up test files

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index fb24141f08a1314a386bc58899ec57ecf6c56e56..623c3c1e8f400f4262414a5cf546143d698840e7 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -17,20 +17,20 @@ class SeqSummaryCommand : public Command {
 public:
        SeqSummaryCommand(string);
        SeqSummaryCommand();
-       ~SeqSummaryCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();
+       ~SeqSummaryCommand(){}
        
+       vector<string> setParameters();
+       string getCommandName()                 { return "summary.seqs";                        }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
 private:
        bool abort;
        string fastafile, outputDir, namefile;
        int processors;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
        map<string, int> nameMap;
        
        struct linePair {
@@ -44,7 +44,6 @@ private:
        
        int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
        int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);       
-       int readNames();
 
        #ifdef USE_MPI
        int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long int>&);