added shared file type to get.groups and remove.groups

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index a62572673c3d7497007ab959157fd41dfb6b124b..c0d368770cfa8df11560d2b89fee200231cb0dc3 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -16,26 +16,36 @@
 class SeqSummaryCommand : public Command {
 public:
        SeqSummaryCommand(string);
-       ~SeqSummaryCommand();
-       int execute();
-       void help();
+       SeqSummaryCommand();
+       ~SeqSummaryCommand(){}
        
+       vector<string> setParameters();
+       string getCommandName()                 { return "summary.seqs";                        }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
+       string getDescription()         { return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }          
 private:
        bool abort;
-       string fastafile, outputDir;
+       string fastafile, outputDir, namefile;
        int processors;
+       vector<string> outputNames;
+       map<string, int> nameMap;
        
        struct linePair {
                unsigned long int start;
-               int num;
-               linePair(unsigned long int i, long int j) : start(i), num(j) {}
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
+
        vector<linePair*> lines;
        vector<int> processIDS;
        
        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 setLines(string);
 
        #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>&);