added namefile to summary.seqs

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 58fbc0a8b4e9dddec4745f65882ac9b6b6dd8002..fb24141f08a1314a386bc58899ec57ecf6c56e56 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -16,29 +16,38 @@
 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();
        
 private:
        bool abort;
-       string fastafile, outputDir;
+       string fastafile, outputDir, namefile;
        int processors;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+       map<string, int> nameMap;
        
        struct linePair {
-               int start;
-               int num;
-               linePair(long int i, long int j) : start(i), num(j) {}
+               unsigned long int start;
+               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);
+       int readNames();
 
        #ifdef USE_MPI
-       int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<long>&);      
+       int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long int>&); 
        #endif