consensus.seqs summary file change

[mothur.git] / screenseqscommand.h

diff --git a/screenseqscommand.h b/screenseqscommand.h
index 071724f79cb45c69bb4c4237c072ddc462188439..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();
        
@@ -24,9 +29,10 @@ private:
 
        struct linePair {
                unsigned long int start;
-               int numSeqs;
-               linePair(unsigned long int i, int j) : start(i), numSeqs(j) {}
+               unsigned long int end;
+               linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
+
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
 
@@ -34,17 +40,23 @@ private:
        int screenGroupFile(set<string>);
        int screenAlignReport(set<string>);
        
-       int driver(linePair*, string, string, string, string, set<string>&);
-       int createProcesses(string, string, string, string, set<string>&);
+       int driver(linePair*, string, string, string, set<string>&);
+       int createProcesses(string, string, string, set<string>&);
        
        #ifdef USE_MPI
-       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&, set<string>&);
+       int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&, set<string>&);
        #endif
 
        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