added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / summarysharedcommand.h

diff --git a/summarysharedcommand.h b/summarysharedcommand.h
index 351b1352b7e865d8c0741ffb56875407070db344..f366d0f62432e0bc34c475b190f946a04ba26335 100644 (file)
--- a/summarysharedcommand.h
+++ b/summarysharedcommand.h
@@ -14,34 +14,44 @@
 #include "sharedrabundvector.h"
 #include "inputdata.h"
 #include "calculator.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
-class GlobalData;
-
 class SummarySharedCommand : public Command {
 
 public:
        SummarySharedCommand(string);
-       ~SummarySharedCommand();
-       int execute();
-       void help();
+       SummarySharedCommand();
+       ~SummarySharedCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "summary.shared";                      }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
+       string getDescription()         { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
        
 private:
-       GlobalData* globaldata;
-       ReadOTUFile* read;
+       struct linePair {
+               int start;
+               int end;
+       };
+       vector<linePair> lines;
        vector<Calculator*> sumCalculators;     
        InputData* input;
-       ValidCalculators* validCalculator;
        
-       bool abort, allLines, mult, all;
+       bool abort, allLines, mult, all, createPhylip;
        set<string> labels; //holds labels to be used
-       string label, calc, groups;
-       vector<string>  Estimators, Groups;
+       string label, calc, groups, sharedfile;
+       vector<string>  Estimators, Groups, outputNames;
        vector<SharedRAbundVector*> lookup;
-       string outputFileName, format, outAllFileName, outputDir;
-       ofstream outputFileHandle, outAll;
-       void process(vector<SharedRAbundVector*>);
+       string format, outputDir;
+       int numGroups, processors;
+       int process(vector<SharedRAbundVector*>, string, string);
+       int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);
 
 };