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

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 537f7916299d36c7f628a9e7e6974821746f3b12..ae38b46c5c1d60a1c6c97b5a618f1eca8d59a417 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -12,7 +12,6 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
 // aka. dist.shared()
@@ -21,36 +20,49 @@
        The user can select the labels they wish to use as well as the groups they would like included.
        They can also use as many or as few calculators as they wish. */
        
-class GlobalData;
 
 class MatrixOutputCommand : public Command {
        
 public:
-       MatrixOutputCommand(string);    
+       MatrixOutputCommand(string);
+       MatrixOutputCommand();  
        ~MatrixOutputCommand();
-       int execute();  
-       void help();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "dist.shared";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Dist.shared"; }
+       string getDescription()         { return "generate a distance matrix that describes the dissimilarity among multiple groups"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       void printSims(ostream&);
+       struct linePair {
+               int start;
+               int end;
+       };
+       vector<linePair> lines;
+       
+       void printSims(ostream&, vector< vector<float> >&);
        int process(vector<SharedRAbundVector*>);
        
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        vector<Calculator*> matrixCalculators;
-       vector< vector<float> > simMatrix;
+       //vector< vector<float> > simMatrix;
        InputData* input;
-       ValidCalculators* validCalculator;
        vector<SharedRAbundVector*> lookup;
-       string exportFileName, output;
-       int numGroups;
+       string exportFileName, output, sharedfile;
+       int numGroups, processors;
        ofstream out;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used
        string outputFile, calc, groups, label, outputDir;
        vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
-       
+       int process(vector<SharedRAbundVector*>, string, string);
+       int driver(vector<SharedRAbundVector*>, int, int, vector< vector<seqDist> >&);
 
 };