paralellized seq.error and dist.shared added some error checks to libshuff and dist...

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 521104c395382d5ce15c61f99510c830ae054f7a..b42cfb92c62a74fdb55b7902c3bfa9644c7359f7 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 +20,47 @@
        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"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       void printSims(ostream&);
-       void process(vector<SharedRAbundVector*>);
+       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> >&);
 
 };