added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / matrixoutputcommand.h

diff --git a/matrixoutputcommand.h b/matrixoutputcommand.h
index 04d0ccbf8e46145591acca443d37039809da88d0..ae38b46c5c1d60a1c6c97b5a618f1eca8d59a417 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -12,36 +12,58 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readotu.h"
 #include "validcalculator.h"
 
+// aka. dist.shared()
+
 /* This command create a tree file for each similarity calculator at distance level, using various calculators to find the similiarity between groups. 
-       The user can select the lines or labels they wish to use as well as the groups they would like included.
+       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();  
        ~MatrixOutputCommand();
-       int execute();  
+       
+       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;
-       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> >&);
+
 };