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 2871d5e31511572ad30fd9a19f28e50ae4c8bb67..ae38b46c5c1d60a1c6c97b5a618f1eca8d59a417 100644 (file)
--- a/matrixoutputcommand.h
+++ b/matrixoutputcommand.h
@@ -32,26 +32,38 @@ public:
        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*>);
        
        vector<Calculator*> matrixCalculators;
-       vector< vector<float> > simMatrix;
+       //vector< vector<float> > simMatrix;
        InputData* input;
        vector<SharedRAbundVector*> lookup;
        string exportFileName, output, sharedfile;
-       int numGroups;
+       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> >&);
+
 };