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

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 3e8fbb01c4df3c34540a11342a5a960a03788145..d2d6c721c72fcc5d96926fc246c31e89743dca58 100644 (file)
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -13,7 +13,6 @@
 #include "command.hpp"
 #include "inputdata.h"
 #include "groupmap.h"
-#include "readotu.h"
 #include "validcalculator.h"
 #include "tree.h"
 #include "treemap.h"
@@ -27,7 +26,6 @@
        The user can select the lines or 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;
 
 typedef list<PCell>::iterator MatData;
 
@@ -35,9 +33,19 @@ class TreeGroupCommand : public Command {
        
 public:
        TreeGroupCommand(string);       
+       TreeGroupCommand();
        ~TreeGroupCommand();
-       int execute();  
-       void help();
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "tree.shared";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
+       string getDescription()         { return "generate a tree file that describes the dissimilarity among groups"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        int createTree();
@@ -45,8 +53,6 @@ private:
        int makeSimsShared();
        int makeSimsDist();
        
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        ReadMatrix* readMatrix;
        SparseMatrix* matrix;
        NameAssignment* nameMap;
@@ -57,10 +63,9 @@ private:
        vector< vector<float> > simMatrix;
        map<int, int> index;  //maps row in simMatrix to vector index in the tree       
        InputData* input;
-       ValidCalculators* validCalculator;
        vector<SharedRAbundVector*> lookup;
        string lastLabel;
-       string format, outputFile, groupNames, filename;
+       string format, outputFile, groupNames, filename, sharedfile, inputfile;
        int numGroups;
        ofstream out;
        float precision, cutoff;