working on current change

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index e23dc777689f80806a8d81e458c9acda7f3ba4aa..a52d3b189354f910c3b92cf65a24aeac4a137c68 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;
 
@@ -35,18 +33,24 @@ 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"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       void createTree();
+       int createTree();
        void printSims(ostream&);
-       void makeSimsShared();
-       void makeSimsDist();
+       int makeSimsShared();
+       int makeSimsDist();
        
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        ReadMatrix* readMatrix;
        SparseMatrix* matrix;
        NameAssignment* nameMap;
@@ -57,10 +61,9 @@ 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;
@@ -68,10 +71,10 @@ private:
        bool abort, allLines;
        set<string> labels; //holds labels to be used
        string phylipfile, columnfile, namefile, calc, groups, label, outputDir;
-       vector<string>  Estimators, Groups; //holds estimators to be used
+       vector<string>  Estimators, Groups, outputNames; //holds estimators to be used
        
        //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
-       void process(vector<SharedRAbundVector*>);
+       int process(vector<SharedRAbundVector*>);