working on current change

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index c61c9fbfa63bf84a2482955ca20aa914f89b9400..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;
 
@@ -37,12 +35,15 @@ public:
        TreeGroupCommand(string);       
        TreeGroupCommand();
        ~TreeGroupCommand();
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       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:
        int createTree();
@@ -50,8 +51,6 @@ private:
        int makeSimsShared();
        int makeSimsDist();
        
-       GlobalData* globaldata;
-       ReadOTUFile* read;
        ReadMatrix* readMatrix;
        SparseMatrix* matrix;
        NameAssignment* nameMap;
@@ -62,14 +61,12 @@ 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;
-       map<string, vector<string> > outputTypes;
 
        bool abort, allLines;
        set<string> labels; //holds labels to be used