added hcluster command and fixed some bugs, namely one with smart distancing.

[mothur.git] / treegroupscommand.h

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 3f145e92b4780fa4f40a45ed1849150dafffc800..3f2822cfae2abe2929b8ac8f2b94b0e5b9236503 100644 (file)
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -34,9 +34,10 @@ typedef list<PCell>::iterator MatData;
 class TreeGroupCommand : public Command {
        
 public:
-       TreeGroupCommand();     
+       TreeGroupCommand(string);       
        ~TreeGroupCommand();
        int execute();  
+       void help();
        
 private:
        void createTree();
@@ -58,11 +59,22 @@ private:
        InputData* input;
        ValidCalculators* validCalculator;
        vector<SharedRAbundVector*> lookup;
+       string lastLabel;
        string format, outputFile, groupNames, filename;
        int numGroups;
        ofstream out;
        float precision, cutoff;
 
+       bool abort, allLines;
+       set<string> labels; //holds labels to be used
+       string phylipfile, columnfile, namefile, calc, groups, label;
+       vector<string>  Estimators, Groups; //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*>);
+       
+       
+
 };