X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classifytreecommand.h;h=ef180babdf12e2a3640ea6157d64b91fe4cc9268;hp=30957af065686f1f8958f7ea84d4be49c187debe;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=d2390ede25cc211f95f99e377d5654bad7e6950e

diff --git a/classifytreecommand.h b/classifytreecommand.h
index 30957af..ef180ba 100644
--- a/classifytreecommand.h
+++ b/classifytreecommand.h
@@ -12,6 +12,7 @@
 #include "command.hpp"
 #include "readtree.h"
 #include "treemap.h"
+#include "counttable.h"
 
 class ClassifyTreeCommand : public Command {
 public:
@@ -22,7 +23,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "classify.tree";				}
 	string getCommandCategory()		{ return "Phylotype Analysis";          }
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Classify.tree"; }
 	string getDescription()		{ return "Find the consensus taxonomy for the descendant of each tree node"; }
     
@@ -30,19 +33,18 @@ public:
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	string treefile, taxonomyfile, groupfile, namefile, outputDir;
+	string treefile, taxonomyfile, groupfile, namefile, countfile, outputDir;
 	bool abort;
 	vector<string> outputNames;
     int numUniquesInName, cutoff;
     map<string, string> nameMap;
     map<string, int> nameCount;
     map<string, string> taxMap;
+    CountTable* ct;
 	
 	int getClassifications(Tree*&);
 	map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);
     string getTaxonomy(set<string>, int&);
-    int readNamesFile(); 
-    int readTaxonomyFile();
 	
 };