changes while testing

[mothur.git] / phylosummary.h

diff --git a/phylosummary.h b/phylosummary.h
index 9ebdf81ac4fbd06490f05d7be7c15b6f6a5d1179..65a467483ddab1ae58757629644162dc83bab254 100644 (file)
--- a/phylosummary.h
+++ b/phylosummary.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "mothurout.h"
 #include "groupmap.h"
+#include "counttable.h"
 
 /**************************************************************************************************/
 
@@ -32,11 +33,15 @@ struct rawTaxNode {
 class PhyloSummary {
 
 public:
-       PhyloSummary(string, string);
-       ~PhyloSummary() { if (groupmap != NULL)  {  delete groupmap;  }  }
+       PhyloSummary(GroupMap*);
+       PhyloSummary(string, GroupMap*);
+    PhyloSummary(CountTable*);
+       PhyloSummary(string, CountTable*);
+       ~PhyloSummary() {}
        
-       void summarize(string);  //pass it a taxonomy file and a group file and it makes the tree
+       int summarize(string);  //pass it a taxonomy file and a group file and it makes the tree
        int addSeqToTree(string, string);
+       int addSeqToTree(string, map<string, bool>);
        void print(ofstream&);
        int getMaxLevel() { return maxLevel; }
        
@@ -47,6 +52,8 @@ private:
        void assignRank(int);
        void readTreeStruct(ifstream&);
        GroupMap* groupmap;
+    CountTable* ct;
+       bool ignore;
        
        int numNodes;
        int numSeqs;