fixes while testing 1.33.0

[mothur.git] / phylosummary.h

diff --git a/phylosummary.h b/phylosummary.h
index 04ba65f8ad6c93a5db879a323a2a6b6ed890a3c5..4d3464f70472cdd2d2f8575934fcb96f6efbb3e5 100644 (file)
--- a/phylosummary.h
+++ b/phylosummary.h
@@ -13,6 +13,7 @@
 #include "mothur.h"
 #include "mothurout.h"
 #include "groupmap.h"
+#include "counttable.h"
 
 /**************************************************************************************************/
 
@@ -32,24 +33,29 @@ struct rawTaxNode {
 class PhyloSummary {
 
 public:
-       PhyloSummary(string);
-       PhyloSummary(string, string);
-       ~PhyloSummary() { if (groupmap != NULL)  {  delete groupmap;  }  }
+       PhyloSummary(GroupMap*, bool);
+       PhyloSummary(string, GroupMap*, bool);
+    PhyloSummary(CountTable*, bool);
+       PhyloSummary(string, CountTable*, bool);
+       ~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, vector<string>);
+       int addSeqToTree(string, map<string, bool>);
        void print(ofstream&);
+    void print(ofstream&, bool);
        int getMaxLevel() { return maxLevel; }
        
 private:
        string getNextTaxon(string&);
        vector<rawTaxNode> tree;
        void print(int, ofstream&);
+    void print(int, ofstream&, bool);
        void assignRank(int);
        void readTreeStruct(ifstream&);
        GroupMap* groupmap;
-       bool ignore;
+    CountTable* ct;
+       bool ignore, relabund;
        
        int numNodes;
        int numSeqs;