added count file to chimera.uchime. found issue with uchime program that indicated...

[mothur.git] / counttable.h

diff --git a/counttable.h b/counttable.h
index ffc08167682bf8aa9f1a4a42267a90d666376250..04e26d775bb84042ea409e2d18694eeaa216c4df 100644 (file)
--- a/counttable.h
+++ b/counttable.h
@@ -37,6 +37,7 @@
 
 
 #include "mothurout.h"
+#include "listvector.hpp"
 
 class CountTable {
     
@@ -46,10 +47,17 @@ class CountTable {
         ~CountTable() {}
     
         int readTable(string);
+        bool testGroups(string file); //used to check if file has group data without reading it.
     
         bool hasGroupInfo() { return hasGroups; }
         int getNumGroups() { return groups.size(); }
         vector<string> getNamesOfGroups() {  return groups;   }  //returns group names, if no group info vector is blank.
+        
+        int push_back(string); //add a sequence 
+        int push_back(string, int); //add a sequence 
+        int push_back(string, vector<int>); //add a sequence with group info
+        int get(string); //returns unique sequence index for reading distance matrices like NameAssignment
+        int size() { return indexNameMap.size(); }
     
         vector<int> getGroupCounts(string);  //returns group counts for a seq passed in, if no group info is in file vector is blank. Order is the same as the groups returned by getGroups function.
         int getGroupCount(string, string); //returns number of seqs for that group for that seq
@@ -58,8 +66,10 @@ class CountTable {
         int getNumSeqs() { return total; } //return total number of seqs
         int getNumUniqueSeqs() { return uniques; } //return number of unique/representative seqs
         int getGroupIndex(string); //returns index in getGroupCounts vector of specific group
+    
         vector<string> getNamesOfSeqs();
         int mergeCounts(string, string); //combines counts for 2 seqs, saving under the first name passed in.
+        ListVector getListVector();
     
     private:
         string filename;