X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=counttable.h;fp=counttable.h;h=68ba8d211cae1a12aa1d39a76f720a0998a87ad9;hb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;hp=04e26d775bb84042ea409e2d18694eeaa216c4df;hpb=f509429e06e545bde69c97cacc0eb436775bd329;p=mothur.git

diff --git a/counttable.h b/counttable.h
index 04e26d7..68ba8d2 100644
--- a/counttable.h
+++ b/counttable.h
@@ -38,36 +38,49 @@
 
 #include "mothurout.h"
 #include "listvector.hpp"
+#include "groupmap.h"
 
 class CountTable {
     
     public:
     
-        CountTable() { m = MothurOut::getInstance(); hasGroups = false; total = 0; }
+        CountTable() { m = MothurOut::getInstance(); hasGroups = false; total = 0; uniques = 0; }
         ~CountTable() {}
     
-        int readTable(string);
+        int createTable(set<string>&, map<string, string>&, set<string>&); //seqNames, seqName->group, groupNames 
+        int createTable(string, string, bool); //namefile, groupfile, createGroup
+        int readTable(string);    
+        int printTable(string);
+        int printHeaders(ofstream&);
+        int printSeq(ofstream&, string);
         bool testGroups(string file); //used to check if file has group data without reading it.
+        int copy(CountTable*);
     
         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 addGroup(string);
         
+        int renameSeq(string, string); //used to change name of sequence for use with trees
+        int setAbund(string, string, int); //set abundance number of seqs for that group for that seq
         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 remove(string); //remove seq
         int get(string); //returns unique sequence index for reading distance matrices like NameAssignment
         int size() { return indexNameMap.size(); }
     
+        vector<string> getGroups(string); //returns vector of groups represented by this sequences
         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
         int getGroupCount(string); // returns total seqs for that group
-        int getNumSeqs(string); //returns total seqs for that seq
+        int getNumSeqs(string); //returns total seqs for that seq, 0 if not found 
         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();
+        vector<string> getNamesOfSeqs(string);
         int mergeCounts(string, string); //combines counts for 2 seqs, saving under the first name passed in.
         ListVector getListVector();