added countable class to read and store count file. added count parameter to make...

[mothur.git] / counttable.h

diff --git a/counttable.h b/counttable.h
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+#ifndef Mothur_counttable_h
+#define Mothur_counttable_h
+
+
+//
+//  counttable.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 6/26/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+//This class is designed to read a count table file and store its data.
+//count table files look like:
+
+/*
+ Representative_Sequence       total   F003D000        F003D002        F003D004        F003D006        F003D008        F003D142        F003D144        F003D146        F003D148        F003D150        MOCK.GQY1XT001  
+ GQY1XT001C296C        6051    409     985     923     937     342     707     458     439     387     464     0       
+ GQY1XT001A3TJI        4801    396     170     413     442     306     769     581     576     497     651     0       
+ GQY1XT001CS2B8        3018    263     226     328     460     361     336     248     290     187     319     0       
+ GQY1XT001CD9IB        2736    239     177     256     405     306     286     263     248     164     392     0       
+ 
+ or if no group info was used to create it
+ 
+ Representative_Sequence       total   
+ GQY1XT001C296C        6051
+ GQY1XT001A3TJI        4801
+ GQY1XT001CS2B8        3018
+ GQY1XT001CD9IB        2736
+ GQY1XT001ARCB1        2183
+ GQY1XT001CNF2P        2796
+ GQY1XT001CJMDA        1667
+ GQY1XT001CBVJB        3758
+ 
+ 
+ */
+
+
+#include "mothurout.h"
+
+class CountTable {
+    
+    public:
+    
+        CountTable() { m = MothurOut::getInstance(); hasGroups = false; total = 0; }
+        ~CountTable() {}
+    
+        int readTable(string);
+    
+        bool hasGroupInfo() { return hasGroups; }
+        int getNumGroups() { return groups.size(); }
+        vector<string> getNamesOfGroups() {  return groups;   }  //returns group names, if no group info vector is blank.
+    
+        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() { 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();
+    
+    private:
+        string filename;
+        MothurOut* m;
+        bool hasGroups;
+        int total, uniques;
+        vector<string> groups;
+        vector< vector<int> > counts;
+        vector<int> totals;
+        vector<int> totalGroups;
+        map<string, int> indexNameMap;
+        map<string, int> indexGroupMap;
+    
+};
+
+#endif