X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=counttable.h;fp=counttable.h;h=8c970199babf9d45f3a624d3456d39732fc3e5e2;hb=fdfbfe59134dd7dd3e49d90609d129128ba2d370;hp=0000000000000000000000000000000000000000;hpb=2ecee16fec29d4c525f740ec19b27962ca09c050;p=mothur.git

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