1 #ifndef Mothur_counttable_h
2 #define Mothur_counttable_h
9 // Created by Sarah Westcott on 6/26/12.
10 // Copyright (c) 2012 Schloss Lab. All rights reserved.
13 //This class is designed to read a count table file and store its data.
14 //count table files look like:
17 Representative_Sequence total F003D000 F003D002 F003D004 F003D006 F003D008 F003D142 F003D144 F003D146 F003D148 F003D150 MOCK.GQY1XT001
18 GQY1XT001C296C 6051 409 985 923 937 342 707 458 439 387 464 0
19 GQY1XT001A3TJI 4801 396 170 413 442 306 769 581 576 497 651 0
20 GQY1XT001CS2B8 3018 263 226 328 460 361 336 248 290 187 319 0
21 GQY1XT001CD9IB 2736 239 177 256 405 306 286 263 248 164 392 0
23 or if no group info was used to create it
25 Representative_Sequence total
39 #include "mothurout.h"
40 #include "listvector.hpp"
47 CountTable() { m = MothurOut::getInstance(); hasGroups = false; total = 0; uniques = 0; }
50 int createTable(set<string>&, map<string, string>&, set<string>&); //seqNames, seqName->group, groupNames
51 int createTable(string, string, bool); //namefile, groupfile, createGroup
52 int readTable(string);
53 int printTable(string);
54 int printHeaders(ofstream&);
55 int printSeq(ofstream&, string);
56 bool testGroups(string file); //used to check if file has group data without reading it.
57 int copy(CountTable*);
59 bool hasGroupInfo() { return hasGroups; }
60 int getNumGroups() { return groups.size(); }
61 vector<string> getNamesOfGroups() { return groups; } //returns group names, if no group info vector is blank.
64 int renameSeq(string, string); //used to change name of sequence for use with trees
65 int setAbund(string, string, int); //set abundance number of seqs for that group for that seq
66 int push_back(string); //add a sequence
67 int push_back(string, int); //add a sequence
68 int push_back(string, vector<int>); //add a sequence with group info
69 int remove(string); //remove seq
70 int get(string); //returns unique sequence index for reading distance matrices like NameAssignment
71 int size() { return indexNameMap.size(); }
73 vector<string> getGroups(string); //returns vector of groups represented by this sequences
74 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.
75 int getGroupCount(string, string); //returns number of seqs for that group for that seq
76 int getGroupCount(string); // returns total seqs for that group
77 int getNumSeqs(string); //returns total seqs for that seq, 0 if not found
78 int getNumSeqs() { return total; } //return total number of seqs
79 int getNumUniqueSeqs() { return uniques; } //return number of unique/representative seqs
80 int getGroupIndex(string); //returns index in getGroupCounts vector of specific group
82 vector<string> getNamesOfSeqs();
83 vector<string> getNamesOfSeqs(string);
84 int mergeCounts(string, string); //combines counts for 2 seqs, saving under the first name passed in.
85 ListVector getListVector();
92 vector<string> groups;
93 vector< vector<int> > counts;
95 vector<int> totalGroups;
96 map<string, int> indexNameMap;
97 map<string, int> indexGroupMap;