added SequenceCountParser class to parse the count table by group. added count parame...

[mothur.git] / sequencecountparser.h

diff --git a/sequencecountparser.h b/sequencecountparser.h
new file mode 100644 (file)
index 0000000..4889ea6
--- /dev/null
+++ b/sequencecountparser.h
@@ -0,0 +1,59 @@
+#ifndef Mothur_sequencecountparser_h
+#define Mothur_sequencecountparser_h
+
+//
+//  sequencecountparser.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 8/7/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "mothur.h"
+#include "mothurout.h"
+#include "sequence.hpp"
+#include "counttable.h"
+
+/* This class reads a fasta and count file and parses the data by group. The countfile must contain group information.
+ 
+ Note: The sum of all the groups unique sequences will be larger than the original number of unique sequences. 
+ This is because when we parse the count file we make a unique for each group instead of 1 unique for all
+ groups. 
+ 
+ */
+
+class SequenceCountParser {
+       
+public:
+       
+    SequenceCountParser(string, string);                       //count, fasta - file mismatches will set m->control_pressed = true
+    SequenceCountParser(string, CountTable&);          //fasta, counttable - file mismatches will set m->control_pressed = true
+    ~SequenceCountParser();
+    
+    //general operations
+    int getNumGroups();
+    vector<string> getNamesOfGroups(); 
+    
+    int getNumSeqs(string);            //returns the number of unique sequences in a specific group
+    vector<Sequence> getSeqs(string); //returns unique sequences in a specific group
+    map<string, int> getCountTable(string); //returns seqName -> numberOfRedundantSeqs for a specific group - the count file format, but each line is parsed by group.
+    
+    int getSeqs(string, string, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false
+    int getCountTable(string, string); //print seqName -> numberRedundantSeqs for a specific group - group, filename
+    
+    map<string, string> getAllSeqsMap(){ return allSeqsMap; }  //returns map where the key=sequenceName and the value=representativeSequence - helps us remove duplicates after group by group processing
+private:
+       
+    CountTable countTable;
+    MothurOut* m;
+       
+    int numSeqs;
+    map<string, string> allSeqsMap;
+    map<string, vector<Sequence> > seqs; //a vector for each group
+    map<string, map<string, int> > countTablePerGroup; //countTable for each group
+    vector<string> namesOfGroups;
+};
+
+
+
+#endif