moving source to source folder

[mothur.git] / source / consensusseqscommand.h

diff --git a/source/consensusseqscommand.h b/source/consensusseqscommand.h
new file mode 100644 (file)
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+++ b/source/consensusseqscommand.h
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+#ifndef CONSENSUSSEQSCOMMAND_H
+#define CONSENSUSSEQSCOMMAND_H
+//test
+/*
+ *  consensusseqscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/23/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "listvector.hpp"
+
+class ConsensusSeqsCommand : public Command {
+public:
+       ConsensusSeqsCommand(string);
+       ConsensusSeqsCommand();
+       ~ConsensusSeqsCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "consensus.seqs";              }
+       string getCommandCategory()             { return "Sequence Processing"; }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Consensus.seqs"; }
+       string getDescription()         { return "create a consensus sequence for each OTU or for a fasta file"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       
+       bool abort, allLines;
+       string fastafile, listfile, namefile, label, outputDir;
+       set<string> labels;
+       vector<string> outputNames;
+       map<string, string> fastaMap;
+       map<string, string> nameMap;
+       map<string, string> nameFileMap;
+       int cutoff;
+       
+       int readFasta();
+       int readNames();
+       int processList(ListVector*&);
+       string getConsSeq(string, ofstream&, string&, int);
+       char getBase(vector<int>, int);
+};
+
+#endif
+
+
+
+