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[mothur.git] / getseqscommand.h

diff --git a/getseqscommand.h b/getseqscommand.h
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+#ifndef GETSEQSCOMMAND_H
+#define GETSEQSCOMMAND_H
+
+/*
+ *  getseqscommand.h
+ *  Mothur
+ *
+ *  Created by Sarah Westcott on 7/8/09.
+ *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+
+class GetSeqsCommand : public Command {
+       
+       public:
+       
+               GetSeqsCommand(string);
+               GetSeqsCommand();
+               ~GetSeqsCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.seqs";                            }
+               string getCommandCategory()             { return "Sequence Processing";         }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
+               string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport, quality or taxonomy file"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
+       private:
+               set<string> names;
+               vector<string> outputNames;
+               string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+               bool abort, dups;
+               
+               int readFasta();
+               int readName();
+               int readGroup();
+               int readAlign();
+               int readAccnos();
+               int readList();
+               int readTax();
+               int readQual();
+               int compareAccnos();
+               
+};
+
+#endif
+