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[mothur.git] / listseqscommand.h

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