Revert to previous commit

[mothur.git] / getlineagecommand.h

diff --git a/getlineagecommand.h b/getlineagecommand.h
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+#ifndef GETLINEAGECOMMAND_H
+#define GETLINEAGECOMMAND_H
+
+/*
+ *  getlineagecommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/24/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+ 
+#include "command.hpp"
+
+class GetLineageCommand : public Command {
+       
+       public:
+       
+               GetLineageCommand(string);
+               GetLineageCommand();
+               ~GetLineageCommand(){}
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "get.lineage";                         }
+               string getCommandCategory()             { return "Phylotype Analysis";          }
+               string getHelpString(); 
+               string getCitation() { return "http://www.mothur.org/wiki/Get.lineage"; }
+               string getDescription()         { return "gets sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
+
+       
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
+       
+       private:
+               set<string> names;
+               vector<string> outputNames, listOfTaxons;
+               string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+               bool abort, dups;
+               
+               int readFasta();
+               int readName();
+               int readGroup();
+               int readAlign();
+               int readList();
+               int readTax();  
+               vector< map<string, float> > getTaxons(string);
+};
+
+#endif
+