--- /dev/null
+#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
+