moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / getlineagecommand.h

diff --git a/getlineagecommand.h b/getlineagecommand.h
deleted file mode 100644 (file)
index a677061..0000000
--- a/getlineagecommand.h
+++ /dev/null
@@ -1,51 +0,0 @@
-#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
-