*/
#include "command.hpp"
+#include "sharedrabundvector.h"
+#include "listvector.hpp"
+
class RemoveLineageCommand : public Command {
vector<string> setParameters();
string getCommandName() { return "remove.lineage"; }
string getCommandCategory() { return "Phylotype Analysis"; }
- string getHelpString();
+
+ string getHelpString();
+ string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Remove.lineage"; }
string getDescription() { return "removes sequences from a list, fasta, name, group, alignreport or taxonomy file from a given taxonomy or set of taxonomies"; }
private:
set<string> names;
vector<string> outputNames, listOfTaxons;
- string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
+ string fastafile, namefile, groupfile, alignfile, listfile, countfile, taxfile, outputDir, taxons, sharedfile, constaxonomy, label;
bool abort, dups;
+ vector<SharedRAbundVector*> lookup;
+ ListVector* list;
int readFasta();
int readName();
int readGroup();
+ int readCount();
int readAlign();
int readList();
- int readTax();
+ int readTax();
+ int readShared();
+ int readConsTax();
+ int readConsList();
+ int getShared();
+ int getListVector();
vector< map<string, float> > getTaxons(string);
};