GetLineageCommand(string);
GetLineageCommand();
- ~GetLineageCommand(){};
- vector<string> getRequiredParameters();
- vector<string> getValidParameters();
- vector<string> getRequiredFiles();
- map<string, vector<string> > getOutputFiles() { return outputTypes; }
- int execute();
- void help();
-
+ ~GetLineageCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "get.lineage"; }
+ string getCommandCategory() { return "Phylotype Analysis"; }
+ string getOutputFileNameTag(string, string);
+ 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;
+ vector<string> outputNames, listOfTaxons;
string fastafile, namefile, groupfile, alignfile, listfile, taxfile, outputDir, taxons;
bool abort, dups;
- map<string, vector<string> > outputTypes;
int readFasta();
int readName();
int readAlign();
int readList();
int readTax();
- string removeConfidences(string);
- vector< map<string, int> > getTaxons(string);
+ vector< map<string, float> > getTaxons(string);
};
#endif