* Mothur
*
* Created by Sarah Westcott on 7/8/09.
- * Copyright 2009 __MyCompanyName__. All rights reserved.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
public:
- GetSeqsCommand(string);
+ GetSeqsCommand(string);
+ GetSeqsCommand();
~GetSeqsCommand(){};
+ vector<string> getRequiredParameters();
+ vector<string> getValidParameters();
+ vector<string> getRequiredFiles();
+ map<string, vector<string> > getOutputFiles() { return outputTypes; }
int execute();
void help();
private:
set<string> names;
- string accnosfile, fastafile, namefile, groupfile, alignfile;
- bool abort;
+ vector<string> outputNames;
+ string accnosfile, accnosfile2, fastafile, namefile, groupfile, alignfile, listfile, taxfile, qualfile, outputDir;
+ bool abort, dups;
+ map<string, vector<string> > outputTypes;
- void readFasta();
- void readName();
- void readGroup();
- void readAlign();
- void readAccnos();
+ int readFasta();
+ int readName();
+ int readGroup();
+ int readAlign();
+ int readAccnos();
+ int readList();
+ int readTax();
+ int readQual();
+ int compareAccnos();
};