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#ifndef CLUSTERFRAGMENTSCOMMAND_H
#define CLUSTERFRAGMENTSCOMMAND_H
/*
* clusterfragmentscommand.h
* Mothur
*
* Created by westcott on 9/23/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "sequence.hpp"
#include "counttable.h"
/************************************************************/
struct seqRNode {
int numIdentical;
int length;
Sequence seq;
string names;
bool active;
seqRNode() = default;
seqRNode(int n, Sequence s, string nm, int l) : numIdentical(n), seq(s), names(nm), active(1), length(l) {}
~seqRNode() = default;
};
/************************************************************/
class ClusterFragmentsCommand : public Command {
public:
ClusterFragmentsCommand(string);
~ClusterFragmentsCommand() = default;
vector<string> setParameters();
string getCommandName() { return "cluster.fragments"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Cluster.fragments"; }
string getDescription() { return "creates a namesfile with sequences that are a fragment of a larger sequence"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
CountTable ct;
bool abort;
string fastafile, namefile, countfile;
int diffs, percent;
vector<seqRNode> alignSeqs;
map<string, string> names; //represents the names file first column maps to second column
map<string, int> sizes; //this map a seq name to the number of identical seqs in the names file
map<string, int>::iterator itSize;
vector<string> outputNames;
int readFASTA();
void readNameFile();
void printData(string, string); //fasta filename, names file name
bool isFragment(string, string);
};
/************************************************************/
#endif
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