1 #ifndef PRECLUSTERCOMMAND_H
2 #define PRECLUSTERCOMMAND_H
9 * Created by westcott on 12/21/09.
10 * Copyright 2009 Schloss Lab. All rights reserved.
15 #include "command.hpp"
16 #include "sequence.hpp"
18 /************************************************************/
23 seqPNode(int s, Sequence q) : numIdentical(s), seq(q) {}
26 /************************************************************/
28 class PreClusterCommand : public Command {
31 PreClusterCommand(string);
39 string fastafile, namefile;
40 vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
41 map<string, string> names; //represents the names file first column maps to second column
42 map<string, int> sizes; //this map a seq name to the number of identical seqs in the names file
43 map<string, bool> active; //maps sequence name to whether it has already been merged or not.
46 int calcMisMatches(string, string);
48 void printData(string, string); //fasta filename, names file name
51 /************************************************************/