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 /************************************************************/
25 seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm), active(1) {}
28 /************************************************************/
30 class PreClusterCommand : public Command {
33 PreClusterCommand(string);
36 vector<string> getRequiredParameters();
37 vector<string> getValidParameters();
38 vector<string> getRequiredFiles();
39 map<string, vector<string> > getOutputFiles() { return outputTypes; }
46 string fastafile, namefile, outputDir;
47 vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
48 map<string, string> names; //represents the names file first column maps to second column
49 map<string, int> sizes; //this map a seq name to the number of identical seqs in the names file
50 map<string, int>::iterator itSize;
51 // map<string, bool> active; //maps sequence name to whether it has already been merged or not.
52 vector<string> outputNames;
53 map<string, vector<string> > outputTypes;
57 //int readNamesFASTA();
58 int calcMisMatches(string, string);
59 void printData(string, string); //fasta filename, names file name
62 /************************************************************/