8 * Created by westcott on 9/8/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
17 #include "alignmentdb.h"
19 /***********************************************************/
20 //This class was created using the algorythms described in
21 //CHIMERA_CHECK version 2.7 written by Niels Larsen.
23 /***********************************************************/
25 class ChimeraCheckRDP : public Chimera {
28 ChimeraCheckRDP(string, string);
31 int getChimeras(Sequence*);
32 void print(ostream&, ostream&);
39 AlignmentDB* templateDB;
41 Sequence closest; //closest is the closest overall seq to query
43 vector<sim> IS; //IS is the vector of IS values for each window for query
45 map<string, string> names;
48 int calcKmers(map<int, int>, map<int, int>);
49 void makeSVGpic(vector<sim>);
50 void readName(string);
52 /***********************************************************/