8 * Created by Sarah Westcott on 7/9/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
15 #include "sequence.hpp"
20 vector<string> leftParent; //keep the name of closest left associated with the two scores
21 vector<string> rightParent; //keep the name of closest right associated with the two scores
22 vector<float> score; //so you can keep last score and calc this score and keep whichever is bigger.
23 vector<float> closestLeft; //keep the closest left associated with the two scores
24 vector<float> closestRight; //keep the closest right associated with the two scores
34 //********************************************************************************************************************
35 //sorts lowest to highest
36 inline bool compareSeqDist(SeqDist left, SeqDist right){
37 return (left.dist < right.dist);
39 //********************************************************************************************************************
51 linePair(int i, int j) : start(i), end(j) {}
55 /***********************************************************************/
63 Chimera(string, string);
65 virtual void setFilter(bool f) { filter = f; }
66 virtual void setCorrection(bool c) { correction = c; }
67 virtual void setProcessors(int p) { processors = p; }
68 virtual void setWindow(int w) { window = w; }
69 virtual void setIncrement(int i) { increment = i; }
70 virtual void setNumWanted(int n) { numWanted = n; }
71 virtual void setKmerSize(int k) { kmerSize = k; }
72 virtual void setSVG(int s) { svg = s; }
73 virtual void setName(string n) { name = n; }
74 virtual void setMatch(int m) { match = m; }
75 virtual void setMisMatch(int m) { misMatch = m; }
76 virtual void setDivR(float d) { divR = d; }
77 virtual void setParents(int p) { parents = p; }
78 virtual void setMinSim(int s) { minSim = s; }
79 virtual void setIters(int i) { iters = i; }
82 virtual void setCons(string){};
83 virtual void setQuantiles(string){};
84 virtual vector<Sequence*> readSeqs(string);
85 virtual vector< vector<float> > readQuantiles();
86 virtual void setMask(string);
87 virtual void runFilter(vector<Sequence*>);
88 virtual void createFilter(vector<Sequence*>);
92 virtual void getChimeras() = 0;
93 virtual void print(ostream&) = 0;
97 bool filter, correction, svg;
98 int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, parents, iters;
100 string seqMask, quanfile, filterString, name;
105 /***********************************************************************/