8 * Created by Sarah Westcott on 7/9/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
15 #include "sequence.hpp"
17 /***********************************************************************/
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
28 /***********************************************************************/
35 /***********************************************************************/
41 /***********************************************************************/
49 float queryToParentLocal;
52 /***********************************************************************/
57 //********************************************************************************************************************
58 //sorts lowest to highest
59 inline bool compareRegionStart(results left, results right){
60 return (left.nastRegionStart < right.nastRegionStart);
62 //********************************************************************************************************************
63 //sorts lowest to highest
64 inline bool compareSeqDist(SeqDist left, SeqDist right){
65 return (left.dist < right.dist);
67 //********************************************************************************************************************
79 linePair(int i, int j) : start(i), end(j) {}
83 /***********************************************************************/
91 Chimera(string, string);
93 virtual void setFilter(bool f) { filter = f; }
94 virtual void setCorrection(bool c) { correction = c; }
95 virtual void setProcessors(int p) { processors = p; }
96 virtual void setWindow(int w) { window = w; }
97 virtual void setIncrement(int i) { increment = i; }
98 virtual void setNumWanted(int n) { numWanted = n; }
99 virtual void setKmerSize(int k) { kmerSize = k; }
100 virtual void setSVG(int s) { svg = s; }
101 virtual void setName(string n) { name = n; }
102 virtual void setMatch(int m) { match = m; }
103 virtual void setMisMatch(int m) { misMatch = m; }
104 virtual void setDivR(float d) { divR = d; }
105 virtual void setParents(int p) { parents = p; }
106 virtual void setMinSim(int s) { minSim = s; }
107 virtual void setMinCoverage(int c) { minCov = c; }
108 virtual void setMinBS(int b) { minBS = b; }
109 virtual void setMinSNP(int s) { minSNP = s; }
110 virtual void setIters(int i) { iters = i; }
111 virtual void setTemplateSeqs(vector<Sequence*> t) { templateSeqs = t; }
112 virtual bool getUnaligned() { return unaligned; }
113 virtual void setTemplateFile(string t) { templateFileName = t; }
115 virtual void setCons(string){};
116 virtual void setQuantiles(string){};
117 virtual void doPrep(){};
118 virtual vector<Sequence*> readSeqs(string);
119 virtual vector< vector<float> > readQuantiles();
120 virtual void setMask(string);
121 virtual void runFilter(Sequence*);
122 virtual void createFilter(vector<Sequence*>);
124 virtual void printHeader(ostream&){};
125 virtual int getChimeras(Sequence*){ return 0; }
126 virtual int getChimeras(){ return 0; }
127 virtual void print(ostream&){};
132 vector<Sequence*> templateSeqs;
133 bool filter, correction, svg, unaligned;
134 int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters;
136 string seqMask, quanfile, filterString, name, outputDir, templateFileName;
137 Sequence* getSequence(string); //find sequence from name
140 /***********************************************************************/