#include "mothur.h"
#include "sequence.hpp"
-
+/***********************************************************************/
struct Preference {
string name;
vector<string> leftParent; //keep the name of closest left associated with the two scores
int midpoint;
};
-
+/***********************************************************************/
+struct score_struct {
+ int prev;
+ int score;
+ int row;
+ int col;
+};
+/***********************************************************************/
+struct trace_struct {
+ int col;
+ int oldCol;
+ int row;
+};
+/***********************************************************************/
+struct results {
+ int regionStart;
+ int regionEnd;
+ int nastRegionStart;
+ int nastRegionEnd;
+ string parent;
+ string parentAligned;
+ float queryToParent;
+ float queryToParentLocal;
+ float divR;
+};
+/***********************************************************************/
struct SeqDist {
Sequence* seq;
float dist;
+ int index;
};
-
+//********************************************************************************************************************
+//sorts lowest to highest
+inline bool compareRegionStart(results left, results right){
+ return (left.nastRegionStart < right.nastRegionStart);
+}
//********************************************************************************************************************
//sorts lowest to highest
inline bool compareSeqDist(SeqDist left, SeqDist right){
public:
- Chimera(){};
- Chimera(string);
- Chimera(string, string);
- virtual ~Chimera(){};
+ Chimera(){ m = MothurOut::getInstance(); }
+ Chimera(string) { m = MothurOut::getInstance(); }
+ Chimera(string, bool, string) { m = MothurOut::getInstance(); }
+ Chimera(string, string) { m = MothurOut::getInstance(); }
+ virtual ~Chimera(){ for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } };
virtual void setFilter(bool f) { filter = f; }
virtual void setCorrection(bool c) { correction = c; }
virtual void setProcessors(int p) { processors = p; }
virtual void setDivR(float d) { divR = d; }
virtual void setParents(int p) { parents = p; }
virtual void setMinSim(int s) { minSim = s; }
+ virtual void setMinCoverage(int c) { minCov = c; }
+ virtual void setMinBS(int b) { minBS = b; }
+ virtual void setMinSNP(int s) { minSNP = s; }
virtual void setIters(int i) { iters = i; }
-
+ virtual bool getUnaligned() { return unaligned; }
+ virtual void setTemplateFile(string t) { templateFileName = t; templateSeqs = readSeqs(t); }
+ virtual int getLength() { return length; }
virtual void setCons(string){};
virtual void setQuantiles(string){};
+ virtual int doPrep(){ return 0; }
virtual vector<Sequence*> readSeqs(string);
virtual vector< vector<float> > readQuantiles();
virtual void setMask(string);
- virtual void runFilter(vector<Sequence*>);
- virtual void createFilter(vector<Sequence*>);
+ virtual map<int, int> runFilter(Sequence*);
+ virtual string createFilter(vector<Sequence*>, float);
+ virtual void printHeader(ostream&){};
+ virtual int getChimeras(Sequence*){ return 0; }
+ virtual int getChimeras(){ return 0; }
+ virtual int print(ostream&, ostream&){ return 0; }
- //pure functions
- virtual void getChimeras() = 0;
- virtual void print(ostream&) = 0;
protected:
- bool filter, correction, svg;
- int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, parents, iters;
+ vector<Sequence*> templateSeqs;
+ bool filter, correction, svg, unaligned;
+ int processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters, length;
float divR;
- string seqMask, quanfile, filterString, name;
-
-
+ string seqMask, quanfile, filterString, name, outputDir, templateFileName;
+ Sequence* getSequence(string); //find sequence from name
+ MothurOut* m;
};
/***********************************************************************/