#include "mothur.h"
#include "sequence.hpp"
-
+/***********************************************************************/
+struct data_struct {
+ float divr_qla_qrb;
+ float divr_qlb_qra;
+ float qla_qrb;
+ float qlb_qra;
+ float qla;
+ float qrb;
+ float ab;
+ float qa;
+ float qb;
+ float lab;
+ float rab;
+ float qra;
+ float qlb;
+ int winLStart;
+ int winLEnd;
+ int winRStart;
+ int winREnd;
+ Sequence querySeq;
+ Sequence parentA;
+ Sequence parentB;
+ float bsa;
+ float bsb;
+ float bsMax;
+ float chimeraMax;
+
+};
+/***********************************************************************/
+struct data_results {
+ vector<data_struct> results;
+ string flag;
+ Sequence trimQuery;
+ //results malignerResults;
+
+ data_results(vector<data_struct> d, string f, map<int, int> s, Sequence t) : results(d), flag(f), trimQuery(t) {}
+ data_results() {}
+};
+/***********************************************************************/
+//sorts lowest to highest first by bsMax, then if tie by chimeraMax
+inline bool compareDataStruct(data_struct left, data_struct right){
+ if (left.bsMax < right.bsMax) { return true; }
+ else if (left.bsMax == right.bsMax) {
+ return (left.chimeraMax < right.chimeraMax);
+ }else { return false; }
+}
/***********************************************************************/
struct Preference {
string name;
- vector<string> leftParent; //keep the name of closest left associated with the two scores
- vector<string> rightParent; //keep the name of closest right associated with the two scores
- vector<float> score; //so you can keep last score and calc this score and keep whichever is bigger.
- vector<float> closestLeft; //keep the closest left associated with the two scores
- vector<float> closestRight; //keep the closest right associated with the two scores
+ string leftParent; //keep the name of closest left
+ string rightParent; //keep the name of closest
+ float score; //preference score
+ float closestLeft; //keep the closest left
+ float closestRight; //keep the closest right
int midpoint;
-
+ Preference() { name = ""; leftParent = ""; rightParent = ""; score = 0.0; closestLeft = 10000.0; closestRight = 10000.0; midpoint = 0; }
+ ~Preference() {}
};
/***********************************************************************/
struct score_struct {
int score;
int row;
int col;
+// int mismatches;
};
/***********************************************************************/
struct trace_struct {
float dist;
int index;
};
+/***********************************************************************/
+struct SeqCompare {
+ Sequence seq;
+ float dist;
+ int index;
+};
//********************************************************************************************************************
//sorts lowest to highest
inline bool compareRegionStart(results left, results right){
return (left.dist < right.dist);
}
//********************************************************************************************************************
-
+//sorts lowest to highest
+inline bool compareSeqCompare(SeqCompare left, SeqCompare right){
+ return (left.dist < right.dist);
+}
+//********************************************************************************************************************
struct sim {
string leftParent;
string rightParent;
};
struct linePair {
- int start;
- int end;
- linePair(int i, int j) : start(i), end(j) {}
+ unsigned long long start;
+ unsigned long long end;
+ linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
linePair(){}
};
+
/***********************************************************************/
class Chimera {
public:
- Chimera(){};
- Chimera(string);
- Chimera(string, bool, string);
- Chimera(string, string);
- virtual ~Chimera(){};
- virtual void setFilter(bool f) { filter = f; }
- virtual void setCorrection(bool c) { correction = c; }
- virtual void setProcessors(int p) { processors = p; }
- virtual void setWindow(int w) { window = w; }
- virtual void setIncrement(int i) { increment = i; }
- virtual void setNumWanted(int n) { numWanted = n; }
- virtual void setKmerSize(int k) { kmerSize = k; }
- virtual void setSVG(int s) { svg = s; }
- virtual void setName(string n) { name = n; }
- virtual void setMatch(int m) { match = m; }
- virtual void setMisMatch(int m) { misMatch = m; }
- 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 void setTemplateSeqs(vector<Sequence*> t) { templateSeqs = t; }
+ Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; byGroup = false; }
+ virtual ~Chimera(){ for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } for (int i = 0; i < filteredTemplateSeqs.size(); i++) { delete filteredTemplateSeqs[i]; } };
virtual bool getUnaligned() { return unaligned; }
- virtual void setTemplateFile(string t) { templateFileName = t; }
virtual int getLength() { return length; }
-
- virtual void setCons(string){};
- virtual void setQuantiles(string){};
- virtual void doPrep(){};
virtual vector<Sequence*> readSeqs(string);
- virtual vector< vector<float> > readQuantiles();
virtual void setMask(string);
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 void print(ostream&, ostream&){};
+ virtual Sequence print(ostream&, ostream&){ Sequence temp; return temp; }
+ virtual Sequence print(ostream&, ostream&, data_results, data_results) { Sequence temp; return temp; }
+ virtual int print(ostream&, ostream&, string){ return 0; }
+ virtual int getNumNoParents(){ return 0; }
+ virtual data_results getResults() { data_results results; return results; }
+
+ #ifdef USE_MPI
+ virtual Sequence print(MPI_File&, MPI_File&){ Sequence temp; return temp; }
+ virtual Sequence print(MPI_File&, MPI_File&, data_results, data_results, bool&){ Sequence temp; return temp; }
+ virtual int print(MPI_File&, MPI_File&, string){ return 0; }
+ #endif
protected:
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, outputDir, templateFileName;
+ vector<Sequence*> filteredTemplateSeqs;
+ bool filter, unaligned, byGroup;
+ int length;
+ string seqMask, filterString, outputDir, templateFileName;
Sequence* getSequence(string); //find sequence from name
+ MothurOut* m;
};
/***********************************************************************/
projects / mothur.git / blobdiff