X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimera.h;h=e187bfc60d8d504d80561d4347f9a838f1ddabee;hp=33e514b0f05d424740f2a660066e1ace6d99d40d;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=c4fb347858dd8cfea4d2933f429fff4130dca65b diff --git a/chimera.h b/chimera.h index 33e514b..e187bfc 100644 --- a/chimera.h +++ b/chimera.h @@ -13,31 +13,118 @@ #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 results; + string flag; + Sequence trimQuery; + //results malignerResults; + + data_results(vector d, string f, map 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 leftParent; //keep the name of closest left associated with the two scores - vector rightParent; //keep the name of closest right associated with the two scores - vector score; //so you can keep last score and calc this score and keep whichever is bigger. - vector closestLeft; //keep the closest left associated with the two scores - vector 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 prev; + int score; + int row; + int col; +// int mismatches; +}; +/***********************************************************************/ +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; }; - +/***********************************************************************/ +struct SeqCompare { + 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){ 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; @@ -46,60 +133,52 @@ struct sim { }; 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, 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 setIters(int i) { iters = i; } - - - virtual void setCons(string){}; - virtual void setQuantiles(string){}; + 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 int getLength() { return length; } virtual vector readSeqs(string); - virtual vector< vector > readQuantiles(); virtual void setMask(string); - virtual void runFilter(vector); - virtual void createFilter(vector); + virtual map runFilter(Sequence*); + virtual string createFilter(vector, float); + virtual void printHeader(ostream&){}; + virtual int getChimeras(Sequence*){ return 0; } + virtual int getChimeras(){ return 0; } + 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 - //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; - float divR; - string seqMask, quanfile, filterString, name; - - + vector templateSeqs; + vector filteredTemplateSeqs; + bool filter, unaligned, byGroup; + int length; + string seqMask, filterString, outputDir, templateFileName; + Sequence* getSequence(string); //find sequence from name + MothurOut* m; }; /***********************************************************************/