X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimera.h;h=e187bfc60d8d504d80561d4347f9a838f1ddabee;hp=9142bacaa09a016d1cabd25560f1e428a699a15c;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=fe346922fe0af5b1a025beacb211078d37598fd4 diff --git a/chimera.h b/chimera.h index 9142bac..e187bfc 100644 --- a/chimera.h +++ b/chimera.h @@ -12,11 +12,132 @@ #include "mothur.h" -#include "sparsematrix.hpp" #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; + 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; + float score; + int midpoint; +}; -typedef list::iterator MatData; -typedef map SeqMap; //maps sequence to all distance for that seqeunce +struct linePair { + unsigned long long start; + unsigned long long end; + linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {} + linePair(){} +}; /***********************************************************************/ @@ -25,80 +146,39 @@ 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 setCons(string) {}; - virtual void setQuantiles(string) {}; - - virtual vector readSeqs(string file) { - try { - ifstream in; - openInputFile(file, in); - vector container; - - //read in seqs and store in vector - while(!in.eof()){ - - Sequence* current = new Sequence(in); - container.push_back(current); - gobble(in); - } - - in.close(); - return container; - } - catch(exception& e) { - errorOut(e, "Chimera", "readSeqs"); - exit(1); - } - } - + 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 void setMask(string); + 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; } - virtual void setMask(string filename) { - try { - - if (filename == "default") { - //default is from wigeon 236627 EU009184.1 Shigella dysenteriae str. FBD013 - seqMask = ".....................................................................................................AAATTGAAGAGTTT-GA--T-CA-T-G-GCTC-AG-AT-TGAA-C-GC--TGG-C--G-GC-A-GG--C----C-T--AACACA-T-GC-A-AGT-CGA-A-CG----------G-TAA-CA-G----------------------------GAAG-A-AG----------------------------------------------------CTT-G----------------------------------------------------------------------------------CT-TCTTT----------------G-CT--G--AC--G--AG-T-GG-C-GG-A--C-------------GGG-TGAGT-A--AT-GT-C-T-G-GG---A-A--A-CT-G--C-C-TGA--TG-G------------------------------------------------------------------A-GG----GGG-AT-AA-CTA-------------------------C-T-G-----------------------GAA-A---CGG-TAG-CTAA-TA---CC-G--C-AT-A----------A--------------------C-------------------------------------GT-C-----------------------------------------------------------------------------------------------------------------------G-CA-A--------------------------------------------------------------------------------------------------------------------------------------G-A-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAA--G-A-G-GG-----G--GA-C-CT--------------------------------------------------------------------------------------------------------------------TCG-G----------------------------------------------------------------------------------------------------------------------G----CC-TC--T---T-G--------------C----C-A---T-CG-G---AT---G-T-----G-CCC-AGA--T-GGG--A------TT--A--G-CT-A----G---TAGG-T-G-GG-G-T----AAC-GG-C-T-C-ACCT--A-GG-C-G--A-CG-A------------TCC-C-T------AG-CT-G-G-TCT-G-AG----A--GG-AT--G-AC-C-AG-CCAC-A-CTGGA--A-C-TG-A-GA-C-AC-G-G-TCCAGA-CTCC-TAC-G--G-G-A-G-GC-A-GC-A-G-TG---GG-G-A-ATA-TTGCA-C-AA-T-GG--GC-GC-A----A-G-CC-T-GA-TG-CA-GCCA-TGCC-G-CG-T---G-T-A--T--GA-A-G--A--A-G-G-CC-----TT-CG---------G-G-T-T-G-T--A---AA-G-TAC--------TT-TC-A-G--C-GGG----GA-G--G---AA-GGGA---GTAA-AG----T--T--AA-T---A----C-----CT-T-TGC-TCA-TT-GA-CG-TT-A-C-CC-G-CA-G---------AA-----------GAAGC-ACC-GG-C-TAA---C--T-CCGT--GCCA--G-C---A--GCCG---C-GG--TA-AT--AC---GG-AG-GGT-GCA-A-G-CG-TTAA-T-CGG-AA-TT-A--C-T--GGGC-GTA----AA-GCGC-AC--G-CA-G-G-C-G------------G--T-TT-G-T-T-AA----G-T-C-A---G-ATG-TG-A-AA-TC--CC-CGG-G--------------------------------------------------------------------CT-C-AA-------------------------------------------------------------------------CC-T-G-GG-AA-C----T-G-C-A-T-C--------T--GA-T-A-C-T-G-GCA--A-G-C---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T-T-G-A-G-T-C-----T-CG--TA-G-A------------G-GG-G-GG-T----AG--AATT-CCA-G-GT--GT-A-GCG-GTGAAA-TG-CGT-AGAG-A-TC-T-GGA--GG-A-AT-A-CC-GG--T--G--GC-GAA-G--G-C---G----G--C-C-CCCTG------G-AC-GA--------------------------------------------------------------AG-A-C-T--GA--CG-----CT-CA-GG--T-G-CGA--AA-G-C--------------G-TGGG-GAG-C-A-AACA--GG-ATTA-G-ATA-C-----CC-T-G-GTA-G-T----C-CA--C-G-CCG-T-AAA--C-GATG-TC--GA-CT---------T-GG--A--G-G-TT-G-TG-C--C--------------------------------------------------------------------------------------CTT-GA--------------------------------------------------------------------------------------------------------------------------------------------------G-G-C-GT--G-G-C-T-TC-C------GG--A----GC-TAA--CG-C-G-T--T--AA-GT--C----G-ACC-GCC-T-G-GG-GAG-TA---CGG-----C-C--G-C-A-A-GGT-T--AAA-ACTC-AAA---------TGAA-TTG-ACGGG-G-G-CCCG----C-A--C-A-A-GCG-GT-G--G--AG-CA-T--GT-GGT-TT-AATT-C-G-ATG-CAAC-G-CG-A-AG-A-A-CC-TT-A-CC-TGGTC-TT-G-AC-A-T-C--------------CAC-G-G-------------A-AG-T-T-T--TC--A-GA-G-A-T--G-A-G--A-A-T-G--T-G-----CC-------------------------------------T--TC-G------------------------------------------GG----A----A---CC-GTG---A--GA---------------------------------------------------C-A-G-G-T-GCTG-CA-TGG-CT--GTC-GTC-A-GC-TC---G-TG-TT-G--TGA-AA-TGT-T-GG-G-TT-AA-GT-CCCGC-AA--------C-GAG-CGC-A-ACC-C-T-TA--TC--C-TTTG--T-T-G-C-C---AG-C-G-----G-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GG---C----C-G------------G----G---A-A--CT---------------C-A-A-A-G-GA-G--AC-T-G-CCA--G-T------------------------------------G-A---TAA----------------------------------A-C-T-G--G-A-GG-A--AGG-T--GGGG-A-TGAC-GTC--AAGT-C---ATC-A-T-G-G-C-C-CTT----AC-G--AC-C-A-GG-GC-TA-CAC-ACGTG-C--TA--CAATG---G-CGCA-T-A--C-AAA-GA-GA--------------------------------------------------------------------------------------------------A-G-C-G-A--C-CTCG-C--G---------------------------------------A-GA-G-C-----------A--A-G-CG---G----------A--CCT-C------A-T-AAAGT-GC-G-T-C-G-TAG-TCC--------GGA-T-TGGAG-TC--T-GCAA-CT-C-------------------------------------------------------------------------------------------------G-ACTCC-A-T-G-AA-G-TC-GGAAT-CG-C-TA--G-TA-AT-C-G-T----GGA-TC-A-G--A------AT--GCC-AC-G-GT-G-AAT-ACGT-T-CCCGGGCCT-TGTA----CACACCG-CCC-GTC-----A---CA--CCA-TG-GG-A--G---TGG-G-TT-GC-AAA--A-GAA------G--T-AGG-TA-G-C-T-T-AA-C-C--------------------------------------------------------------TT----C-------------------------------------------------------------------------------------------------G--GG-A--GG-G--C---GC-TTA--CC--ACT-T----T-GTG-AT-TCA------------------------TG--ACT-GGGG-TG-AAG-TCGTAACAA-GGTAA-CCGT-AGGGGAA-CCTG-CGGT-TGGATCACCTCCTTA................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................"; - }else{ - ifstream infile; - openInputFile(filename, infile); - - while (!infile.eof()) { - Sequence temp(infile); - seqMask = temp.getAligned(); - - gobble(infile); - } - - infile.close(); - } - } - catch(exception& e) { - errorOut(e, "Chimera", "setMask"); - exit(1); - } - } + #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; - int processors, window, increment; - string seqMask; - - + vector templateSeqs; + vector filteredTemplateSeqs; + bool filter, unaligned, byGroup; + int length; + string seqMask, filterString, outputDir, templateFileName; + Sequence* getSequence(string); //find sequence from name + MothurOut* m; }; /***********************************************************************/