#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<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;
+ 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<PCell>::iterator MatData;
-typedef map<int, float> 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(){}
+};
/***********************************************************************/
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<Sequence*> readSeqs(string file) {
- try {
- ifstream in;
- openInputFile(file, in);
- vector<Sequence*> 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<Sequence*> readSeqs(string);
+ 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 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<Sequence*> templateSeqs;
+ 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