#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);
- 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 setTemplate(string t) { templateFile = 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 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; }
+
+ #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 templateFile;
-
-
+ 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