#include "mothur.h"
-#include "sparsematrix.hpp"
#include "sequence.hpp"
-typedef list<PCell>::iterator MatData;
-typedef map<int, float> SeqMap; //maps sequence to all distance for that seqeunce
+/***********************************************************************/
+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;
+};
+/***********************************************************************/
+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;
+};
+//********************************************************************************************************************
+//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);
+}
+//********************************************************************************************************************
+struct sim {
+ string leftParent;
+ string rightParent;
+ float score;
+ int midpoint;
+};
+
+struct linePair {
+ unsigned long int start;
+ unsigned long int end;
+ linePair(unsigned long int i, unsigned long int 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; }
+ Chimera(){ m = MothurOut::getInstance(); length = 0; unaligned = false; }
+ //Chimera(string) { m = MothurOut::getInstance(); }
+ //Chimera(string, bool, string) { m = MothurOut::getInstance(); }
+ //Chimera(string, string) { m = MothurOut::getInstance(); }
+ virtual ~Chimera(){ for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i]; } };
+ //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 bool getUnaligned() { return unaligned; }
+ //virtual void setTemplateFile(string t) { templateFileName = t; templateSeqs = readSeqs(t); }
+ virtual int getLength() { return length; }
- virtual void setCons(string) {};
- virtual void setQuantiles(string) {};
+ //virtual void setCons(string){};
+ //virtual void setQuantiles(string){};
+ //virtual int doPrep(){ return 0; }
+ 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 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);
- }
- }
+ virtual void printHeader(ostream&){};
+ virtual int getChimeras(Sequence*){ return 0; }
+ virtual int getChimeras(){ return 0; }
+ virtual int print(ostream&, ostream&){ return 0; }
+ #ifdef USE_MPI
+ virtual int print(MPI_File&, MPI_File&){ return 0; }
+ #endif
- //pure functions
- virtual void getChimeras() = 0;
- virtual void print(ostream&) = 0;
protected:
- bool filter, correction;
- int processors, window, increment;
-
-
+ vector<Sequence*> templateSeqs;
+ bool filter, unaligned; // correction, svg,
+ int length; //processors, window, increment, numWanted, kmerSize, match, misMatch, minSim, minCov, minBS, minSNP, parents, iters,
+ //float divR;
+ string seqMask, filterString, outputDir, templateFileName; //quanfile, name,
+ Sequence* getSequence(string); //find sequence from name
+ MothurOut* m;
};
/***********************************************************************/
projects / mothur.git / blobdiff