+++ /dev/null
-#ifndef CHIMERA_H
-#define CHIMERA_H
-
-/*
- * chimera.h
- * Mothur
- *
- * Created by Sarah Westcott on 7/9/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-
-#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<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;
-};
-
-struct linePair {
- 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(){ 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){ Sequence temp; return temp; }
- virtual int print(MPI_File&, MPI_File&, string){ return 0; }
- #endif
-
-
- protected:
-
- 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;
-};
-
-/***********************************************************************/
-
-#endif
-
projects / mothur.git / blobdiff