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scores.h
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//***************SCORES.H************************
//
//Some utility functions used to compute scores, map functions, string functions
//
//
//Author: Rong She
//Date: April 2007
//***********************************************
#if defined(_MSC_VER)
#pragma warning(disable: 4786)
#pragma warning(disable: 4503)
#endif
#ifndef SCORES_H /* SCORES_H */
#define SCORES_H
#include "c45extern.h"
#include "struct.h"
#include <string>
#include <set>
#include <map>
#include <vector>
#include <fstream>
#include <iostream>
#include <algorithm>
using namespace std;
//not currently used parameters
const float HSP_ALPHA = 0.5f;
const float GENE_BETA = 0.5f;
const float GENE_OL_GAMA = 0;
//used parameters
extern float HSP_SK_ALPHA;
extern float GENE_MS_BETA;
extern float MAX_OVERLAP_PER; //no longer used
extern int MAX_GAP_BTWN_HSP;
extern int TOP_RANK_NUM;
extern float MIN_GENE_COVER_PER;
extern float MIN_GENE_SCORE;
extern bool USE_MIN_GENE_SCORE;
extern int MIN_EXON_SIZE;
extern int MIN_INTRON_SIZE;
extern int MAX_EXON_SIZE;
extern int MAX_INTRON_SIZE;
extern int MAX_EXON_HSP_DIFF;
extern int MAX_INTRON_HSP_DIFF;
//extern int MIN_INTRON_LEN;
extern int START_CODON_CHECK_LEN;
extern int MAX_NUM_SPLICE_SITES;
extern int SPLICE_LEN;
//extern int MIN_INTERNAL_EXON_LEN;
extern string PHASE1_VERSION;
extern string PHASE1_OUTPUT;
extern string PHASE2_VERSION;
extern int SPLICE_SEGMENT_VERSION;
extern float TREE_CLS_THRESHOLD;
extern int TREE_DATA_SHIFT;
extern int TREE_DATA_DISTORT;
extern int ALIGN_SCORE_MATRIX[28][28]; //map<string, int> ALIGN_SCORE_MATRIX;
extern string QUERY_SEQ_FILE;
extern int END_EXON_LEN;
extern int MID_EXON_LEN;
extern int EXPLORE_END_EXON_LEN;
extern float EXPLORE_END_EXON_PER;
extern int REPAIR_HSP_MIN_INIT_SCORE;
extern int REPAIR_HSP_EXTEND_SCORE_DROP;
extern bool EXTEND_HSP_BY_SCORE;
extern int REPAIR_HSP_AFTER_EXON;
extern bool VERBOSE;
extern bool GENBLASTG_NEED_PID;
extern bool OUTPUT_Protein, OUTPUT_GFF, OUTPUT_cDNA;
extern string USER_ID;
extern bool phase1_only;
extern bool GENEWISE_COMMAND;
extern bool EXONERATE_COMMAND;
extern map<string, multiset<long> > genewise_ug_exons;
extern map<string, multiset<long> > genewise_g_exons;
extern map< string, map< pair<long, long>, multiset<long> > > wormbase_exons;
extern ofstream of_perform;
extern bool GAPPED;
extern int chromosome_start_pos; //keep track of the start position (on the chromosome sequence) of the current group region
//extern bool GBLASTG_FOUND;
//=================================================================================//
/* CONSTANT DEFINITIONS */
const int DELIMIT = '\t';
const string OUT_EXT = ".gblast";
const int MAX_CHAR_PER_LINE = 80;
const int MAX_CHAR_NAME = 32;
const int MAX_LINE = 1<<12; //4096;//each chromosome string has up to MAX_LINE chars (2^12)
const string START_CODON = "atg";
const string STOP_CODONS[3] = {"tag", "tga", "taa"};
const string START_CODON_REV = "gta";
const string STOP_CODONS_REV[3] = {"gat", "agt", "aat"};
const string DONOR_SITE[2] = {"gt", "gc"};
const string ACCEPTOR_SITE[1] = {"ag"};
const string DONOR_SITE_REV[2] = {"tg", "cg"};
const string ACCEPTOR_SITE_REV[1] = {"ga"};
//utility functions
extern float Score(int, int, float);
extern float Penalty_old(float HSP_skip_penalty, float gene_missing_penalty );
extern float Penalty_new(float HSP_skip_penalty, float gene_missing_penalty, float gene_overlap_penalty );
extern void MyMapInsert(const int pos, const int index, const bool isStart, map<int, vector<int> >& myMap);
extern void MyMapInsert( const string sort_key, const long value, map<string, multiset<long> >& myMap);
extern void MyMapInsert( const string sort_key, const long value, multimap<string, multiset<long> >& myMap);
extern void MyMapInsert( const int pos, const int pos_end, const float PID, const bool isStart, map<int, vector<pair<float, int> > >& myMap);
extern void MyMapInsert( const string sort_key, const string chr_seq, const int start, const int end,
map<string, pair<string, set< pair<int, int> > > >& myMap);
extern int CountCharInStr(const string& str, char ch);
extern void GetSubstrFromVecStrs(vector<string>& chr_seq, bool isPosStrand, const int start_pos, const int len, string& resultStr);
extern int GetSubstrFromVecStrs_ForRepair(vector<string>& chr_seq, bool isPosStrand, const int start_pos, const int len, string& resultStr);
extern void GetSubstrFromVecStrs(vector<string>& chr_seq, bool isPosStrand, const int start_pos, const int len, string& resultStr,
string& prev_2nt, string& next_2nt);
extern void GetSubstrFromVecStrs_ForRepair(vector<string>& chr_seq, bool isPosStrand, const int start_pos, const int len, string& resultStr,
string& prev_2nt, string& next_2nt);
extern void GetSubstrFromVecStrs_NegRev(vector<string>& chr_seq, bool isPosStrand, const int start_pos, const int len, string& resultStr);
extern int GetSubstrFromVecStrs_NegRev_ForRepair(vector<string>& chr_seq, bool isPosStrand, const int start_pos, const int len, string& resultStr);
extern void StrToComplement(string& resultStr);
extern void StrToReverseComplement(string& resultStr);
extern void BackwardSearch(string& segStr, int start_pos, bool isPos, const string* matchStrs, int num_matchStrs, vector<int>& results, bool is_donor, ofstream& outFile);
extern void ForwardSearch(string& segStr, int start_pos, bool isPos, const string* matchStrs, int num_matchStrs, vector<int>& results, bool is_donor, ofstream& outFile);
//extern void BackwardSearch(string& segStr, int start_pos, bool isPos, const string* matchStrs, int num_matchStrs, vector<int>& results, bool is_donor);
//extern void ForwardSearch(string& segStr, int start_pos, bool isPos, const string* matchStrs, int num_matchStrs, vector<int>& results, bool is_donor);
extern void BackwardSearch_nPerBorder(string& segStr, int start_pos, bool isPos, const string* matchStrs, int num_matchStrs, vector<int>& results, bool is_donor, vector<string>& site_2nt, ofstream& outFile,
string& prev_2nt, string& next_2nt);
extern void ForwardSearch_nPerBorder(string& segStr, int start_pos, bool isPos, const string* matchStrs, int num_matchStrs, vector<int>& results,
bool is_donor, vector<string>& site_2nt, ofstream& outFile, string& prev_2nt, string& next_2nt);
extern map<string, string> DNA_CODON_TBL;
extern map<string, char> DNA_CODON_TBL_SL;
extern void LoadCodonMap();
extern void LoadCodonMap_SingleLetterAA();
extern void TranslateDNACodons(string& dna, string& protein);
extern bool FindRealPos(string& alignStr, int align_start, int align_end, int search_start, int search_end,
int& search_start_pos, int& search_end_pos, int& extra_front, int& extra_end);
extern void GetPenaltyFromMatchStr(string& alignStr, int align_start, int align_end, int search_start, int search_end,
string& matchStr, int& exact_match, int& gap, int& pos_match,
int query_start, string& queryStr, set< pair<int, int> >& query_match_pos, bool& end_is_match);
extern void GetPenaltyFromMatchStr(int search_start_pos, int search_end_pos, int extra_front, int extra_end,
string& matchStr, int& exact_match, int& gap, int& pos_match);
extern void FindTgtStrPos(string& targetStr, int cur_pos, int search_start, int search_end, int& start_index, int& end_index);
//extern void FillFrontExtArea(string& matchStr, int exon_index, int& ext, vector<string>& chr_seq, int exon_pos,
// vector<string>& strChrs, string& queryStr, string& targetStr);
//extern void FillEndExtArea(string& matchStr, int exon_index, int& ext, vector<string>& chr_seq, int exon_pos,
// vector<string>& strChrs, string& queryStr, string& targetStr);
//extern void FillExonArea(vector<string>& strChrs, string& queryStr, string& matchStr, string& targetStr, vector<string>& chr_seq,
// bool isPosStrand, int exon_pos, int front_gap, int frame, int start_index, int end_index);
//extern void FillFromTargetStr(vector<string>& chr_seq, bool isPosStrand, int start_pos, int length, bool revStr, vector<string>& strChrs);
//extern void FillFrontFixedLenExt(vector<string>& chr_seq, int& ext, int exon_pos, vector<string>& strChrs);
//extern void FillEndFixedLenExt(vector<string>& chr_seq, int& ext, int exon_pos, vector<string>& strChrs);
extern void StrToLower(string& str);
extern int LenOfStrVec(vector<string>& str_vec);
extern void ProteinToDNAStyle(string& str);
extern int ProteinPosToDNAStylePos(int pos);
extern int DNAToProteinStylePos_StartSite(int pos);
extern int DNAToProteinStylePos_EndSite(int pos);
extern void GetStopCodonIndexes(string& cur_chr_seq, vector<int>& stop_indexes, const string* stop_codons);
extern int FindHSPNo(vector<int>& sites, vector<int>& site_hsp_no, int site);
extern int FindMax(vector<int>& hsp_no);
extern bool RegionOverlap(int cur_region_start, int cur_region_end, set< pair<int,int> >& regions);
extern int GetSingleStrFromVecStrs(vector<string>& chr_seq, bool isPosStrand,
const int vecIndex, const int start_pos, string& resultStr, int& leftover);
extern bool IsSorted(vector<int>& vec);
extern bool IsUnique(vector<int>& vec);
extern void BackwardSearch(string& segStr, int start_pos, bool isPos, const string* matchStrs, int num_matchStrs,
vector<int>& results, bool is_donor, ofstream& outFile, int seg_index, vector<int>& segs);
extern void ForwardSearch(string& segStr, int start_pos, bool isPos, const string* matchStrs, int num_matchStrs,
vector<int>& results, bool is_donor, ofstream& outFile, int seg_index, vector<int>& segs);
//extern void CombineInFrameSpliceSites(int border, vector<int>& sites, vector<int>& final_sites,
// vector<int>& site_regions, int region, bool is_acceptor, vector<int>& site_head_tail);
extern void CombineSpliceSites(int border, vector<int>& sites, vector<int>& final_sites, vector<int>& site_regions,
int region, bool is_acceptor, vector<int>& site_head_tail, int frame_reference,
vector<string>& site_2nt, vector<string>& final_site_2nt, ofstream& os);
//extern void CombineSpliceSites_S1(int border, vector<int>& sites, vector<int>& final_sites, vector<int>& site_regions,
// int region, bool is_acceptor, vector<int>& site_head_tail, int frame_reference,
// int hsp_ID, vector<int>& acceptor_HSP_ID, vector<int>& donor_HSP_ID,
// vector<string>& site_2nt, vector<string>& final_site_2nt);
extern bool FindRealPos_DNA(string& alignStr, int align_start, int align_end, int search_start, int search_end,
int& search_start_pos, int& search_end_pos);
extern void GetGaps(const string& str, vector<int>& gap_starts, vector<int>& gap_ends);
extern int GetMatches(const string& str, vector<int>& match_starts, vector<int>& match_ends, vector<int>& id);
extern int ConvertToNoGappedPos(int pos, vector<int>& gap_starts, vector<int>& gap_ends, bool need_after_gap_pos);
extern int ConvertToGappedPos(int pos, vector<int>& gap_starts, vector<int>& gap_ends);
extern int ComputeBackId(int pos, vector<int>& match_starts, vector<int>& match_ends, vector<int>& match_id, int total_id);
extern int ComputeFrontId(int pos, vector<int>& match_starts, vector<int>& match_ends, vector<int>& match_id, int total_id);
extern void GetSegments(Tree T, vector<int>& gap_starts, vector<int>& gap_ends, int hsp_start,
//multimap<int, pair<int, int> >& donor_segments,
vector<SegmentsInThreeBounds>& donor_segments_pair,
vector< vector<int> >& donor_acceptor_HSP_ID, //vector<int>& donor_acceptor_HSP_ID, //vector<int>& acceptor_HSP_ID,
int hsp_ID, //int& prev_hsp_ID,
int& last_segment_start, int& last_segment_end,
bool& lastLeafIsExon); //, vector<int>& segment_hsp_start, bool& isFirstLeaf);
extern void ProcSegmentsByLens(multimap<int, pair<int, int> >& donor_segments,
int& last_segment_start, vector<int>& segment_hsp_start, int& last_hsp_start);
extern bool GetAlignPairStr(string& curStr, char t, char q, bool open_gap);
extern void remove_trailing_cr_lf(string& str);
extern int remove_trailing_cr_lf(char* str, int len);
extern bool all_white_space(string& str);
extern void DNA2AA(string& target_seq, int start_index, string& result_seq);
extern bool TranslateTargetDNA(string& str);
extern bool HasInFrameStop(string& str, bool frame_start_at_str_beginning, int& stop_pos, bool ignore_last_codon);
extern void EraseAll(string& str, char ch);
extern bool HasStopCodon(int acceptor_site, int donor_site, vector<string>& seq, int& frame, //int& site_before_stop,
int& site_after_stop,
string& align, int prev_donor_site, string& left_chars,
bool output_DNA, ofstream& DNA_os, bool temp_DNA, string& temp_DNA_string,
bool is_last_exon, bool& found_stop);
extern void HasStopCodon_KeepStopCodon(int acceptor_site, int donor_site, vector<string>& seq, int& frame,
string& align, string& left_chars);
extern void CombineConsecutiveSpaces(string& str);
extern int similarity_score(char a,char b, bool opengap, bool& opengap_cur);
#endif /* SCORES_H */