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About
Functions and their possible use
Input-Output functions
Working with strings
Working with graphs
Auxiliary functions
This document contains general data on CBioInfCpp.h library.
The documents About_CBioInfCpp.pdf, CBioInfCpp.h, About_CBioInfCpp.rtf (all of them are placed in this directory) constitute a single Work (i.e. this Work is divided into these 3 files), and this Work is distributed under Creative Commons Attribution 4.0 International Public License (CC BY) (hyperlink to the License: https://creativecommons.org/licenses/by/4.0/legalcode.ru).
CBioInfCpp.h, About_CBioInfCpp.rtf, About_CBioInfCpp.pdf are written by Sergey Chernouhov (chernouhov@rambler.ru).
CBioInfCpp.h contains a number of functions that may be used as in bioinformatics as well as in other fields related to working with graphs and strings.
All the function are defined in the only file CBioInfCpp.h. Also the libraries iostream, fstream, string, vector, set, algorithm, queue, map, cmath, stack, limits.h, cstdlib, ctime, float.h, unordered_map, unordered_set, utility, functional are included. Yes, this way may be considered as “not the only best”, but it allows to start immediately by writing “include CBioInfCpp.h” at the program beginning.
The data structures "Adjacency vector" and "Adjacency map" to represent a graph are used in the CBioInfCpp (see the section “Working with graphs”).
PS The current version of CBioInfCpp.h contains not so many functions. But it would be nice if this library grows up.
int FastaRead (std::ifstream & fin, std::vector < std::string> & IndexS, std::vector < std::string> & DataS)
Reads FASTA dataset from file. Returns 0 if the number of indexes of strings =
number of strings, the first string in dataset is index (starts with ">") and in
dataset there is no 2 indexes one-by-one without a data string in between.
Otherwise returns -1.
IndexS: Here indexes of strings will be contained
DataS: Here data strings will be contained
void StringsRead (std::ifstream & fin, std::vector <std::string> & DataS)
Reads all strings from file to vector DataS
int MatrixCout (std::vector <std::vector <int>> & B, char g = ' ')
"Couts" Matrix (int) to screen. Returns -1 if the Matrix is empty.
The Matrix may have lines of different length. In this case the "missing" values to the end for the "shorter lines" are filled with the char g.
int MatrixCout (std::vector <std::vector <long long int>> & B, char g = ' ')
"Couts" Matrix (long long int) to screen. Returns -1 if the Matrix is empty.
The Matrix may have lines of different length. In this case the "missing" values to the end for the "shorter lines" are filled with the char g.
int MatrixCout (std::vector <std::vector <double>> & B, unsigned int prec = 4, char g = ' ', bool scientifique = false)
"Couts" Matrix (double) to screen. Returns -1 if the Matrix is empty.
The Matrix may have lines of different length. In this case the "missing" values to the end for the "shorter lines" are filled with the char g.
If bool scientifique == false, the precision will be set as prec;
if bool scientifique == true, scientific notation will be applied.
int MatrixCout (std::vector <std::vector <long double>> & B, unsigned int prec = 4, char g = ' ', bool scientifique = false)
"Couts" Matrix (long double) to screen. Returns -1 if the Matrix is empty.
The Matrix may have lines of different length. In this case the "missing" values to the end for the "shorter lines" are filled with the char g.
If bool scientifique == false, the precision will be set as prec;
if bool scientifique == true, scientific notation will be applied.
int MatrixFout (std::vector <std::vector <double>> & B, std::ofstream & fout, unsigned int prec = 4, char g = ' ', bool scientifique = false)
"Fouts" Matrix (double) to file. Returns -1 if the Matrix is empty.
The Matrix may have lines of different length. In this case the "missing" values to the end for the "shorter lines" are filled with the char g.
If bool scientifique == false, the precision will be set as prec;
if bool scientifique == true, scientific notation will be applied.
int MatrixFout (std::vector <std::vector <long double>> & B, std::ofstream & fout, unsigned int prec = 4, char g = ' ', bool scientifique = false)
"Fouts" Matrix (long double) to file. Returns -1 if the Matrix is empty.
The Matrix may have lines of different length. In this case the "missing" values to the end for the "shorter lines" are filled with the char g.
If bool scientifique == false, the precision will be set as prec;
if bool scientifique == true, scientific notation will be applied.
int MatrixFout (std::vector < std::vector <int>> & B, std::ofstream & fout, char g = ' ')
"Fouts" Matrix (int) to file. Returns -1 if the Matrix is empty.
The Matrix may have lines of different length. In this case the "missing" values to the end for the "shorter lines" are filled with the char g.
int MatrixFout (std::vector < std::vector <long long int>> & B, std::ofstream & fout, char g = ' ')
"Fouts" Matrix (long long int) to file. Returns -1 if the Matrix is empty.
The Matrix may have lines of different length. In this case the "missing" values to the end for the "shorter lines" are filled with the char g.
int VectorCout (const std::vector <int> &P)
"Couts" vector (int) to screen. Returns -1 if the vector is empty
int VectorFout (const std::vector <int> &P, std::ofstream &fout)
"Fouts" vector (int) to file. Returns -1 if the vector is empty
int VectorCout (const std::vector <long long int> &P)
"Couts" vector (long long int) to screen. Returns -1 if the vector is empty
int VectorFout (const std::vector <long long int> &P, std::ofstream &fout)
"Fouts" vector (long long int) to file. Returns -1 if the vector is empty
int VectorCout (const std::vector <double> &P, unsigned int prec = 4, bool scientifique = false)
"Couts" vector (double) to screen. Returns -1 if the vector is empty
If bool scientifique == false, the precision will be set as prec;
if bool scientifique == true, scientific notation will be applied.
int VectorFout (const std::vector <double> &P, std::ofstream &fout, unsigned int prec = 4, bool scientifique = false)
"Fouts" vector (double) to file. Returns -1 if the vector is empty
If bool scientifique == false, the precision will be set as prec;
if bool scientifique == true, scientific notation will be applied.
int VectorCout (const std::vector <long double> &P, unsigned int prec = 4, bool scientifique = false)
"Couts" vector (long double) to screen. Returns -1 if the vector is empty
If bool scientifique == false, the precision will be set as prec;
if bool scientifique == true, scientific notation will be applied.
int VectorFout (const std::vector <long double> &P, std::ofstream &fout, unsigned int prec = 4, bool scientifique = false)
"Fouts" vector (long double) to file. Returns -1 if the vector is empty
If bool scientifique == false, the precision will be set as prec; if bool scientifique == true, scientific notation will be applied.
int VectorCout (const std::vector <std::string> &P)
"Couts" vector (string) to screen. Returns -1 if the vector is empty
int VectorFout (const std::vector <std::string> &P, std::ofstream &fout)
"Fouts" vector (string) to file. Returns -1 if the vector is empty
int PairVectorCout (const std::pair < std::vector<int>, std::vector<double>> & P, unsigned int prec = 4, bool scientifique = false)
Modification of the function VectorCout (see it above) for not-integer (double) weights of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2*i, 2*i+1 in the first vector has its weight set as i-th element in the second one.
int PairVectorFout (const std::pair < std::vector<int>, std::vector<double>> & P, std::ofstream &fout, unsigned int prec = 4, bool scientifique = false)
Modification of the function VectorFout (see it above) for not-integer (double) weights of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2*i, 2*i+1 in the first vector has its weight set as i-th element in the second one.
int GraphCout (const std::vector <int> &P, const bool weighted)
"Couts" a graph that is set by Adjacency vector A to screen: one edge in one line.
Parameter "weighted" sets if the graph A is weighted or no.
Returns -1 if input data is not correct. Otherwise returns 0.
int GraphFout (const std::vector <int> &P, const bool weighted, std::ofstream &fout)
"Fouts" a graph that is set by Adjacency vector A to file: one edge in one line.
Parameter "weighted" sets if the graph A is weighted or no.
Returns -1 if input data is not correct. Otherwise returns 0.
int GraphCout (const std::pair < std::vector<int>, std::vector<double>> & P, unsigned int prec = 4, bool scientifique = false)
Modification of the function GraphCout (see it above) for not-integer (double) weights of edges of a graph. Parameter "weighted" sets if the graph A is weighted or no.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights.
But weights are set in the second one. So an edge that is set by the pair of vertices indexed as 2i, 2i+1 in the first vector has its weight set as i-th element in the second one.
int GraphFout const std::pair < std::vector<int>, std::vector<double>> & P, std::ofstream &fout, unsigned int prec = 4, bool scientifique = false)
Modification of the function GraphFout (see it above) for not-integer (double) weights of edges of a graph.
Parameter "weighted" sets if the graph A is weighted or no.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights.
But weights are set in the second one. So an edge that is set by the pair of vertices indexed as 2i, 2i+1 in the first vector has its weight set as i-th element in the second one.
int GraphCout (const std::map <std::pair < int, int> , int> &P)
"Couts" a graph that is set by Adjacency map P to screen: one edge in one line.
Returns -1 if input data is not correct. Otherwise returns 0.
int GraphFout (const std::map <std::pair < int, int> , int> &P, std::ofstream &fout)
"Fouts" a graph that is set by Adjacency map P to file: one edge in one line. Returns -1 if input data is not correct. Otherwise returns 0.
int GraphCout (const std::map <std::pair < int, int> , double> &P, unsigned int prec = 4, bool scientifique = false)
Modification of the function GraphCout for Adjacency map (see it above) for not-integer (double) weights of edges.
int GraphFout (const std::map <std::pair < int, int> , double> &P, std::ofstream &fout, unsigned int prec = 4, bool scientifique = false)
Modification of the function GraphFout for Adjacency map (see it above) for not-integer (double) weights of edges.
int GraphCout (const std::map <std::pair < int, int> , std::vector<int> > &P, bool in_line=false)
"Couts" a graph that is set by Adjacency mega-map P to screen.
Adjacency mega-map is an extended version of Adjacency map (and it is built basing on std::map too) for containing graphs that have multiply loops and multiply edges.
In doing so, the key value of the map is a pair of integers that sets edge(s) between them and the mapped value is a vector that contains weights of all edges between these vertices.
Parameter "in_line" sets how to print mapped value of the edges: all values of the mapped vector in one line or key value + every value of the mapped vector as separate line.
Returns -1 if input data is not correct. Otherwise returns 0.
int GraphFout (const std::map <std::pair < int, int> , std::vector<int> > &P, std::ofstream &fout, bool in_line=false)
"Fouts" a graph that is set by Adjacency mega-map P to file.
Adjacency mega-map is an extended version of Adjacency map (and it is built basing on std::map too) for containing graphs that have multiply loops and multiply edges.
In doing so, the key value of the map is a pair of integers that sets edge(s) between them and the mapped value is a vector that contains weights of all edges between these vertices.
Parameter "in_line" sets how to print mapped value of the edges: all values of the mapped vector in one line or key value + every value of the mapped vector as separate line.
Returns -1 if input data is not correct. Otherwise returns 0.
int GraphCout (const std::map <std::pair < int, int> , std::vector<double> > &P, bool in_line=false, unsigned int prec = 4, bool scientifique = false)
Modification of the function GraphCout for mega-map (see it above) for not-integer (double) weights of edges.
int GraphFout (const std::map <std::pair < int, int> , std::vector <double> > &P, std::ofstream &fout, bool in_line=false, unsigned int prec = 4, bool scientifique = false)
Modification of the function GraphFout for mega-map (see it above) for not-integer (double) weights of edges.
int CoutSuffixTree (const std::vector <int> & Tree, const std::string DataS, bool tree=true, bool strings = true)
"Couts" the suffix tree set by Tree (its format see at SuffixTreeMake' s description). The string itself is set by DataS. No checking of input data correctness is here.
If "tree" = true couts every 4 numbers that set each edge of the tree in line. If "strings" = true couts every substring that relevant to each edge in line.
int FoutSuffixTree (const std::vector <int> & Tree, const std::string DataS, std::ofstream &fout, bool tree=true, bool strings = true)
"Fouts" the suffix tree set by Tree (its format see at SuffixTreeMake' s description). The string itself is set by DataS. No checking of input data correctness is here.
If "tree" = true couts every 4 numbers that set each edge of the tree in line. If "strings" = true couts every substring that relevant to each edge in line.
int HmDist (const std::string &s1, const std::string &s2)
Counts Hamming Distance; returns -1 if any string is empty or they have different length.
int RComplDNA (const std::string& s, std::string & sr)
Generates reverse complement of string s as string sr, returns -1 and empty string sr if string s is empty or it is not DNA
int RComplRNA (const std::string& s, std::string & sr)
Generates reverse complement of string s as string sr, returns -1 and empty string sr if string s is empty or it is not RNA
std::string rp (const std::string& s)
Generates reverse complement of DNA without any checking of input data correctness
std::string rpr (const std::string& s)
Generates reverse complement of RNA without any checking of input data correctness
double gcDRNA (const std::string &s)
Counts DNA/RNA GC-content; in case any symbol not DNA/RNA-nucleotide or string s is empty returns -1.0.
int RNAfromDNA (const std::string &s, std::string & sr)
Generates RNA from DNA, returns -1 and empty string sr if the input string s is empty or it is not DNA
int DNAfromRNA (const std::string &s, std::string & sr)
Generates DNA from RNA, returns -1 and empty string sr if the input string s is empty or it is not RNA
std::string RNAg (const std::string &s)
Generates RNA from DNA without any checking of input data correctness
std::string DNAg (const std::string &s)
Generates DNA from RNA without checking of data correctness
std::string StrToCircular (const std::string& s, int tail = INT_MAX)
Returns a circular string of minimal length of a string s; if length of s <3 returns s itself. One may set "tail" i.e. maximal overlap "tail-to-beginning" of the string s (nonpositive values of "tail" will be ignored).
int TandemRepeatsFinding (const std::string &s, std::vector <int> &Result, int MaxWordLength = 4, int limit = 5)
Finds all tandem repeats in the string s as follows:
- the repeat has its lenght >= limits,
- the repeat should be formed by j-mers: j in [1; MaxWordLength], MaxWordLength in [2; 6]
- limit should be more than MaxWordLength (if no the limit's value will be set as MaxWordLength+1).
Returns 0 and vector Result: every even position of Result contains the starting position of tandem repeat in the s (0-based indexing) and every odd position of Result contain the lenghts of the repeat that have its starting position as previous element in the Result.
Returns -1 and empty Result if input data is incorrect.
void GMapCodonRNA (std::map < std::string, std::string> & MapCodon)
Generates codon table for RNA in the map MapCodon ("$" means stop codon). MapCodon format: Codon -> Amino acid.
void GMapCodonRNA_A (std::map <std::string, std::vector<std::string>> & MapCodon)
Generates codon table for RNA in the map MapCodon ("$" means stop codon). MapCodon format: Amino acid -> vector of relevant codons.
void GMapMonoisotopicMassTableLD (std::map <char, long double> & MassTable)
Generates Monoisotopic mass table in the map (long double)
int GPFM (std::vector <std::string> &s, std::vector <std::vector <int>> & B, const std::string &Alph)
Generates position frequency matrix (PFM) B upon an array of strings s and given Alphabet (Alphabet is set via string Alph that contains the sequence of its symbols);
Ordering of the rows in B corresponds to sequence of symbols in Alph.
If s contains 1 or 0 items or strings have not equal length or even the only string contains symbol that not belongs to Alphabet or if there are any identical symbols in the Alphabet - returns -1 and empty B.
int GPPM (const std::vector <std::string> &s, std::vector <std::vector <long double>> & B, const std::string &Alph, long double z = 0.0, long double d = 2.0)
Generates a position probability matrix (PPM) B upon an array of strings s and given Alphabet (Alphabet is set via string Alph that contains the sequence of its symbols);
Ordering of the rows in B corresponds to sequence of symbols in Alph.
If s contains 0 items or its strings have not equal length or even the only string contains symbol that not belongs to Alphabet or if there are any identical symbols in the Alphabet - returns -1 and empty B. If success returns 0 and generated B.
z and d are pseudocount parameters: (Ns+z)/(N+d*z) is used
double PDist (const std::string& s1, const std::string& s2)
Counts p-distance without checking of the input data correctness
int GDistanceMatrix (std::vector <std::string> &s, std::vector <std::vector <double>> & B)
Generates DistanceMatrix "B" upon array of strings s; if s contains 1 or 0 items or strings have not equal length returns -1 and empty B.
int ConsStringQ1 (std::vector <std::string> &DataS, std::vector<std::string> &QDataS, std::string &TempS, std::string &QTempS, const int method = 1, const std::string &Alph = "ACGT", const int Phred=33)
Generates a consensus string upon std::vector std::string DataS as an input collection of strings and QDataS as their quality.
The result will be as TempS as consensus string and QTempS as its quality string.
If multiply consensus strings exist returns the one of them. The parameter "Alph" set an alphabet, by default Alph = "ACGT" (other symbols are not considered for forming the consensus string).
The parameter "Phred" sets the quality scale (by default as Phred33).
There are 4 methods to construct the consensus string (set by the parameter "method"): 0 - default - the symbol that has the maximal average probability (quality) for a given position in consensus string will be chosen. It will have the same quality. 1 - the symbol that has the maximal sum of probability (quality) for a given position in consensus string will be chosen. it will have the quality = sum of probability (quality) of this char / number of times that the char occurs at given position. 2 - the symbol that has the maximal sum of probability (quality) for a given position in consensus string will be chosen. it will have the max quality (probability) of this char at given position. 3 - the symbol that has the maximal probability (quality) for a given position in consensus string will be chosen. It will have the same quality.
One may set QDataS as empty: in this case quality will considered as "some equal" for every symbol at every position.
So in order to find a consensus string upon a given collection without quality one may choose method №1 or №2 and empty QDataS.
If no symbol of the Alph has been found at a given position - the ' ' will be set there both in the consensus string TempS and in quality string QTempS.
If any input data is incorrect returns -1 and empty TempS and QTempS, otherwise returns 0.
int ConsStringQ2 (std::vector <std::string> &DataS, std::vector<std::string> &QDataS, std::string &TempS, std::string &QTempS, const int method = 1, const std::string &Alph = "ACGT", const char tr = '^', const int Phred=33)
Modification of ConsStringQ1 (see it above) for all the version of consensus string. For that every position may have >= 1 symbols (if different symbols may be chosen for this position).
The positions are separated by the symbol tr (by default is set as '^').
int JoinOverlapStrings (std::multimap <long long int, std::string> & Locuses, std::map <long long int, std::string> & JoinedLocuses, const bool Aggregate = false, const bool NoQuality = false, const int method = 0, const std::string &Alph = "ACGT", const int Phred=33)
The function joins overlapping strings from Locuses (contain substrings of the unknown string as pairs: start position -> string) and writes the resulting collection of the joined strings to JoinedLocuses (has the same format).
The overlaps are to constructed as consensus strings:
- using ConsStringQ1 (if any one version of result needed, set bool Aggregate = false for it) or using ConsStringQ2 (if all the version needed, set bool Aggregate = true for it), see info on ConsStringQ1 and ConsStringQ2 for details.
- using the chosen method of consensus generating (set by parameter "method", see info on ConsStringQ1 and ConsStringQ2 for details).
- taking into account quality (NoQuality=false, scale is set by parameter "Phred") or no (NoQuality=true). NOTE that if we take quality into account (NoQuality=false) it is expected that the first half of every string in Locuses means the string to be joined itself, and the other half – its quality.
- the Alphabet should be set by the string Alph. In doing so, only symbols of the Alph will be taken into account for consensus string generation.
If NoQuality = true method #1 will be used always.
So, if we need to join collection 0->ACGT, 1->TGTA, 1->TT, 10->TT, 11->TCA in any way without any additional info, we should set NoQuality = true, Aggregate = false, and have the result: 0->ATGTA, 10->TTC.
long double ProfileProbableMer (const std::string &s, int n, const std::vector <std::vector <long double>> & B, std::vector <std::string> & DataS, long double d = 0.0000001, std::string Alph = "ACGT")
Finds all most probable n-mer of the given string s upon position probability matrix (PPM) B and the Alphabet Alph. Returns their probability and all these n-mers contained in DataS. If any data incorrect returns empty DataS and -1.0. Parameter d sets precision for doubles comparison.
int MedianString (const int WordLenght, const std::vector <std::string> & DataS, std::vector <std::string> & MedianS, std::string Alph = "ACGT")
Finds all median strings (having length = WordLenght) upon given array of strings in the vector DataS and given Alphabet set by the string Alph.
Returns distance between found median string(s) annd the pattern (i.e. DataS), all found median strings will contained in the vector MedianS.
If any data incorrect returns empty MedianS and -1.
int EditDist (const std::string &s1, const std::string &s2)
Computes Edit Distance (Levenshtein distance) between two strings (strings may be empty too).
int EditDistA (const std::string &s1, const std::string &s2, std::string &sr1, std::string &sr2)
Extended version of the function EditDist (see it above). Returns also Edit Distance Alignment of s1 and s2 as sr1 and sr2 (one possible version if many exists).
void EDistForFindMR (const std::string &s1, const std::string &s2, const int D, const int L, int l, int b, std::set <std::pair <int, int>> &Result)
An auxiliary function for FindMutatedRepeatsED, see its info for details (below, the following one).
int FindMutatedRepeatsED (std::string &StrShort, std::string &StrLong, int D, std::set <std::pair <int, int>> &Result)
The function finds all the substrings of a string StrLong, that have Edit Distance to a string StrShort <= D. Gap and mistmatch penalties are set as "1" here.
If dataset is correct returns 0 and set <std::pair <int, int>> Result, that contains pairs of integers: first one is a start position of a required substring in StrLong (0-based indexing) and the second one is its length.
If dataset is not correct (any string is empty of StrShort is longer than StrLong or StrShort's length <= D) returns -1 and empty Result.
The algorithm idea is:
- To find all start positions of such substrings. To do so we should reverse both strings and then do Edit Distance Alignment but with no gap penalty at the beginning: The required substring may start at every position of the longer string so here are no penalty fo gapping at start.
- For each start position the maximal possible length for the required
substring (<= StrShort.length+D, but within StrLong).
Note that the required substrings may have length <= StrShort.length+D and >= StrShort.length-D because gap penalty = 1. - If such maximal possible length meets this condition, let a string TempS be a substring of StrLong of this length (TempS starts from relevant start position in StrLong).
And then let's do Edit Distance Alignment between TempS and StrShort in order to find prefixes of TempS, that require the statement of problem to be solved here.
bool CompStrDLO (const std::string & s1, const std::string & s2)
Comparing function for arranging an array (vector) of strings in descending length order
int SuffixTreeMake (const std::string &DataS, std::vector <int> & Tree, int b=1)
Suffix Tree constructing upon a string DataS. If DataS is empty returns -1, if success returns 0.
Suffix Tree will be contained in the vector Tree, every edge as quartet of integers: number of tne start-vertex of edge, number of end-vertex of edge, starting position of substring in DataS, the length of this substring.
"b" sets the number to start numerating of vertices of suffix tree.
std::string ShortSuperstringGr (std::vector <std::string> DataS)
Generates shortest superstring of an array (vector) of strings DataS via implementing greedy algorithm. In doing so, every string that is a substring of any another one of DataS is to be excluded.
DataS is copied (not linked) here as it will be changed here.
Returns empty string if DataS is empty or all strings of DataS are empty.
int TrieMake (std::vector <std::string> &DataS, std::vector <int> & Trie)
Trie constructing upon vector of strings DataS
Trie: Here the Trie will be contained as a number of triplets of integers (a = Trie [3i], b = Trie [3i+1], c = Trie [3i+2], i = 0, 1, ...). Each triplet means an edge a->b marked with symbol (char) c. Vertices in the Tree are numerated starting with "1".
void Num (std::string & Numbers, std::vector <double> & A)
Converts string of numbers (separated by spaces) to a vector of numbers
void Num (std::string & Numbers, std::vector <long double> & A)
Converts string of numbers (separated by spaces) to a vector of numbers
void Num (std::string & Numbers, std::vector <int> & A)
Converts string of numbers (separated by spaces) to a vector of numbers
void Num (std::string & Numbers, std::vector <long long int> & A)
Converts string of numbers (separated by spaces) to a vector of numbers
int Num (std::string & Numbers, int &a1,int &a2, double &a3)
Converts a string to 3 numbers (2 integers and 1 double; they should be separated by spaces in the string and the string should’t contain any other symbols) to int a1,int a2, double a3.
Returns -1 if input data is incorrect (no 3 "candidates to numbers" are found).
But note that here is NO checking if a substring to be converted to a number contains digits and decimal point only.
void Num (std::string & Numbers, std::vector <std::string> & A)
Modification of "Num"-functions (see them above) for strings.
Converts string that consists of some strings (separated by spaces) to a vector of strings.
The "Adjacency vector" is a data structure to represent a graph is used in the library CBioInfCpp.
Let "Adjacency vector" of unweighted graph be a data structure, that contains array of integers such as а[2i], a[2i+1],... (0-basing indexing).
So such array contains even number of elements. Every pair а[2i], a[2i+1] means an edge between vertex а[2i] and а[2i+1] (~ "Edge list as one String"). This format don't identify the graph as directed or undirected (both cases may be). If the graph is considered as directed, its edges should be considered as а[2i] -> a[2i+1].
Let "Adjacency vector" of weighted graph (all weights are integers) be a data structure, that contains array of integers such as а[3i], a[3i+1], a[3i+2],... (0- basing indexing).
So such array contains 3n number of elements. Every pair а[3i], a[3i+1] means an edge between vertex а[3i] and а[3i+1] with weight a[3i+2]("Edge list as one String").
This format don't identify the graph as directed or undirected (both cases may be). If the graph is considered as directed, its edges should be considered as а[3i] -> a[3i+1].
As we are not able to create an array (or a vector) that contains both integers and doubles let’s do the following. Let a graph is represented here as a pair of 2 vectors (i.e. std::pair < std::vector, std::vector>). The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2*i, 2*i+1 in the first vector has its weight set as i-th element in the second one.
The "Adjacency vector" may be considered as another one data structure to represent a graph. It is compact, smaller than Adjacency Matrix (for sparse graphs), simple to implement and it may be a convenient one for some tasks and problems solving.
By the way, vertices of a graph may be marked by both positive and non-positive numbers here. In order to implement some function vertices may be renumbered to get started from "0" or "1"; in doing so, the vertices will be assigned their original numbers before the function is complete.
Also any graph may have multiple edges and multiple loops.
Since Summer of 2019 CBioInfCpp also have a modification of Adjacency vector - Adjacency map. Adjacency map allows to have quicker access to edge’s weight (the key is a pair of vertices numbers (int), mapped value, i.e. weight, may be int or double). As Adjacency map can’t deal with multiple edges, its extended version i.e. Adjacency mega-map may be used in such cases. In doing so, the key value of the map is a pair of integers that sets edge(s) between them and the mapped value is a vector that contains weights (int or double) of all edges between these vertices.
int UWGraphRead (std::ifstream & fin, std::vector <int> & A)
Reads Edge list to "Adjacency vector" of unweighted graph (i.e. to vector A). Let "Adjacency vector" of unweighted graph be a data structure, that contains array of integers such as а[2i], a[2i+1],... / 0-basing indexing in array /.
So such array contains even number of elements. Every pair а[2i], a[2i+1] means an edge between vertex а[2i] and а[2i+1] (~ "Edge list as one String").
This format don't identify the graph as directed or undirected (both cases may be). If the graph is considered as directed, its edges should be considered as а[2i] -> a[2i+1].
Input file should be in edge list format, every edge in new line.
Returns -1 and empty "Adjacency vector" A if any line contains number of elements that !=2.
int WGraphRead (std::ifstream & fin, std::vector <int> & A)
Reads Edges list to "Adjacency vector" of weighted graph. Let "Adjacency vector" of weighted graph be a data structure, that contains array of integers such as а[3i], a[3i+1], a[3i+2],... / 0-basing indexing in array /.
So such array contains 3n number of elements. Every pair а[3i], a[3i+1] means an edge between vertex а[3i] and а[3i+1] with weight a[3i+2]("Edge list as one String").
This format don't identify the graph as directed or undirected (both cases may be). If the graph is considered as directed, its edges should be considered as а[3i] -> a[3i+1].
Input file should be in edge list format, every edge in new line.
Returns -1 and empty "Adjacency vector" A if any line contains number of elements of any line that !=3.
int WGraphRead (std::ifstream & fin, std::pair < std::vector<int>, std::vector<double>> & A)
Modification of the function WGraphRead (see it above) for not-integer (double) weihgts of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2*i, 2*i+1 in the first vector has its weight set as i-th element in the second one.
int RangeVGraph (std::vector <int> & A, int & mx, int & mn, const bool weighted, bool IgnoreWeighted = false)
Finds max (i.e. mx) and min (i.e. mn) value of numbers that assigned to vertices
Graph must be set as "Adjacency vector", bool "weighted" sets if the graph is weighted or no.
If (IgnoreWeighted = true) the function looks at every element in A without any dataset checking
int RenumVGraph (std::vector <int> & A, const int d, const bool weighted, bool IgnoreWeighted = false)
Renumerates vertices adding d-parameter (d may be non-negative or negative)
Graph must be set as "Adjacency vector", bool "weighted" sets if the graph is weighted or no.
If (IgnoreWeighted = true) the function adds d to every element in A without any dataset checking
int AdjVector2AdjMatrix (std::vector <int> & A, std::vector <std::vector <int>> &B, const bool weighted, const bool directed)
Converts "Adjacency vector" A to "Adjacency matrix" B.
bool "weighted" sets if the graph is weighted or no. bool "directed" sets if the graph is directed or no.
In case of multiple edges for a weighted graph only the last edge will be written to Adjacency matrix, others will be lost.
Loops for undirected unweighted graph counts as 2 edges
In this function zero-value of any item of Adjacency matrix means no edge both for unweighted and weighted graph
Returns 0 if success. Returns -1 and empty B if no.
int AdjVector2AdjMatrix (std::pair < std::vector<int>, std::vector<double>> & A, std::vector <std::vector <double>> &B, const bool directed)
Modification of the function AdjVector2AdjMatrx (see it above) for not-integer (double) weights of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2*i, 2*i+1 in the first vector has its weight set as i-th element in the second one.
Note that undirected graph may have only zeros lower than the Main diagonal of its Adjacency matrix here
int AdjMatrix2AdjVector (std::vector <int> & A, std::vector <std::vector <int>> &B, const bool weighted, const bool directed)
Converts "Adjacency matrix" B to "Adjacency vector" A.
bool "weighted" sets if the graph is weighted or no. bool "directed" sets if the graph is directed or no.
For a weighted graph here are no multiple edges.
Loops for an undirected unweighted graph counts as 2 edges (so if the Main diagonal of the matrix B contain any odd number for such graph the function will return -1)
For an undirected graph the data that is lower than the Main diagonal of the matrix B is ignored
In this function zero-value of any item of Adjacency matrix means "no such edge" both for unweighted and weighted graph
Returns 0 if success. Returns -1 and empty A if no.
int AdjMatrix2AdjVector (std::pair < std::vector<int>, std::vector<double>> & A, const std::vector <std::vector <double>> &B, const bool directed)
Modification of the function AdjMatrix2AdjVector (see it above) for not-integer (double) weights of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2*i, 2*i+1 in the first vector has its weight set as i-th element in the second one.
For an undirected graph the data that is lower than the Main diagonal of the matrix B is ignored
int AdjVectorToAdjMap (const std::vector <int> &A, std::map <std::pair < int, int> , int> &G2, const bool weighted, const bool directed = true)
Converts Adjacency vector A to Adjacency map G2. Multiple edges will be joined together. Parameter "weighted" sets if the graph A is weighted or no. Weights may be only integers. Parameter "directed" sets if the graph A is directed or no. For undirected graph numers of nodes of every edge will be written to G2 in increasing order.
If A is unweighted we consider that every edge have its weight = 1.
Returns -1 if input data is not correct. Otherwise returns 0.
int AdjVectorToAdjMap (const std::pair < std::vector<int>, std::vector<double>> & A, std::map <std::pair < int, int> , double> &G2, const bool directed = true)
Converts Adjacency vector A to Adjacency map G2. Multiple edges will be joined together.
Parameter "directed" sets if the graph A is directed or no. For undirected graph numbers of nodes of every edge will be written to G2 in increasing order.
Returns -1 if input data is not correct. Otherwise returns 0.
int AdjMapToAdjVector (std::vector <int> &A, const std::map <std::pair < int, int> , int> &G1)
Converts Adjacency map G1 to Adjacency vector A. A is considered as weighted, all weights are integers.
Returns -1 if input data is not correct. Otherwise returns 0.
int AdjMapToAdjVector (std::pair < std::vector<int>, std::vector<double>> & A, const std::map <std::pair < int, int> , double> &G1)
Modification of the function AdjMapToAdjVector (see it above) for not-integer (double) weights of edges of a graph.
Converts Adjacency map G1 to Adjacency vector A. A is considered as weighted, all weights are double.
Returns -1 if input data is not correct. Otherwise returns 0.
int AdjVectorToAdjMegaMap (const std::vector <int> &A, std::map <std::pair < int, int> , std::vector<int> > &G2, const bool weighted, const bool directed = true)
Converts Adjacency vector A to Adjacency mega-map G2.
Adjacency mega-map is an extended version of Adjacency map (and it is built basing on std::map too) for containing graphs that have multiply loops and multiply edges.
In doing so, the key value of the map is a pair of integers that sets edge(s) between them and the mapped value is a vector that contains weights of all edges between these vertices.
Parameter "weighted" sets if the graph A is weighted or no. Weights may be only integers. If A is unweighted we consider that every edge have its weight = 1.
Parameter "directed" sets if the graph A is directed or no. For undirected graph numers of nodes of every edge will be written to G2 in increasing order.
Returns -1 if input data is not correct. Otherwise returns 0.
int AdjVectorToAdjMegaMap (const std::pair < std::vector<int>, std::vector<double>> & A, std::map <std::pair < int, int> , std::vector<double> > &G2, const bool directed = true)
Modification of the function AdjVectorToAdjMegaMap (see it above) for not-integer (double) weights of edges of a graph.
int AdjMegaMapToAdjVector (std::vector <int> &A, const std::map <std::pair < int, int> , std::vector <int> > &G1)
Converts Adjacency mega-map G1 to Adjacency vector A. A is considered as weighted, all weights are integers.
Adjacency mega-map is an extended version of Adjacency map (and it is built basing on std::map too) for containing graphs that have multiply loops and multiply edges.
In doing so, the key value of the map is a pair of integers that sets edge(s) between them and the mapped value is a vector that contains weights of all edges between these vertices.
Returns -1 if input data is not correct. Otherwise returns 0.
int AdjMegaMapToAdjVector (std::pair < std::vector<int>, std::vector<double>> & A, const std::map <std::pair < int, int> , std::vector<double> > &G1)
Modification of the function AdjVectorToAdjMegaMap (see it above) for not-integer (double) weights of edges of a graph.
int CheckUnvisit (vector <int> & Visited)
An auxiliary function that finds the first unmarked vertex in the graph (0 means unmarked)
void EcycleDGraph (int t, std::vector <int> & R, const int V, std::vector <std::vector<int>> &B)
An auxiliary function that finds Eulerian cycle in the DIRECTED graph without without checking of input data correctness (i.e. (1) the graph includes Eulerian cycle, (2) its vertices numbers start from "1", (3) the graph doesn't contain any isolated vertices).
B is the Adjacency matrix, containing the number of edges between the vertices. V is the max number assigned to vertices.
int EPathDGraph (std::vector <int> & A, std::vector <int> & R, const bool weighted, std::vector <int> & Isolated)
Finding Eulerian Cycle or Path in directed graph (weighted or non-weighted) that may contain multiple edges and multiple loops.
Returns Path/ Cycle as R, isolated vertices as Isolated. Returns value "1" if Eulerian cycle has been found or value "2" if Eulerian path has been found or "-1" together with empty R and Isolates if no cycle/ path found.
If any vertex has loops only, such a vertex is not considered as an isolated one.
Vertices may be numbered in different ways (they may be marked by both negative and non-negative integers). In doing so, we set that the graph contains vertices marked by all the integers from min (1, minimal number assigned to vertices) to maximal number assigned to vertices inclusive.
In order to implement the function vertices may be renumbered to get started from "1"; after search is completed, the vertices will be assigned their original numbers.
int EPathDGraph (std::pair < std::vector<int>, std::vector<double>> & A, std::vector <int> & R, std::vector <int> & Isolated)
Modification of the function EPathDGraph (see it above) for not-integer (double) weights of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2*i, 2*i+1 in the first vector has its weight set as i-th element in the second one.
int DistanceBFA (std::vector <long long int> &A, std::vector <int> & D, const int b, std::vector <int> & Prev, const bool weighted, int V = INT_MIN)
The function counts the shortest distances from the vertex b to all vertices in the graph (these distances are to be contained in vector D, i.e. D[i] means the shortest distance from b to I).
By default vector D is filled with LLONG_MAX.
Vector Prev is intended to contain the number of the previous vertex for every vertex in such shortest paths ("-1" value is set by default and means "this vertex doesn't included in any such path").
The Breadth-first search method is used here.
The input graph should be directed, both weighted or unweighted (in case of unweighted graph we consider every edge's weight as "1".) The graph may have loops and multiple edges.
Input data: Adjacency vector A (it is supposed that vertices are numbered starting from 0) and the maximum vertex number V (V may be not set, in this case it will be the maximum vertex number of Adjacency vector A)
The edges may have weight of 0, >0, <0.
In case we found a negative weight cycle as well as input data is incorrect the function returns "-1" and empty D and Prev.
int DistanceBFA (std::pair < std::vector<int>, std::vector<double>> & A, std::vector <long double> & D, const int b, std::vector <int> & Prev, int V = INT_MIN)
Modification of the function DistanceBFA (see it above) for not-integer (double) weights of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2*i, 2*i+1 in the first vector has its weight set as i-th element in the second one.
int DistanceBFA (std::vector <int> &A, std::vector <long long int> & D, const int b, const bool weighted, int V = INT_MIN)
Modification of the function DistanceBFA (used Bellman–Ford algorithm instead of Breadth-First Search and here is no search for previous vertices for every vertex in such shortest paths).
The function counts the shortest distances from the vertex b to all vertices in the graph (these distances are to be contained in vector D, i.e. D[i] means the shortest distance from b to I). By default vector D is filled with LLONG_MAX.
The Bellman–Ford algorithm is used here.
The input graph should be directed, both weighted or unweighted (in case of unweighted graph we consider every edge's weight as "1".) The graph may have loops and multiple edges.
Input data: Adjacency vector A (it is supposed that vertices are numbered starting from 0) and the maximum vertex number V (V may be not set, in this case it will be the maximum vertex number of Adjacency vector A)
The edges may have weight of 0, >0, <0.
In case we found a negative weight cycle as well as input data is incorrect the function returns "-1" and empty D.
int DistanceBFA (std::pair < std::vector<int>, std::vector<double>> & A, std::vector <long double> & D, const int b, int V = INT_MIN)
Modification of the function DistanceBFA (used Bellman–Ford algorithm instead of Breadth-First Search and here is no search for previous vertices for every vertex in such shortest paths) for not-integer (double) weights of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2i, 2i+1 in the first vector has its weight set as i-th element in the second one.
int DFSTS (const std::vector <int> & A, const int b, std::vector <int> & Visited, std::vector <int> & order, const bool weighted)
An auxiliary function for the function TSortHP. Works without any checking of input data correctness. Vertices in the input directed graph (it is set by the Adjacency vector A) are to be numbered starting from 1.
The graph may contain loops (they will be ignored).
During building topological sorting we shall colour vertices (using vector Visited): 0 = unvisited (white), 1 = visited, but not still finished yet (grey), 2 = finished (black).
Bool "weighted" should be set as "true" for weighted graph, "false" for unweighted.
If the graph contains cycle - returns 1 and empty "order".
int CycleToPath (std::vector <int> Cycle, std::vector<int> &Path)
The function integrate cycle Cycle to the path Path (starting vertex will be the first from the Cycle that may be found in the Path)
Returns 0 if success. Returns -1 if it is impossible or input data are incorrect.
int TSortHP (std::vector <int> & A, std::vector <int> & R, std::vector <int> & order, std::vector <int> & Isolated, const bool weighted, const bool OnlyTS = false)
The function finds topological sorting of directed graph (returned as vector "order").
ONLY IF topological sorting exists AND OnlyTS == false the function also checks for Hamiltonian path (returned as vector R) and list of Isolated vertices (returned as vector Isolated).
The graph is set by Adjacency vector A, may be weighted or no (bool weighted).
The graph may contain loops (they will be ignored).
If any vertex has loops only, such a vertex is not considered as an isolated one.
The graph may contain multiple edges.
Vertices may be numbered in different ways (they may be marked by both negative and non-negative integers). In doing so, we set that the graph contains vertices marked by all the integers from min (1, minimal number assigned to vertices) to maximal number assigned to vertices inclusive.
In order to implement the function vertices may be renumbered to get started from "1"; after search is completed, the vertices will be assigned their original numbers.
So if OnlyTS == false:
- the function returns 0 if both topological sorting and Hamiltonian path found.
- the function returns -1 and empty Isolated, order, R if the graph contains cycle.
- the function returns 1 if topological sorting found and, upon that, Hamiltonian path doesn't exist.
If OnlyTS == true, both R and Isolated will be returned empty (to make this function faster). The function returns 0 if topological sorting is found and -1 otherwise.
int TSortHP (std::pair < std::vector<int>, std::vector<double>> & A, std::vector <int> & R, std::vector <int> & order, std::vector <int> & Isolated, const bool OnlyTS = false)
Modification of the function TSortHP (see it above) for not-integer (double) weights of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2*i, 2*i+1 in the first vector has its weight set as i-th element in the second one.
int DFS_for_NBPaths (const std::vector <int> & A, const bool w, const int b, const int bconst, std::vector <int> & Visited, std::vector <int> & Path)
An auxiliary function for NBPaths (see it below): DFS for finding isolated cycles
void Circuit_for_NBPaths (const std::vector <int> & A, const bool w, int V, std::vector <std::vector<int> >&Paths, std::vector <int> & Visited)
An auxiliary function for NBPaths (see it below): finding isolated cycles
int NBPaths (std::vector <int> & A, bool w, std::vector <std::vector<int> >&Paths, bool directed = true)
Finds all maximal non-branching Paths in a graph, that is set by Adjacency vector A.
Parameter "w" sets if A is a weighted graph or no. Parameter "directed" sets if A is a weighted graph or no.
The result will be in std::vector <std::vector > Paths. If input data is incorrect returns -1 and empty Paths.
If input data is correct returns 0.
Vertices may be numbered in different ways (they may be marked by both negative and non-negative integers).
In order to implement the function vertices may be renumbered to get started from "1"; after search is completed, the vertices will be assigned their original numbers.
The input graph A may have multiple edges (multiple edges will be considered as non branching paths) and multiple loops (any loop will considered as a non branching path).
long long int MaxFlowGraph (std::vector <int> A, const bool weighted, int b, int e, std::vector <std::vector<int> >&Paths, std::vector <int> &Flows, std::vector < std::pair < int, int> > &MinCut)
Finds maximal flow from vertex b to vertex e in the graph A (set by Adjacency vector A).
Parameter "weighted" sets if A is a weighted graph or no. All vertices of A should have only non-negative marks.
For a weighted graph edges should have only positive values. Graph A may have multiple edges (multiple edges will be considered as one joined edge that have its weight = sum of the weights of all joined edges) and multiple loops (loops will be ignored).
Returnes:
- maximal flow value and 3 vectors: vector Paths (contains all the paths of the maximal flow network (one of the possible solutions if >1 solutions exist))
- vector Flows (contains values of a flow for a index-relevant Path (i.e. Flows[0] for Paths [0], etc)),
- vector MinCut (contains the max-flow min-cut as an array of edges: every edge is set as a pair of its vertices).
If input data is incorrect or there are no path from b to e or there are no such vertices (b or e) in the graph returns -1 and empty Paths, Flows, MinCut.
long double MaxFlowGraph (std::pair < std::vector<int>, std::vector<double>> A, int b, int e, std::vector <std::vector<int> >&Paths, std::vector <double> &Flows, std::vector < std::pair < int, int> > &MinCut)
Modification of the function MaxFlowGraph (see it above) for not-integer (double) weights of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2i, 2i+1 in the first vector has its weight set as i-th element in the second one.
int SubGraphsInscribed (std::vector <int> A, std::vector <int> B, std::set<std::vector <int>> & Result, const bool directed = true)
The function finds all inscribed subgraphs in unweighted graph A that are isomorphic to unweighted graph B. "Inscribed" means here that
(1) this subgraph is "glued" to other parts of A only by edges that connected to its vertices that are begin/ end ones of any max-length non-branching path of this subgraph
and/ or
(2) graph A may have some other connected components.
I.e. for graph B = {0->2, 10->2, 2->3, 3->4, 4->5, 4->6} we will find only A1 = {0->2, 1->2, 2->3, 3->4, 4->5, 4->6} as inscribed isomorphic subgraph of A = {0->2, 7->1, 1->2, 2->3, 3->4, 4->5, 4->6}.
But if we add edge 3->8 to A (in this case A = {3->8, 0->2, 7->1, 1->2, 2->3, 3->4, 4->5, 4->6}), we couldn't find any inscribed isomorphic to B subgraph of A.
Graph A is set by an Adjacency vector.
Graph B is set by an Adjacency vector.
Both A and B are unweighted.
Bool "directed" sets if A and B are directed graphs or no.
Result: a set for containing all subgraphs of A found (set by Adjacency vectors), i.e. this set to contain results.
The function returns the number of different subgraphs of A that are isomorphic to B and subgraphs themselves in Result; if input data are incorrect returns -1 and empty Result.
A and B may have >=1 connected components; also A and B may have multiply edges.
int DistanceTS (std::vector <int> &A, std::vector <long long int> & D, const int b, std::vector <int> & Prev, const bool weighted, int V = INT_MIN)
The function counts the shortest distances from the vertex b to all vertices in the graph (these distances are to be contained in vector D, i.e. D[i] means the shortest distance from b to i).
By default vector D is filled with LLONG_MAX.
In doing so, vector Prev is intended to contain the number of the previvous vertex for every vertex in such shortest paths ("-1" value is set by default and means "this vertex doesn't included in any such path").
This function seems to be faster than DistanceBFA, but DistanceTS works only with graphs containing no cycles (except loops, multiple loops).
The input graph should be directed, both weighted or unweighted (in this case we consider every edge's weight as "1".) The graph may have loops and multiple edges.
Input data: Adjacency vector A (it is supposed that vertices are numbered starting from 0) and the maximum vertex number V (V may be not set, in this case it will be the maximum vertex number of Adjacency vector A)
The edges of a weighted graph may have weight of 0, >0, <0, but only less than INT_MAX (<INT_MAX).
In case we found a cycle as well as input data is incorrect the function returns "-1" and empty D and Prev.
int DistanceTS (std::pair < std::vector<int>, std::vector<double>> & A, std::vector <long double> & D, const int b, std::vector <int> & Prev, int V = INT_MIN)
Modification of the function DistanceTS (see it above) for not-integer (double) weights of edges of a graph.
Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2*i, 2*i+1 in the first vector has its weight set as i-th element in the second one.
int MakeSubgraphSetOfVertices (const std::vector <int>&A, std::vector <int>&Subgraph, const std::set <int> &Vertices, const bool weighted)
The function makes a subgraph Subgraph from the graph A as follows: we take only vertices from the set Vertices. Graph A is set by Adjacency vector A. It may be weighted or no (set by "weighted"), weights may be integers only.
int MakeSubgraphSetOfVertices (const std::vector <int>&A, std::vector <int>&Subgraph, const std::unordered_set <int> &Vertices, const bool weighted)
The function makes a subgraph Subgraph from the graph A as follows: we take only vertices from the unordered_set Vertices. Graph A is set by Adjacency vector A. It may be weighted or no (set by "weighted"), weights may be integers only.
int MakeSubgraphSetOfVertices (const std::pair < std::vector<int>, std::vector<double>> & A, std::pair < std::vector<int>, std::vector<double>> &Subgraph, const std::set <int> &Vertices)
Modification of the function MakeSubgraphSetOfVertices (see it above) for not-integer (double) weights of edges of a graph.
int MakeSubgraphSetOfVertices (const std::pair < std::vector<int>, std::vector<double>> & A, std::pair < std::vector<int>, std::vector<double>> &Subgraph, const std::unordered_set <int> &Vertices)
Modification of the function MakeSubgraphSetOfVertices (see it above) for not-integer (double) weights of edges of a graph and unordered_set Vertices.
int AdjVectorEdgesMultiplicity (const std::vector <int> &A, std::map <std::pair < int, int> , int> &G2, const bool weighted, bool directed = true)
Counts multiplicity of edges of a graph that is set by Adjacency vector A.
Parameter "weighted" sets if the graph A is weighted or no. Weights may be only integers. If A is unweighted we consider that every edge have its weight = 1.
Parameter "directed" sets if the graph A is directed or no.
For a DIRECTED graph the result will be formed in the map G2 as follows: key is the pair of integers corresponding to the source and the sink vertices of an edge, and the value is its multiplicity. For example "G2[std::pair <int, int>(1, 2)] = 3" means that directed edge 1->2 has its multiplicity = 3.
For UNDIRECTED graph G2 will contain edge multiplicity for both keys std::pair <int, int> (vertex1, vertex 2) and std::pair <int, int> (vertex2, vertex 1).
For example for undirected graph will be so: "G2 [std::pair <int, int>(1, 2)] = G2 [std::pair <int, int>(2, 1)] = 3".
Returns -1 and empty G2 if input data is not correct. Otherwise returns 0.
int AdjVectorEdgesMultiplicity (const std::pair < std::vector<int>, std::vector<double>> & A, std::map <std::pair < int, int> , int> &G2, bool directed = true)
Modification of the function AdjVectorEdgesMultiplicity (see it above) for not-integer (double) weights of edges of a graph. Graph is represented here as a pair of 2 vectors. The first one is an "Adjacency vector" without weights. But weights are set in the second one.
So an edge that is set by the pair of vertices indexed as 2i, 2i+1 in the first vector has its weight set as i-th element in the second one.
Returns -1 and empty G2 if input data is not correct. Otherwise returns 0.
int DFSSCC1 (const std::vector <int> & A, const int b, std::vector <int> & Visited, std::vector <int> & order, const bool weighted)
An auxiliary function to order vertices of a graph for the function SCCGraph_Vertices
int DFSSCC2 (const std::vector <int> & A, const int b, std::vector <int> & Visited, std::vector <int> & order,std::set <int> & R, const bool weighted)
An auxiliary function to find vertices of a graph for a strongly connected component (for the function SCCGraph_Vertices).
int NeighborJoiningUndirectedGraph (const std::vector <std::vector <int>> B, std::pair < std::vector<int>, std::vector<double>> &A)
Generates a tree (undirected graph) using Neighbor Joining method (as an Adjacency vector A, 1-based indexing of vertices) upon a distance matrix B.
If any data incorrect (B has zero lines (i.e. empty) or has negative values or is not a square matrix) returns empty A and -1. If success returns 0.
int UPGMA_UndirectedGraph (const std::vector <std::vector <int>> B, std::pair < std::vector<int>, std::vector<double>> &A)
Generates a tree (undirected graph) using UPGMA method (as an Adjacency vector A, 1-based indexing of vertices) upon a distance matrix B.
If any data incorrect (B has zero lines (i.e. empty) or has negative values or is not a square matrix) returns empty A and -1. If success returns 0.
void DFSAllPathsDGraph (std::vector <int>&A, std::vector <int> &Visited, const int &b, const int &e, const bool weighted, std::set <std::vector <int>> & GPath, std::vector <int> &Path)
An auxiliary function for AllPathsDGraph (see it below)
int AllPathsDGraph (std::vector <int>&A, const int &b, const int &e, const bool weighted, std::set <std::vector <int>> & GPath)
An experimental function to find all paths from the vertex b to the vertex e of directed graph that is set by Adjacency vector A. May be too slow or have some mistakes.
Graph A may be weighted or no (set by weighted).
Returns 0 and set of paths found in GPath, if input data are incorrect returns -1 and empty GPath.
int DFS_for_Circles (const std::vector <int> & A, const bool w, const int b, const int bconst, std::vector <int> & Visited, std::vector <int> & Path, std::set <std::vector <int>> &GPath, int &mn, const bool &directed)
An auxiliary function for Circles_in_Graph (see it below): DFS for finding cycles
int Circles_in_Graph (std::vector <int> & A, const bool w, std::set <std::vector<int> >&Paths, std::set <int> &StartV, const bool directed = true)
An experimental function to find all cycles in graph that is set by Adjacency vector A. May be too slow or have some mistakes.
A may be weighted or no (set by w) and directed or no (set be directed).
If StartV is not empty, the function searches only for cycles that contain any vertex in StartV.
Returns 0 and set of cycles found in Paths, if input data are incorrect returns -1 and empty Paths.
int NeighborJoiningUndirectedGraph (const std::vector <std::vector <double>> B, std::pair < std::vector<int>, std::vector<double>> &A)
Modification for distance matrix B of doubles.
int UPGMA_UndirectedGraph (const std::vector <std::vector <double>> B, std::pair < std::vector<int>, std::vector<double>> &A)
Modification for distance matrix B of doubles.
int SCCGraph_Vertices (std::vector <int> & A, std::vector <std::set <int>> & G, const bool weighted, int mn = 0, int V = INT_MIN)
The function finds collection of vertices for each strongly connected component of the directed graph, that is set by an Adjacency vector A.
These collections are to be contained in vector G, i.e. G[i] contains a collection of vertices of the i-th strongly connected component.
Input data: Adjacency vector A, the maximum vertex number V (V may be not set, in this case it will be the maximum vertex number of Adjacency vector A), the minimum vertex number mn (== 0 by default), bool weighted, that sets if the graph is weighted.
If input data is incorrect the function returns "-1" and empty G.
int CCGraph_Vertices (std::vector <int> & A, std::vector <std::set <int>> & R, const bool weighted, int mn = 0, int V = INT_MIN)
The function finds collection of vertices for each connected component of the undirected graph, that is set by an Adjacency vector A.
These collections are to be contained in vector R, i.e. R[i] contains a collection of vertices of the i-th connected component.
Input data: Adjacency vector A, the maximum vertex number V (V may be not set, in this case it will be the maximum vertex number of Adjacency vector A), the minimum vertex number mn (== 0 by default), bool weighted, that sets if the graph is weighted.
If input data is incorrect the function returns "-1" and empty R.
int MatrixSet (std::vector <std::vector <double>> & B, const int NLines, const int NColumns, const double i)
Sets (resets) matrix NLines x NColumns filled value "i" (double). Returns -1 if NLines or NColumns <=0
int MatrixSet (std::vector <std::vector <long double>> & B, const int NLines, const int NColumns, const long double i)
Sets (resets) matrix NLines x NColumns filled value "i" (long double). Returns -1 if NLines or NColumns <=0
int MatrixSet (std::vector <std::vector <int>> & B, const int NLines, const int NColumns, const int i)
Sets (resets) matrix NLines x NColumns filled value "i" (int). Returns -1 if NLines or NColumns <=0
int MatrixSet (std::vector <std::vector <long long int>> & B, const int NLines, const int NColumns, const long long int i)
Sets (resets) matrix NLines x NColumns filled value "i" (long long int). Returns -1 if NLines or NColumns <=0
int FindIn (std::vector <int> &D, int a, int step = 1, int start = 0)
Returns index in vector (int) of the first element = a. Search starts from index "start" with step = "step". If step<1 step will be set as 1. If start<0 start will be set as 0. If no such element found the function returns -1.
int FindIn (std::vector <long long int> &D, long long int a, int step = 1, int start = 0)
Returns index in vector (long long int) of the first element = a. Search starts from index "start" with step = "step". If step<1 step will be set as 1. If start<0 start will be set as 0. If no such element found the function returns -1.
int FindIn (std::vector <double> &D, double a, int step = 1, int start = 0)
Returns index in vector (double) of the first element = a. Search starts from index "start" with step = "step". If step<1 step will be set as 1. If start<0 start will be set as 0. If no such element found the function returns -1.
Yes, operation like (a==b) may be not correct for doubles. But this function may be considered as an useful one in some cases.
The following version of the function finds the first element, that differs from "a" less than "d".
int FindIn (std::vector <double> &D, double a, double d, int step = 1, int start = 0)
Returns index in vector (double) of the first element, that differs from "a" less than nonnegative double "d".
Search starts from index "start" with step = "step". If step<1 step will be set as 1. If start<0 start will be set as 0. If no such element found the function returns -1.
int FindIn (std::vector <long double> &D, long double a, int step = 1, int start = 0)
Returns index in vector (long double) of the first element = a. Search starts from index "start" with step = "step". If step<1 step will be set as 1. If start<0 start will be set as 0. If no such element found the function returns -1.
Yes, operation like (a==b) may be not correct for doubles. But this function may be considered as an useful one in some cases. The following version of the function finds the first element, that differs from "a" less than "d".
int FindIn (std::vector <long double> &D, long double a, long double d, int step = 1, int start = 0)
Returns index in vector (long double) of the first element, that differs from "a" less than nonnegative long double "d".
Search starts from index "start" with step = "step". If step<1 step will be set as 1. If start<0 start will be set as 0. If no such element found the function returns -1.
int FindIn (std::vector <string> &D, std::string a, int step = 1, int start = 0)
Returns index in vector (string) of the first element = a. Search starts from index "start" with step = "step". If step<1 step will be set as 1. If start<0 start will be set as 0. If no such element found the function returns -1.
int SwapInVector (std::vector <int> & A1, unsigned int f, unsigned int l)
Swaps 2 elements in vector (int). Returns -1 if some index out of vector's range or vector is empty
int SwapInVector (std::vector <long long int> & A1, unsigned int f, unsigned int l)
Swaps 2 elements in vector (long long int). Returns -1 if some index out of vector's range or vector is empty
int SwapInVector (std::vector <double> & A1, unsigned int f, unsigned int l)
Swaps 2 elements in vector (double). Returns -1 if some index out of vector's range or vector is empty
int SwapInVector (std::vector <long double> & A1, unsigned int f, unsigned int l)
Swaps 2 elements in vector (long double). Returns -1 if some index out of vector's range or vector is empty
int SwapInVector (std::vector < std::string> & A1, unsigned int f, unsigned int l)
Swaps 2 elements in vector (string). Returns -1 if some index out of vector's range or if the vector is empty
int GraphVerticesNumbersCompress (std::vector <int> & P, const bool weighted)
Renumbering of vertices of the graph P (set by Adjacency vector P) to make the sequence of numbers of vertices as a row of not-negative integers with no blanks. Weighted sets if the graph P is weighted.
std::string CIGAR1 (const std::string &S0, const std:: string & S2, int npos = 0)
Generates CIGAR-string as a result of "fitting" of the string S2 to s0 (starting position == npos). If any data is incorrect returns empty string.
int ScoreStringMatrix (const std::vector <std::string> &s)
Returnes a score (i.e. total number of mismatches) upon a vector of strings s.
If input data is incorrect returns 0.
int GenRandomUWGraph (std::vector <int> &P, int v, int e, int b=0)
An auxiliary function that generates a random unweighted graph P (set by Adjacency vector P). e means the number of edges, v means the number of vertices, b means the minimal number to be assigned to vertex
int PartitionOfNumber (std::vector <std::vector <int>> &B, int n)
Generates partitions of int n (i.e. representing n as a sum of positive integers) in B. If n<=0 returns empty B and "-1"
int PartitionOfNumberL (std::vector < std::vector <int>> &B, int n, int l=-1)
Generates partitions of int n (i.e. representing n as a sum of positive integers) in B. Extended version: one may set l>0 as a length of partitions (i.e. number of summands).
In this case "0" will be added to the end of the shorter partitions. If n<=0 returns empty B and "-1"
std::string GenerateAlphabet (const std::vector <std::string> &DataS)
Generates an alphabet upon the given vector of strings DataS. Symbols will be ordered under ASCII.
std::string GenerateAlphabet (const std::string &DataS)
Generates an alphabet upon the given string DataS. Symbols will be ordered under ASCII.